<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE article PUBLIC "-//NLM//DTD Journal Publishing DTD v2.3 20070202//EN" "journalpublishing.dtd">
<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" article-type="review-article">
<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Cell. Neurosci.</journal-id>
<journal-title>Frontiers in Cellular Neuroscience</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Cell. Neurosci.</abbrev-journal-title>
<issn pub-type="epub">1662-5102</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fncel.2014.00446</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Neuroscience</subject>
<subj-group>
<subject>Review Article</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Epigenetic regulation in the inner ear and its potential roles in development, protection, and regeneration</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name><surname>Layman</surname> <given-names>Wanda S.</given-names></name>
<xref ref-type="aff" rid="aff1"/>
<uri xlink:href="http://community.frontiersin.org/people/u/190789"/>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name><surname>Zuo</surname> <given-names>Jian</given-names></name>
<xref ref-type="aff" rid="aff1"/>
<xref ref-type="author-notes" rid="fn001"><sup>&#x0002A;</sup></xref>
<uri xlink:href="http://community.frontiersin.org/people/u/192089"/>
</contrib>
</contrib-group>
<aff id="aff1"><institution>Department of Developmental Neurobiology, St. Jude Children&#x02019;s Research Hospital</institution> <country>Memphis, TN, USA</country></aff>
<author-notes>
<fn fn-type="edited-by"><p>Edited by: Andy Groves, Baylor College of Medicine, USA</p></fn>
<fn fn-type="edited-by"><p>Reviewed by: Neil Segil, University of Southern California, USA; Alain Dabdoub, Sunnybrook Research Institute/University of Toronto, Canada</p></fn>
<fn fn-type="corresp" id="fn001"><p>&#x0002A;Correspondence: Jian Zuo, Department of Developmental Neurobiology, St. Jude Children&#x02019;s Research Hospital, MS323, 262 Danny Thomas Place, Memphis, TN 38105, USA e-mail: <email>jian.zuo&#x00040;stjude.org</email></p></fn>
<fn fn-type="other" id="fn002"><p>This article was submitted to the journal Frontiers in Cellular Neuroscience.</p></fn>
</author-notes>
<pub-date pub-type="epreprint">
<day>22</day>
<month>11</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="epub">
<day>07</day>
<month>01</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="collection">
<year>2014</year>
</pub-date>
<volume>8</volume>
<elocation-id>446</elocation-id>
<history>
<date date-type="received">
<day>31</day>
<month>10</month>
<year>2014</year>
</date>
<date date-type="accepted">
<day>11</day>
<month>12</month>
<year>2014</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#x000A9; 2015 Layman and Zuo.</copyright-statement>
<copyright-year>2015</copyright-year>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution and reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract><p>The burgeoning field of epigenetics is beginning to make a significant impact on our understanding of tissue development, maintenance, and function. Epigenetic mechanisms regulate the structure and activity of the genome in response to intracellular and environmental cues that direct cell-type specific gene networks. The inner ear is comprised of highly specialized cell types with identical genomes that originate from a single totipotent zygote. During inner ear development specific combinations of transcription factors and epigenetic modifiers must function in a coordinated manner to establish and maintain cellular identity. These epigenetic regulatory mechanisms contribute to the maintenance of distinct chromatin states and cell-type specific gene expression patterns. In this review, we highlight emerging paradigms for epigenetic modifications related to inner ear development, and how epigenetics may have a significant role in hearing loss, protection, and regeneration.</p></abstract>
<kwd-group>
<kwd>hair cells</kwd>
<kwd>auditory</kwd>
<kwd>histone acetylation</kwd>
<kwd>histone methylation</kwd>
<kwd>DNA methylation</kwd>
<kwd>ototoxicity</kwd>
<kwd>histone deacetylase inhibitors</kwd>
<kwd>cellular reprogramming</kwd>
</kwd-group>
<counts>
<fig-count count="3"/>
<table-count count="1"/>
<equation-count count="0"/>
<ref-count count="133"/>
<page-count count="11"/>
<word-count count="9705"/>
</counts>
</article-meta>
</front>
<body>
<sec sec-type="introduction" id="s1">
<title>Introduction</title>
<p>In 1942, C. H. Waddington coined the term epigenetics by combining the words epigenesis and genetics (Waddington, <xref ref-type="bibr" rid="B116">2012</xref>). Epigenesis refers to the sequence of events that occur during differentiation of cells from their initial totipotent state to a fully developed multicellular organism. The physical nature of genes and their role in heredity was unknown at the time Waddington coined this term. However, he used the term epigenetics to refer to the increasing irreversibility of cellular differentiation as a cell becomes more differentiated during development. The field of developmental biology continues striving to better understand how a single totipotent cell containing one genome has the ability to generate millions of highly specialized fully differentiated cells with very different gene regulatory networks.</p>
<p>The definition of epigenetics has evolved over the years and continues to be debated by scientists. Epigenetics was classically defined as heritable changes in gene function that cannot be explained by changes in DNA sequence and typically referred to DNA methylation related to parental genomic imprinting. However, this definition has changed drastically in recent years to encompass non-heritable changes that alter gene function including dynamic chromatin states regulated by various histone modifications and chromatin remodeling proteins. The development of the &#x0201C;omics era&#x0201D; has greatly impacted the way scientists now view epigenetics since many human developmental disorders and cancer have been correlated with the misregulation of specific epigenetic events and has driven the development of epigenetic therapeutics.</p>
<p>Although a vast amount of data about epigenetics exists for other tissues, there is a noticeable lack of information about epigenetic modifications in the inner ear. Proper epigenetic modifications are required for normal developmental processes. Gene expression must be coordinated in a temporal and cell-type specific manner and requires multiple levels of gene regulation. Although transcription factors are a primary source of gene regulation, epigenetic modifications regulate transcription factor access to target genes. This concept is apparent from studies looking at direct cellular reprogramming through ectopic expression of defined transcription factors, which show that direct reprogramming is a slow and inefficient process with most cells failing to reprogram (Huangfu et al., <xref ref-type="bibr" rid="B38">2008</xref>; Mikkelsen et al., <xref ref-type="bibr" rid="B75">2008</xref>). In the auditory field, ectopic expression of transcription factors such as <italic>Atoh1</italic> has been used to convert mammalian non-sensory epithelial cells into cells that express many endogenous hair cell markers (Zheng and Gao, <xref ref-type="bibr" rid="B130">2000</xref>; Izumikawa et al., <xref ref-type="bibr" rid="B43">2005</xref>; Gubbels et al., <xref ref-type="bibr" rid="B29">2008</xref>). However, the reprogramming process of transforming supporting cells into hair cells may not be solely about genetic transformation, but also epigenetic transformation. Studies using induced pluripotent stem cells (iPSCs) have shown that they retain the epigenetic memory of their somatic cell of origin (Kim et al., <xref ref-type="bibr" rid="B51">2010</xref>; Lister et al., <xref ref-type="bibr" rid="B68">2011</xref>). The epigenetic memory retained by iPSCs can interfere with their potential for differentiation into other cell types (Li et al., <xref ref-type="bibr" rid="B65">2009</xref>; Kim et al., <xref ref-type="bibr" rid="B51">2010</xref>; Lister et al., <xref ref-type="bibr" rid="B68">2011</xref>). Additionally, iPSCs derived from aged mice have a decreased potential for reprogramming compared to iPSCs derived from juvenile mice (Li et al., <xref ref-type="bibr" rid="B65">2009</xref>; Lister et al., <xref ref-type="bibr" rid="B68">2011</xref>). Although ectopic expression of transcription factors (<italic>Atoh1</italic>) can convert neonatal non-sensory epithelial cells into hair cell-like cells, loss of cellular plasticity at later postnatal ages could largely impact clinical application of this method (Kelly et al., <xref ref-type="bibr" rid="B48">2012</xref>; Liu et al., <xref ref-type="bibr" rid="B70">2012b</xref>).</p>
<p>In this review, we discuss the different types of epigenetic modifications and regulatory mechanisms in regards to development, disease, protection, and cellular reprogramming.</p>
</sec>
<sec id="s2">
<title>Histone modifications</title>
<p>Nucleosomes form the fundamental repeating units of eukaryotic chromatin, which is used to package large eukaryotic genomes into the nucleus while still ensuring appropriate access to the chromatin (Kornberg, <xref ref-type="bibr" rid="B57">1974</xref>; Kornberg and Thomas, <xref ref-type="bibr" rid="B58">1974</xref>). Nucleosomes are folded through a series of successively higher order structures to both compact DNA and create an added layer of regulatory control ensuring correct gene expression. The nucleosome is comprised of approximately 147 base pairs of DNA wrapped around eight histone core subunits consisting of two copies each of the core histones H2A, H2B, H3, and H4 (Luger et al., <xref ref-type="bibr" rid="B71">1997</xref>). Histone H3 and H4 have long tails that protrude from the nucleosome and can be covalently modified at several sites (Figure <xref ref-type="fig" rid="F1">1</xref>; Vaquero et al., <xref ref-type="bibr" rid="B113">2003</xref>; Campos and Reinberg, <xref ref-type="bibr" rid="B14">2009</xref>; Bannister and Kouzarides, <xref ref-type="bibr" rid="B3">2011</xref>). These histone tails are subjected to post-translational modification including acetylation, methylation, phosphorylation, ubiquitination, sumoylation, or ADP-ribosylation which is mediated by the counteracting activities of enzymes that add or remove such modifications (Vaquero et al., <xref ref-type="bibr" rid="B113">2003</xref>; Campos and Reinberg, <xref ref-type="bibr" rid="B14">2009</xref>; Bannister and Kouzarides, <xref ref-type="bibr" rid="B3">2011</xref>).</p>
<fig id="F1" position="float">
<label>Figure 1</label>
<caption><p><bold>Cartoon diagram indicates potential sites of modification at specific residues along the histones tail</bold>. The tails of histone H3 and H4 have the largest number of potential modification sites including lysine (K)-specific methylation and acetylation sites and arginine (R)-specific methylation sites. The tail of histone H3 is subject to both repressive lysine (K)-specific methylation marks (K9 and K27) as well as activating lysine (K)-specific methylation marks (K4, K36, and K79).</p></caption>
<graphic xlink:href="fncel-08-00446-g0001.tif"/>
</fig>
<sec id="s2-1">
<title>Histone acetylation</title>
<p>Posttranslational histone modifications alter histones interaction with DNA and nuclear proteins. Histone acetylation of specific lysine residues plays a fundamental role in transcriptional regulation. The enzymes responsible for maintaining proper histone acetylation states include histone acetyltransferases (HATs) and histone deacetylases (HDACs). Histones undergo acetylation to yield a more relaxed chromatin conformation resulting from a net change in the overall charge and reduced electrostatic interactions. HATs transfer the acetyl moiety from acetyl coenzyme A to specific lysine residues on the histone tail. Acetylated histones also act as a signal that recruits bromodomain-containing proteins, which are primarily transcription factors and cofactors to target genes activating their transcription (Zeng and Zhou, <xref ref-type="bibr" rid="B127">2002</xref>). The HDACs act in opposition to the HATs by removing the acetyl groups from histone tails allowing histones to interact with DNA more tightly to form a compacted nucleosome structure. This increased rigidity of the chromatin prevents the incorporation of transcriptional machinery, effectively silencing gene transcription (Figure <xref ref-type="fig" rid="F2">2</xref>).</p>
<fig id="F2" position="float">
<label>Figure 2</label>
<caption><p><bold>Chromatin state.</bold> Cartoon diagram depicting the open relaxed chromatin of an actively transcribed gene (upper portion), compared to the nucleosome dense compacted chromatin associated with a silenced gene (bottom portion). HMT&#x02014;histone methyltransferase, HAT&#x02014;histone acetyltransferase, TBP&#x02014;TATA-binding protein, TAF&#x02014;TBP-associated factors, TF&#x02014;transcription factor, HDAC&#x02014;histone deacetylase, KDM&#x02014;lysine (K)-specific demethylase, DNMT&#x02014;DNA methyltransferase, MBD&#x02014;methyl-CpG-binding domain.</p></caption>
<graphic xlink:href="fncel-08-00446-g0002.tif"/>
</fig>
</sec>
<sec id="s2-2">
<title>Histone methylation and demethylation</title>
<p>Histone methylation, depending on both the histone and residue modified, contributes to either active or repressive chromatin configurations (Figure <xref ref-type="fig" rid="F2">2</xref>). Although histone methylation is not as well understood as acetylation, histones H3 and H4 are common methylation targets that can be methylated on arginine and lysine residues (Figure <xref ref-type="fig" rid="F1">1</xref>). While lysine can receive only one acetyl group, it can receive up to three methyl groups, and does not affect the overall charge of the residue. Specific histone methylation states serve as binding sites for the recruitment of additional regulatory proteins such as chromatin remodelers (Zhang and Dent, <xref ref-type="bibr" rid="B129">2005</xref>; Wu and Zhang, <xref ref-type="bibr" rid="B122">2009</xref>; Helin and Dhanak, <xref ref-type="bibr" rid="B33">2013</xref>). As a general rule of thumb, sites of methylation that are typically associated with active gene transcription are H3K4me2/3 (promoter), H3K36me3 (3&#x02032; end gene body), and H3K79me2 (5&#x02032; end of gene body) (Azuara et al., <xref ref-type="bibr" rid="B2">2006</xref>; Kolasinska-Zwierz et al., <xref ref-type="bibr" rid="B54">2009</xref>; Onder et al., <xref ref-type="bibr" rid="B81">2012</xref>; Fuchs et al., <xref ref-type="bibr" rid="B26">2014</xref>). Whereas methylation marks associated typically with silenced genes are H3K9me2/3 (promoter and enhancer), H3K27me3 (promoter and enhancer), and H4K20me3 (promoter) (Azuara et al., <xref ref-type="bibr" rid="B2">2006</xref>; Kolasinska-Zwierz et al., <xref ref-type="bibr" rid="B54">2009</xref>). These common active and repressive histone marks are further illustrated in relation to the gene region in which they are detected in Figure <xref ref-type="fig" rid="F3">3</xref>.</p>
<fig id="F3" position="float">
<label>Figure 3</label>
<caption><p><bold>Chromatin modifications are distributed in specific gene regulatory regions. (A)</bold> The normal distribution of DNA methylation, DNA hydroxymethylation, and histone marks in the enhancer, promoter, and gene body of actively transcribed genes. Actively transcribed genes carry typically have chromatin modifications within the gene body to facilitate transcription initiation and elongation. <bold>(B)</bold> Common chromatin modifications found in the enhancer, promoter, and gene body of silenced genes. <bold>(C)</bold> Bivalent/poised genes have both activating and silencing chromatin modifications to facilitate rapid changes in gene expression during development.</p></caption>
<graphic xlink:href="fncel-08-00446-g0003.tif"/>
</fig>
<p>Studies of histone methylation marks in mouse pluripotent embryonic stem cells (ESCs) have defined a class of developmentally regulated genes as &#x0201C;bivalent&#x0201D; since these genes are marked with both active (H3K4me3) and repressive (H3K27me3) histone modifications (Figure <xref ref-type="fig" rid="F3">3</xref>; Azuara et al., <xref ref-type="bibr" rid="B2">2006</xref>; Bernstein et al., <xref ref-type="bibr" rid="B5">2006</xref>; Mikkelsen et al., <xref ref-type="bibr" rid="B76">2007</xref>; Voigt et al., <xref ref-type="bibr" rid="B115">2013</xref>). By exhibiting both active and repressive features, bivalent genes are posited as being in a poised state, enabling them to be rapidly activated upon suitable developmental cues and/or environmental stimuli. Although bivalent genes were first described for ESCs, where the marks are most prevalent, later observations also detected bivalent domains in cell types of restricted potency such as neural progenitor cells (Mikkelsen et al., <xref ref-type="bibr" rid="B76">2007</xref>; Rugg-Gunn et al., <xref ref-type="bibr" rid="B91">2010</xref>).</p>
<p>The enzymes responsible for maintaining proper histone methylation status are histone lysine/arginine methyltransferases and histone lysine/arginine demethylases. Lysine-specific histone methyltransferases (HMTs) are subdivided into SET (<bold>S</bold>u(var)3&#x02013;9, <bold>E</bold>nhancer of Zeste, <bold>T</bold>rithorax) domain-containing and non-SET domain-containing proteins. The argine-specific protein arginine methyltransferases (PRMTs) are responsible for methylating arginine residues on the histones. HMTs and PRMTs together have over 60 different family members all of which use S-Adenosyl methionine (SAM) as a cofactor and methyl donor group (Helin and Dhanak, <xref ref-type="bibr" rid="B33">2013</xref>).</p>
<p>Histone methylation for many years was considered to be a permanent and irreversible histone modification due to the low turnover rate of methylated histones (Byvoet et al., <xref ref-type="bibr" rid="B9">1972</xref>). However, the discovery of lysine specific demethylase 1 (LSD1, officially known as KDM1A) and later the JmjC-domain-containing lysine demethylase family has completely changed this view (Kooistra and Helin, <xref ref-type="bibr" rid="B56">2012</xref>). Interestingly, LSD1 can catalyze the demethylation of H3K4me1/2 and H3K9me1/2, which means that LSD1 has the ability to both silence and activate gene transcription (Zhang and Dent, <xref ref-type="bibr" rid="B129">2005</xref>; Wu and Zhang, <xref ref-type="bibr" rid="B122">2009</xref>; Helin and Dhanak, <xref ref-type="bibr" rid="B33">2013</xref>). LSD1 is also reported to demethylate non-histone target proteins such as p53, DNMT1, and E2F1 (Huang et al., <xref ref-type="bibr" rid="B37">2007</xref>; Wang et al., <xref ref-type="bibr" rid="B117">2009</xref>; Kontaki and Talianidis, <xref ref-type="bibr" rid="B55">2010</xref>; Helin and Dhanak, <xref ref-type="bibr" rid="B33">2013</xref>; Mosammaparast et al., <xref ref-type="bibr" rid="B77">2013</xref>). LSD1 and its close relative LSD2 belong to the superfamily of flavin adenine dinucleotide (FAD)-dependent monooxidases. Unlike the LSD demethylases, the JmjC-domain-containing demethylases can also demethylate trimethylated lysines. This catalysis involves an oxidative mechanism requiring iron and 2-oxoglutarate as co-factors and is posited to occur through direct hydroxylation of the affected methyl group.</p>
</sec>
<sec id="s2-3">
<title>Histone variants</title>
<p>Although histones have a conserved role as general DNA packaging agents, it has become clear that another key function of these proteins is to confer variation in chromatin structure to ensure dynamic patterns of transcriptional regulation. Some histone variants have distinct biophysical characteristics that are thought to alter the properties of nucleosomes, while other variants are targeted to specific regions of the genome. Specific histone variants are exchanged with the pre-existing histones during critical periods of development and differentiation (Brandt et al., <xref ref-type="bibr" rid="B8">1979</xref>; Grove and Zweidler, <xref ref-type="bibr" rid="B28">1984</xref>; Wunsch et al., <xref ref-type="bibr" rid="B123">1991</xref>; Bosch and Suau, <xref ref-type="bibr" rid="B6">1995</xref>). This replacement can often result in the variants becoming the predominant species in the differentiated cell (Pina and Suau, <xref ref-type="bibr" rid="B82">1987</xref>; Wunsch et al., <xref ref-type="bibr" rid="B123">1991</xref>). Mutations in specific histone variants and their associated chaperone machinery contribute to human disease such as cancer (Maze et al., <xref ref-type="bibr" rid="B72">2014</xref>), suggesting an essential function for regulation of histone variants during specific aspects of cellular differentiation.</p>
</sec>
</sec>
<sec id="s3">
<title>DNA methylation</title>
<p>Methylation at the 5-positon of cytosine (5-mC) is one of the best studied and most mechanistically understood epigenetic modifications that is well conserved among most plant, animal and fungal models (Feng et al., <xref ref-type="bibr" rid="B25">2010</xref>). Three conserved DNA methyltransferase enzymes, DNA methyltransferase 1 (DNMT1), DNMT3A and DNMT3B, are responsible for the deposition and maintenance of DNA methylation and are essential for normal development (Li et al., <xref ref-type="bibr" rid="B64">1992</xref>; Okano et al., <xref ref-type="bibr" rid="B80">1999</xref>). Mammalian genomes are globally CpG-depleted and roughly 60&#x02013;80% of the 28 million CpGs in the human genome are generally methylated (Smith and Meissner, <xref ref-type="bibr" rid="B99">2013</xref>). Less than 10% of CpGs occur in the CG-dense regions called CpG islands (Deaton and Bird, <xref ref-type="bibr" rid="B20">2011</xref>). CpG islands are prevalent at transcription start sites (TSSs) of housekeeping genes and genes involved in developmental processes (Deaton and Bird, <xref ref-type="bibr" rid="B20">2011</xref>). Most genomic DNA methylation patterns are static across tissues and throughout life and only change in localized contexts as specific cellular processes are activated or repressed (Figure <xref ref-type="fig" rid="F3">3</xref>). However, the exception to this is in the germ line and during pre-implantation embryonic development, when DNA methylation levels are globally reset (Smith and Meissner, <xref ref-type="bibr" rid="B99">2013</xref>).</p>
<p>Numerous assays have been developed since DNA methylation was originally postulated as an epigenetic regulator to study cytosine methylation (Holliday and Pugh, <xref ref-type="bibr" rid="B35">1975</xref>; Riggs, <xref ref-type="bibr" rid="B86">1975</xref>). This includes assays such as methylation-sensitive restriction enzyme mapping, deamination of unmethylated cytosines with sodium bisulphite, and targeting methylated DNA directly using antibodies for enrichment. High-throughput sequencing has enabled complete methylomes to be elucidated, such that methylation sites are now mapped at base-pair resolution across development from zygote to terminally differentiated adult cells. However, global DNA methylation patterns during development and aging are tissue and cell type-specific (Calvanese et al., <xref ref-type="bibr" rid="B10">2012</xref>).</p>
<p>DNMT1 is critical for maintaining DNA methylation during mitosis. During DNA replication, DNMT1 is positioned at the replication fork and transfers the methylation marks to the newly synthesized daughter strand and is essential for stable repression of genes after cell division. Although DNA methylation maintenance ensures epigenetic inheritance at established positions, there are many instances in which methylation must be specifically targeted and others in which methylation must be inhibited or removed. DNMT3A and DNMT3B are responsible for establishing <italic>de novo</italic> DNA methylation, primarily at CpG dinucleotides (Jurkowska et al., <xref ref-type="bibr" rid="B47">2011</xref>). DNMT3A and DNMT3B target promoters in complex with other epigenetic repressors, including HDACs and repressive HMTs such as EZH2 and G9a. Additionally, crosstalk exists between some site-specific transcription factors and DNMTs for example DNMT1, DNMT3A, and DNMT3B have been shown to interact with transcription factors such as E2F1, E2F6, and Atoh1 to facilitate or prevent DNA methylation at specific target genes (Robertson et al., <xref ref-type="bibr" rid="B89">2000</xref>; Bossuyt et al., <xref ref-type="bibr" rid="B7">2009</xref>; Velasco et al., <xref ref-type="bibr" rid="B114">2010</xref>). Loss of all three DNMTs in ESCs does not affect their survival or stem cell molecular identity, but the ability to differentiate is completely inhibited (Jackson et al., <xref ref-type="bibr" rid="B44">2004</xref>; Tsumura et al., <xref ref-type="bibr" rid="B110">2006</xref>). ESCs lacking DNA methylation fail to up-regulate germ layer associated markers and are unable to efficiently silence pluripotency genes (Jackson et al., <xref ref-type="bibr" rid="B44">2004</xref>). Typically the transcriptional network associated with pluripotency is rapidly silenced upon differentiation through both maintenance and <italic>de novo</italic> methylation, since embryonic programs must be resolved towards specific cell lineages.</p>
<p>5-mC was initially the only known DNA-specific epigenetic mark, then in 2009, 5-hydroxymethylcytosine (5-hmC) was discovered as another relatively abundant cytosine modification in mouse Purkinje neurons and ESCs (Kriaucionis and Heintz, <xref ref-type="bibr" rid="B59">2009</xref>; Tahiliani et al., <xref ref-type="bibr" rid="B107">2009</xref>). The ten-eleven translocation (TET) proteins mediate the oxidation of 5-mC to 5-hmC (Tahiliani et al., <xref ref-type="bibr" rid="B107">2009</xref>; Wang et al., <xref ref-type="bibr" rid="B118">2012</xref>), which is then further oxidized in a stepwise manner to 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC; He et al., <xref ref-type="bibr" rid="B32">2011</xref>; Ito et al., <xref ref-type="bibr" rid="B42">2011</xref>). An emerging finding is that 5-mC and 5-hmC are dynamically regulated both within and across cell types (Kriaucionis and Heintz, <xref ref-type="bibr" rid="B59">2009</xref>; Tahiliani et al., <xref ref-type="bibr" rid="B107">2009</xref>; Szulwach et al., <xref ref-type="bibr" rid="B104">2011</xref>; Shen and Zhang, <xref ref-type="bibr" rid="B95">2013</xref>). Although 5-hmC may simply act as a DNA demethylation intermediate, studies have shown that 5-hmC not only impairs the binding of 5-mC binding proteins (Valinluck et al., <xref ref-type="bibr" rid="B111">2004</xref>), but also has its own unique binding protein, MBD3, (Yildirim et al., <xref ref-type="bibr" rid="B124">2011</xref>) and shows unique distribution patterns in the genome (Stroud et al., <xref ref-type="bibr" rid="B101">2011</xref>; Szulwach et al., <xref ref-type="bibr" rid="B104">2011</xref>). 5-hmC is enriched in gene dense euchromatic regions, and particularly at TSSs, promoters, and enhancers (Shen and Zhang, <xref ref-type="bibr" rid="B95">2013</xref>). Additionally, 5-hmC is specifically enriched at gene promoters associated with bivalent domains marked with both the permissive mark H3K4me2/3 and the repressive mark H3K27me3, but is absent from heterochromatin marked by H3K9me3 (Shen and Zhang, <xref ref-type="bibr" rid="B95">2013</xref>).</p>
<p>Recent genome-wide analysis of DNA methylation in human cells has identified a widespread distribution of 5-mC and, paradoxically, has shown hypermethylation in the gene bodies of actively transcribed genes (Figure <xref ref-type="fig" rid="F3">3</xref>; Lister et al., <xref ref-type="bibr" rid="B67">2009</xref>; Stadler et al., <xref ref-type="bibr" rid="B100">2011</xref>; Hon et al., <xref ref-type="bibr" rid="B36">2013</xref>; Ziller et al., <xref ref-type="bibr" rid="B133">2013</xref>) and hypomethylation was found at active enhancers (Lister et al., <xref ref-type="bibr" rid="B67">2009</xref>; Stadler et al., <xref ref-type="bibr" rid="B100">2011</xref>; Hon et al., <xref ref-type="bibr" rid="B36">2013</xref>; Ziller et al., <xref ref-type="bibr" rid="B133">2013</xref>). 5-hmC is also significantly enriched at distal cis-regulatory sequences, suggesting that dynamic DNA methylation at these regions is likely mediated by interplays between DNMT mediated methylation and TET mediated demethylation processes (Stroud et al., <xref ref-type="bibr" rid="B101">2011</xref>; Szulwach et al., <xref ref-type="bibr" rid="B104">2011</xref>; Yu et al., <xref ref-type="bibr" rid="B125">2012</xref>). Together, these studies have underscored the diverse roles that DNA methylation has in gene regulation and the need for systematic mapping and characterization of DNA methylomes in different tissues and cell types during development and aging. Since proper maintenance of 5-mC and 5-hmC by DNMT and TET proteins has been shown to be critical for proper neurodevelopment and memory (Wang et al., <xref ref-type="bibr" rid="B118">2012</xref>), aberrant alterations in DNA methylation are also correlated with diseases such as diabetes, schizophrenia, multiple sclerosis, cancer, and cellular senescence (Jurkowska et al., <xref ref-type="bibr" rid="B47">2011</xref>).</p>
</sec>
<sec id="s4">
<title>Chromatin remodelers</title>
<p>At least three processes control the assembly and regulation of chromatin: histone modifications, DNA methylation, and ATP-dependent chromatin remodeling. ATP-dependent chromatin remodelers alter the physical state of chromatin by either sliding nucleosomes in relation to the DNA or exchanging nucleosomes into and out of DNA. Chromatin remodelers act as &#x0201C;readers&#x0201D; of the histone modifications to regulate chromatin structure and gene expression. Approximately 30 genes encode the ATP-dependent chromatin remodeling subunits in mammals. With few exceptions, the ATP-dependent chromatin remodeling proteins appear to be genetically non-redundant.</p>
<p>Mutations in ATP-dependent chromatin remodeling genes often have severe effects on the early embryo or give rise to maternal-effect phenotypes in which the phenotype of the embryo reflects the genotype of the mother. In many cases, the genes encoding the ATP-dependent chromatin remodeling proteins or their subunits are haploinsufficient, which indicates that their role in specific developmental processes is likely rate limiting. For instance, heterozygous mutation in the chromodomain helicase DNA binding protein 7 (CHD7) causes CHARGE syndrome, a multiple anomaly disorder that is a common cause of deaf-blindness in humans (Zentner et al., <xref ref-type="bibr" rid="B128">2010</xref>), whereas duplication or overexpression of <italic>CHD7</italic> is associated with multiple forms of cancer including colorectal cancer, pancreatic cancer, small-cell lung cancer, and gastric cancer (Pleasance et al., <xref ref-type="bibr" rid="B83">2010</xref>; Kim et al., <xref ref-type="bibr" rid="B50">2011</xref>; Colbert et al., <xref ref-type="bibr" rid="B18">2014</xref>; Tahara et al., <xref ref-type="bibr" rid="B106">2014</xref>). These data together suggest that many cell types may be highly sensitive to chromatin remodeler dosage during development and aging.</p>
</sec>
<sec id="s5">
<title>Epigenetics and hearing loss</title>
<p>Hereditary hearing loss or deafness has been associated with mutations in genes whose proteins regulate the chromatin state and include genes involved in DNA methylation, histone modification and chromatin remodeling (Table <xref ref-type="table" rid="T1">1</xref>). Autosomal dominant cerebellar ataxia, deafness, and narcolepsy (ADCADN) and hereditary sensory neuropathy type IE (HSN1E) are both caused by heterozygous mutation in the DNMT1 gene (Sun et al., <xref ref-type="bibr" rid="B102">2014</xref>). ADCADN is characterized by late onset (age 30&#x02013;40 years) narcolepsy&#x02013;cataplexy, sensorineural deafness, cerebellar ataxia, dementia, psychosis, optic atrophy, and other symptoms (Winkelmann et al., <xref ref-type="bibr" rid="B120">2012</xref>). Narcolepsy and deafness are typically the first symptoms to appear followed by ataxia (Winkelmann et al., <xref ref-type="bibr" rid="B120">2012</xref>). People with HSN1E develop hearing loss that is caused by abnormalities in the inner ear leading to sensorineural hearing loss (Wright and Dyck, <xref ref-type="bibr" rid="B121">1995</xref>; Hojo et al., <xref ref-type="bibr" rid="B34">1999</xref>; Klein et al., <xref ref-type="bibr" rid="B53">2011</xref>). Hearing loss worsens over time and usually progresses to moderate or severe deafness between the ages of 20 and 35 (Wright and Dyck, <xref ref-type="bibr" rid="B121">1995</xref>; Hojo et al., <xref ref-type="bibr" rid="B34">1999</xref>; Klein et al., <xref ref-type="bibr" rid="B53">2011</xref>). Mutations in DNMT1 typically cause bilateral hearing loss but unilateral hearing loss has also been reported (Melberg et al., <xref ref-type="bibr" rid="B73">1995</xref>).</p>
<table-wrap id="T1" position="float">
<label>Table 1</label>
<caption><p><bold>Epigenetic factors associated with hearing loss in humans</bold>.</p></caption>
<table frame="hsides" rules="groups">
<thead>
<tr>
<th align="left">Human disease</th>
<th align="left">Gene</th>
<th align="left">Type of hearing loss</th>
</tr>
</thead>
<tbody>
<tr>
<td/>
<td colspan="3" align="left"><italic>DNA methyltransferase</italic></td>
<td/>
</tr>
<tr>
<td align="left">Autosomal dominant cerebellar ataxia, deafness, and narcolepsy (ADCADN)</td>
<td align="left">DNMT1</td>
<td align="left">Sensorineural</td>
</tr>
<tr>
<td align="left">Hereditary sensory neuropathy type IE (HSN1E)</td>
<td align="left">DNMT1</td>
<td align="left">Sensorineural</td>
</tr>
<tr>
<td/>
<td colspan="3" align="left"><italic>Histone methyltransferase</italic></td>
</tr>
<tr>
<td align="left">Sotos syndrome</td>
<td align="left">NSD1</td>
<td align="left">Conductive</td>
</tr>
<tr>
<td align="left">Weaver syndrome</td>
<td align="left">EZH2</td>
<td align="left">Conductive</td>
</tr>
<tr>
<td align="left">Kleefstra syndrome</td>
<td align="left">EHMT1</td>
<td align="left">Sensorineural,</td>
</tr>
<tr>
<td align="left">Kabuki syndrome</td>
<td align="left">KMT2D</td>
<td align="left">Sensorineural Conductive, or Mixed</td>
</tr>
<tr>
<td/>
<td colspan="3" align="left"><italic>Histone acetyltransferase</italic></td>
<td/>
<td/>
</tr>
<tr>
<td align="left">Say-Barber-Biesecker variant of Ohdo syndrome</td>
<td align="left">KAT6B</td>
<td align="left">Sensorineural</td>
</tr>
<tr>
<td align="left">Genitopatellar syndrome (GPS)</td>
<td align="left">KAT6B</td>
<td align="left">Sensorineural</td>
</tr>
<tr>
<td/>
<td align="left">Chromatin remodeler</td>
<td/>
<td/>
</tr>
<tr>
<td align="left">CHARGE syndrome</td>
<td align="left">CHD7</td>
<td align="left">Sensorineural</td>
</tr>
</tbody>
</table>
<table-wrap-foot>
<p><italic>Human diseases associated with hereditary hearing loss or deafness caused by heterozygous mutation in genes whose protein product is involved in DNA methylation, histone modification, or chromatin remodeling</italic>.</p>
</table-wrap-foot>
</table-wrap>
<p>Mutations in HMT have also been associated with hearing loss. Overgrowth disorders, Sotos syndrome and Weaver syndrome, are caused by heterozygous mutations in the HMT NSD1 (Sotos and Weaver syndromes) and EZH2 (Weaver syndrome) (Tatton-Brown and Rahman, <xref ref-type="bibr" rid="B108">2013</xref>; Tatton-Brown et al., <xref ref-type="bibr" rid="B109">2013</xref>). Sotos syndrome is frequently associated with conductive hearing loss while only a few cases of hearing loss have been reported for Weaver syndrome (Tatton-Brown et al., <xref ref-type="bibr" rid="B109">2013</xref>). Although a large degree of phenotypic overlap exists between Sotos syndrome and Weaver syndrome, NSD1 and EZH2 regulate different methylation sites. NSD1 has been shown to preferentially dimethylate H3K36 and H4K20, the impact of dimethylation at either of these two lysine residues is not entirely clear at this time (Qiao et al., <xref ref-type="bibr" rid="B84">2011</xref>). However, EZH2 has been well characterized as it functions as the catalytic subunit for the polycomb repressive complex 2 (PRC2) and is a critical regulator of H3K27me3.</p>
<p>Kleefstra syndrome is a developmental disorder characterized by intellectual disability, childhood hypotonia, distinctive facial features and sensorineural hearing loss (Kleefstra et al., <xref ref-type="bibr" rid="B52">2005</xref>). Heterozygous mutation in euchromatic histone-lysine N-methyltransferase 1 (EHMT1) is causative for Kleefstra syndrome (Kleefstra et al., <xref ref-type="bibr" rid="B52">2005</xref>). EHMT1 is part of the E2F6 complex which represses transcription via methylation of histone H3K9 (Tachibana et al., <xref ref-type="bibr" rid="B105">2005</xref>).</p>
<p>Heterozygous mutation in lysine (K)-specific methyltransferase 2D (KMT2D, also known as MLL2/MLL4) is associated with Kabuki syndrome (Ng et al., <xref ref-type="bibr" rid="B79">2010</xref>). Kabuki syndrome is characterized by distinctive facial features, mild to moderate mental impairment, microcephaly, hypertonia, skeletal abnormalities, heart abnormalities, and hearing loss (Ng et al., <xref ref-type="bibr" rid="B79">2010</xref>). Hearing loss is a common finding in Kabuki syndrome and can be conductive, sensorineural or mixed (Barozzi et al., <xref ref-type="bibr" rid="B4">2009</xref>). KMT2D is a histone methyltransferase that has been shown to mono- and dimethylate H3K4 (Lee et al., <xref ref-type="bibr" rid="B63">2013</xref>). Approximately 6 percent of Kabuki syndrome cases are caused by heterozygous mutation in lysine (K)-specific demethylase 6A (KDM6A). KDM6A catalyzes the demethylation of H3K27me3. Although, KMT2D and KDM6A have different functions at different lysine residues, both ultimately act as transcriptional activators (Jiang et al., <xref ref-type="bibr" rid="B46">2013</xref>; Lee et al., <xref ref-type="bibr" rid="B63">2013</xref>).</p>
<p>Heterozygous mutations in lysine acetyltransferase 6B (KAT6B, also known as MYST4) are associated with both genitopatellar syndrome (GPS) and Say-Barber-Biesecker variant of Ohdo syndrome (Campeau et al., <xref ref-type="bibr" rid="B11">2012a</xref>; Simpson et al., <xref ref-type="bibr" rid="B96">2012</xref>). These KAT6B-related disorders have phenotypic overlap that includes significant global developmental delay/intellectual disability, hypotonia, cryptorchidism, patellar hypoplasia/agenesis, congenital heart defects, dental anomalies, hearing loss, and thyroid anomalies (Campeau et al., <xref ref-type="bibr" rid="B11">2012a</xref>; Simpson et al., <xref ref-type="bibr" rid="B96">2012</xref>). KAT6B is a HAT that also has transcriptional activation activity in the N-terminal end of the protein and transcriptional repression activity in the C-terminal end of the protein (Campeau et al., <xref ref-type="bibr" rid="B12">2012b</xref>). Mutations leading to GPS occur in the proximal portion of the last exon and lead to the expression of a protein without a C-terminal domain, while mutations leading to Say-Barber-Biesecker variant of Ohdo syndrome occur either throughout the gene, leading to nonsense-mediated decay, or more distally in the last exon (Campeau et al., <xref ref-type="bibr" rid="B12">2012b</xref>).</p>
<p>CHD7 has been more extensively characterized in regards to inner ear development than the epigenetic factors listed above. CHD7 haploinsufficiency causes CHARGE syndrome, the most consistent clinical feature associated with CHARGE is inner ear defects, including semicircular canal dysplasia that typically affects all three canals, and a Mondini form of cochlear hypoplasia (Layman et al., <xref ref-type="bibr" rid="B61">2010</xref>; Zentner et al., <xref ref-type="bibr" rid="B128">2010</xref>). Inner ear phenotypes observed in mouse models of CHARGE syndrome are similar to those reported in CHARGE patients and include semicircular canal defects, innervation defects, and vestibular dysfunction (Kiernan et al., <xref ref-type="bibr" rid="B49">2002</xref>; Hawker et al., <xref ref-type="bibr" rid="B31">2005</xref>; Adams et al., <xref ref-type="bibr" rid="B1">2007</xref>; Hurd et al., <xref ref-type="bibr" rid="B39">2007</xref>). Complete absence of CHD7 results in decreased expression of patterning and pro-neural genes including <italic>Otx2, Fgf10, Ngn1, NeuroD</italic>, <italic>Islet1, Rarb</italic>, and <italic>Rxrg</italic> genes leading to reduced proliferation of developing neuroblasts and inner ear malformations (Hurd et al., <xref ref-type="bibr" rid="B40">2010</xref>; Micucci et al., <xref ref-type="bibr" rid="B74">2014</xref>). Additionally, a recent report found that CHD7 deficiency triggers both p53 expression and activation (Van Nostrand et al., <xref ref-type="bibr" rid="B112">2014</xref>). These data together provide a basis for understanding how CHD7 deficiency results in the profound yet variable phenotypes associated with CHARGE syndrome and potential targets for therapeutic development.</p>
</sec>
<sec id="s6">
<title>Epigenetics: damage and protection</title>
<p>Auditory hair cells have repeatedly been shown to be susceptible to ototoxicity from a multitude of drugs including aminoglycoside antibiotics such as gentamicin, loop diuretics such as furosemide, platinum-based chemotherapy agents such as cisplatin, and a number of non-steroidal anti-inflammatory drugs (NSAIDS). Additionally, noise is one of the most common causes of hearing loss, and one of the most common occupational illnesses in the United States. The formation of reactive oxygen species (ROS) is the major cause that underlies the molecular pathology of hair cell death related to noise induced trauma as well as aminoglycoside antibiotic and cisplatin treatment (Cheng et al., <xref ref-type="bibr" rid="B16">2005</xref>; Schacht et al., <xref ref-type="bibr" rid="B94">2012</xref>). ROS production is associated with increased DNA damage and chromosomal degradation with alterations of both hypermethylation and hypomethylation of the DNA (Campos et al., <xref ref-type="bibr" rid="B13">2007</xref>; Lim et al., <xref ref-type="bibr" rid="B66">2008</xref>; Donkena et al., <xref ref-type="bibr" rid="B21">2010</xref>; Ziech et al., <xref ref-type="bibr" rid="B132">2010</xref>, <xref ref-type="bibr" rid="B131">2011</xref>). Aminoglycoside antibiotics have also been shown to cause increased histone deacetylation in mammalian hair cells through recruitment of HDACs to the chromatin (Jiang et al., <xref ref-type="bibr" rid="B45">2006</xref>; Chen et al., <xref ref-type="bibr" rid="B15">2009</xref>).</p>
<p>HDAC inhibitors were originally used as anti-cancer agents and some are approved by the FDA for use in the treatment of specific types of cancer in humans. However, broad spectrum and HDAC-specific inhibitors are also known to have protective effects in a concentration dependent manner in inflammation, neurodegeneration, and oxidative stress models (Ryu et al., <xref ref-type="bibr" rid="B92">2003</xref>; Liu et al., <xref ref-type="bibr" rid="B69">2012a</xref>; Robert and Rassool, <xref ref-type="bibr" rid="B88">2012</xref>). HDAC inhibitors are primarily thought to modulate chromatin condensation by regulating histone acetylation and thus affect gene expression. HDAC inhibitors have also been shown to affect the post-translational modification of some important intracellular non-histone proteins, such as heat shock protein 90 and Rel-A/p65 (Yu et al., <xref ref-type="bibr" rid="B126">2002</xref>; Faraco et al., <xref ref-type="bibr" rid="B24">2009</xref>). In the inner ear, HDAC inhibitors also have a protective effect on hair cells subjected to aminoglycosides <italic>in vitro</italic> (Chen et al., <xref ref-type="bibr" rid="B15">2009</xref>) and cisplatin <italic>in vivo</italic> (Drottar et al., <xref ref-type="bibr" rid="B22">2006</xref>). However, the precise mechanism underlying their protective effect in the inner ear remains unknown.</p>
</sec>
<sec id="s7">
<title>Cellular reprogramming and hair cell regeneration</title>
<p>Reprogramming cell fate through transcription factor(s) over-expression is a general and powerful approach for regenerative medicine (Cohen and Melton, <xref ref-type="bibr" rid="B17">2011</xref>). However, direct reprogramming through ectopic expression of defined transcription factors is a slow and inefficient process that requires weeks, with most cells failing to reprogram (Huangfu et al., <xref ref-type="bibr" rid="B38">2008</xref>; Mikkelsen et al., <xref ref-type="bibr" rid="B75">2008</xref>). Additionally, the efficiency and yield of cellular reprogramming rapidly declines with increasing age and differentiation status of the donor cell (Hanna et al., <xref ref-type="bibr" rid="B30">2010</xref>; Kim et al., <xref ref-type="bibr" rid="B51">2010</xref>; Lister et al., <xref ref-type="bibr" rid="B68">2011</xref>). A large reconfiguration of the chromatin structure, from DNA methylation to histone modifications and nucleosome remodeling, occurs during somatic cell reprogramming to a pluripotent state. These layers of epigenetic regulation are often used as repressive mechanisms in somatic cells to prevent unwanted gene expression from other lineages. How these epigenetic barriers to reprogramming are overcome is a key question, since the epigenetic memory of the somatic cell largely impacts its capacity for cellular reprogramming. Several lines of evidence support the notion that the process of reprogramming involves rare stochastic epigenetic events. Studies have shown that inhibitors of epigenetic events such as DNA methylation, histone deacetylation, and histone methylation are able to improve reprogramming efficiency (Huangfu et al., <xref ref-type="bibr" rid="B38">2008</xref>; Mikkelsen et al., <xref ref-type="bibr" rid="B75">2008</xref>; Hanna et al., <xref ref-type="bibr" rid="B30">2010</xref>; Kim et al., <xref ref-type="bibr" rid="B51">2010</xref>; Lister et al., <xref ref-type="bibr" rid="B68">2011</xref>).</p>
<p>The epigenetic modifications made during inner ear development remain mostly unknown at this time. However, cofactors of repressive complexes such as NuRD and PRC2 have been reported to be present in the neonatal mouse organ of Corti. The NuRD cofactors including LSD1 are present throughout most of the organ of Corti from E18.5 until P4, then completely absent by P7, and are detectable again from P8 through P21 (Layman et al., <xref ref-type="bibr" rid="B62">2013</xref>). The PRC2 enzymatic subunit, EZH2 is also highly present from E18.5 to P0 in the mouse organ of Corti, absent between P2 and P4, and is evident again throughout the organ of Corti by P6 and persists through P21 (Layman et al., <xref ref-type="bibr" rid="B62">2013</xref>). The presence of these repressive complexes also correlates with transcriptional silencing of known target genes of LSD1 and EZH2 including genes required for proliferation (mTert) and cell fate specification (Atoh1), which is consistent with reports related to organ of Corti quiescence and maturation during neonatal development. Additionally, DNMT3A and DNMT3B are also reported to have a dramatic increase in expression after the first postnatal week in the mouse organ of Corti (Mutai et al., <xref ref-type="bibr" rid="B78">2009</xref>; Layman et al., <xref ref-type="bibr" rid="B62">2013</xref>). DNA methylation is one of the most common and irreversible epigenetic modifications that control gene expression. DNA methylation may repress genes encoding drug metabolizing enzymes, drug transporters, or even drug target genes, which may alter the pharmacokinetics and pharmacodynamics of drugs that may be ototoxic or drugs designed to facilitate hearing regeneration. A better understanding of how the genes in the inner ear are regulated epigenetically will allow researchers the ability to design therapeutic agents that may bypass or alter the chromatin state making it more amenable to cellular reprogramming.</p>
<p>Unlike mammalian hair cells, hair cells in the avian basilar papilla and utricle are rapidly regenerated after ototoxic injury (Corwin and Oberholtzer, <xref ref-type="bibr" rid="B19">1997</xref>). New avian hair cells are generated from the epithelial supporting cells through renewed supporting cell proliferation and by direct cellular conversion from a supporting cell to a hair cell (Raphael, <xref ref-type="bibr" rid="B85">1992</xref>; Weisleder and Rubel, <xref ref-type="bibr" rid="B119">1993</xref>; Roberson et al., <xref ref-type="bibr" rid="B87">2004</xref>). However, pharmacological inhibition of HDACs results in decreased proliferation of avian vestibular supporting cells, both in dissociated culture and in intact utricles (Slattery et al., <xref ref-type="bibr" rid="B97">2009</xref>). The reduction in supporting cell proliferation causes a reduction in the number of regenerated hair cells but does not directly affect hair cell differentiation (Slattery et al., <xref ref-type="bibr" rid="B97">2009</xref>). These data indicate that HDACs have a critical function in regulating gene expression in non-sensory epithelial cells responding to ototoxic insult during normal regenerative processes. Further analysis is needed to determine which genes are being regulated by HDACs and whether each specific gene is critical for the proliferative response in supporting cells. Naturally regenerating systems such as the avian basilar papilla and utricle provide much needed information about the regulatory networks that are required for hair cell regeneration. Ideally, a comparison of the DNA methylome and histone modifications between the naturally regenerating system and the mammalian system following ototoxic insult would provide vital information about the types of epigenetic events that must occur to achieve complete mammalian hair cell regeneration.</p>
<p>The cell type specific distribution of histone modifications, DNA methylation, and chromatin remodeling events needs to be characterized during inner ear development from a multipotent progenitor cell to a terminally differentiated cell. The mammalian inner ear offers unique challenges for evaluating the epigenome given the limited number of cells across a diversity of cell types. Transcriptomic analysis of the mammalian inner ear during development by microarray or RNA-seq may provide a starting point for analyzing epigenetic modifications that may regulate the expression of specific target genes and microRNAs (Elkan-Miller et al., <xref ref-type="bibr" rid="B23">2011</xref>; Smeti et al., <xref ref-type="bibr" rid="B98">2012</xref>; Rudnicki et al., <xref ref-type="bibr" rid="B90">2014</xref>). Emerging evidence has shown that more than one hundred microRNAs are regulated by epigenetic mechanisms, and about 50% of them are modulated by DNA methylation (Saito et al., <xref ref-type="bibr" rid="B93">2006</xref>; Kunej et al., <xref ref-type="bibr" rid="B60">2011</xref>; Suzuki et al., <xref ref-type="bibr" rid="B103">2011</xref>). Additionally, a subgroup of microRNAs has been shown to directly target the enzymatic effectors of epigenetic modifications, which adds more complexity to the epigenetic regulatory network (Garzon et al., <xref ref-type="bibr" rid="B27">2009</xref>; Iorio et al., <xref ref-type="bibr" rid="B41">2010</xref>).</p>
</sec>
<sec id="s8">
<title>Conclusions</title>
<p>Given that epigenetics is a cornerstone of development and cellular reprogramming, it seems likely that understanding and manipulating the epigenome holds enormous promise for preventing and treating hearing loss in humans. Epigenetics also offers an important window to understanding how ototoxic compounds and noise affect gene regulatory networks and how these epigenetic modifications may be manipulated and overcome utilizing epigenetic therapeutics. Understanding epigenetic mechanisms has become a major focus for research in most biological systems. The field of hearing research could greatly benefit from the vast amounts of information that can be garnered from epigenetic work in other biological systems to gain a better understanding of the complex gene regulatory networks being regulated in the inner ear.</p>
</sec>
<sec id="s9">
<title>Conflict of interest statement</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
</body>
<back>
<ref-list>
<title>References</title>
<ref id="B1"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Adams</surname> <given-names>M. E.</given-names></name> <name><surname>Hurd</surname> <given-names>E. A.</given-names></name> <name><surname>Beyer</surname> <given-names>L. A.</given-names></name> <name><surname>Swiderski</surname> <given-names>D. L.</given-names></name> <name><surname>Raphael</surname> <given-names>Y.</given-names></name> <name><surname>Martin</surname> <given-names>D. M.</given-names></name></person-group> (<year>2007</year>). <article-title>Defects in vestibular sensory epithelia and innervation in mice with loss of Chd7 function: implications for human CHARGE syndrome</article-title>. <source>J. Comp. Neurol.</source> <volume>504</volume>, <fpage>519</fpage>&#x02013;<lpage>532</lpage>. <pub-id pub-id-type="doi">10.1002/cne.21460</pub-id><pub-id pub-id-type="pmid">17701983</pub-id></citation></ref>
<ref id="B2"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Azuara</surname> <given-names>V.</given-names></name> <name><surname>Perry</surname> <given-names>P.</given-names></name> <name><surname>Sauer</surname> <given-names>S.</given-names></name> <name><surname>Spivakov</surname> <given-names>M.</given-names></name> <name><surname>Jorgensen</surname> <given-names>H. F.</given-names></name> <name><surname>John</surname> <given-names>R. M.</given-names></name> <etal/></person-group>. (<year>2006</year>). <article-title>Chromatin signatures of pluripotent cell lines</article-title>. <source>Nat. Cell Biol.</source> <volume>8</volume>, <fpage>532</fpage>&#x02013;<lpage>538</lpage>. <pub-id pub-id-type="doi">10.1038/ncb1403</pub-id><pub-id pub-id-type="pmid">16570078</pub-id></citation></ref>
<ref id="B3"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Bannister</surname> <given-names>A. J.</given-names></name> <name><surname>Kouzarides</surname> <given-names>T.</given-names></name></person-group> (<year>2011</year>). <article-title>Regulation of chromatin by histone modifications</article-title>. <source>Cell Res.</source> <volume>21</volume>, <fpage>381</fpage>&#x02013;<lpage>395</lpage>. <pub-id pub-id-type="doi">10.1038/cr.2011.22</pub-id><pub-id pub-id-type="pmid">21321607</pub-id></citation></ref>
<ref id="B4"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Barozzi</surname> <given-names>S.</given-names></name> <name><surname>Di Berardino</surname> <given-names>F.</given-names></name> <name><surname>Atzeri</surname> <given-names>F.</given-names></name> <name><surname>Filipponi</surname> <given-names>E.</given-names></name> <name><surname>Cerutti</surname> <given-names>M.</given-names></name> <name><surname>Selicorni</surname> <given-names>A.</given-names></name> <etal/></person-group>. (<year>2009</year>). <article-title>Audiological and vestibular findings in the Kabuki syndrome</article-title>. <source>Am. J. Med. Genet. A</source> <volume>149A</volume>, <fpage>171</fpage>&#x02013;<lpage>176</lpage>. <pub-id pub-id-type="doi">10.1002/ajmg.a.32610</pub-id><pub-id pub-id-type="pmid">19161135</pub-id></citation></ref>
<ref id="B5"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Bernstein</surname> <given-names>B. E.</given-names></name> <name><surname>Mikkelsen</surname> <given-names>T. S.</given-names></name> <name><surname>Xie</surname> <given-names>X.</given-names></name> <name><surname>Kamal</surname> <given-names>M.</given-names></name> <name><surname>Huebert</surname> <given-names>D. J.</given-names></name> <name><surname>Cuff</surname> <given-names>J.</given-names></name> <etal/></person-group>. (<year>2006</year>). <article-title>A bivalent chromatin structure marks key developmental genes in embryonic stem cells</article-title>. <source>Cell</source> <volume>125</volume>, <fpage>315</fpage>&#x02013;<lpage>326</lpage>. <pub-id pub-id-type="doi">10.1016/j.cell.2006.02.041</pub-id><pub-id pub-id-type="pmid">16630819</pub-id></citation></ref>
<ref id="B6"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Bosch</surname> <given-names>A.</given-names></name> <name><surname>Suau</surname> <given-names>P.</given-names></name></person-group> (<year>1995</year>). <article-title>Changes in core histone variant composition in differentiating neurons: the roles of differential turnover and synthesis rates</article-title>. <source>Eur. J. Cell Biol.</source> <volume>68</volume>, <fpage>220</fpage>&#x02013;<lpage>225</lpage>. <pub-id pub-id-type="pmid">8603674</pub-id></citation></ref>
<ref id="B7"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Bossuyt</surname> <given-names>W.</given-names></name> <name><surname>Kazanjian</surname> <given-names>A.</given-names></name> <name><surname>De Geest</surname> <given-names>N.</given-names></name> <name><surname>Van Kelst</surname> <given-names>S.</given-names></name> <name><surname>De Hertogh</surname> <given-names>G.</given-names></name> <name><surname>Geboes</surname> <given-names>K.</given-names></name> <etal/></person-group>. (<year>2009</year>). <article-title>Atonal homolog 1 is a tumor suppressor gene</article-title>. <source>PLoS Biol.</source> <volume>7</volume>:<fpage>e39</fpage>. <pub-id pub-id-type="doi">10.3410/f.1157437.617596</pub-id><pub-id pub-id-type="pmid">19243219</pub-id></citation></ref>
<ref id="B8"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Brandt</surname> <given-names>W. F.</given-names></name> <name><surname>Strickland</surname> <given-names>W. N.</given-names></name> <name><surname>Strickland</surname> <given-names>M.</given-names></name> <name><surname>Carlisle</surname> <given-names>L.</given-names></name> <name><surname>Woods</surname> <given-names>D.</given-names></name> <name><surname>Von Holt</surname> <given-names>C.</given-names></name></person-group> (<year>1979</year>). <article-title>A histone programme during the life cycle of the sea urchin</article-title>. <source>Eur. J. Biochem.</source> <volume>94</volume>, <fpage>1</fpage>&#x02013;<lpage>10</lpage>. <pub-id pub-id-type="doi">10.1111/j.1432-1033.1979.tb12864.x</pub-id><pub-id pub-id-type="pmid">571333</pub-id></citation></ref>
<ref id="B9"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Byvoet</surname> <given-names>P.</given-names></name> <name><surname>Shepherd</surname> <given-names>G. R.</given-names></name> <name><surname>Hardin</surname> <given-names>J. M.</given-names></name> <name><surname>Noland</surname> <given-names>B. J.</given-names></name></person-group> (<year>1972</year>). <article-title>The distribution and turnover of labeled methyl groups in histone fractions of cultured mammalian cells</article-title>. <source>Arch. Biochem. Biophys.</source> <volume>148</volume>, <fpage>558</fpage>&#x02013;<lpage>567</lpage>. <pub-id pub-id-type="doi">10.1016/0003-9861(72)90174-9</pub-id><pub-id pub-id-type="pmid">5063076</pub-id></citation></ref>
<ref id="B10"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Calvanese</surname> <given-names>V.</given-names></name> <name><surname>Fernandez</surname> <given-names>A. F.</given-names></name> <name><surname>Urdinguio</surname> <given-names>R. G.</given-names></name> <name><surname>Suarez-Alvarez</surname> <given-names>B.</given-names></name> <name><surname>Mangas</surname> <given-names>C.</given-names></name> <name><surname>Perez-Garcia</surname> <given-names>V.</given-names></name> <etal/></person-group>. (<year>2012</year>). <article-title>A promoter DNA demethylation landscape of human hematopoietic differentiation</article-title>. <source>Nucleic Acids Res.</source> <volume>40</volume>, <fpage>116</fpage>&#x02013;<lpage>131</lpage>. <pub-id pub-id-type="doi">10.1093/nar/gkr685</pub-id><pub-id pub-id-type="pmid">21911366</pub-id></citation></ref>
<ref id="B11"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Campeau</surname> <given-names>P. M.</given-names></name> <name><surname>Kim</surname> <given-names>J. C.</given-names></name> <name><surname>Lu</surname> <given-names>J. T.</given-names></name> <name><surname>Schwartzentruber</surname> <given-names>J. A.</given-names></name> <name><surname>Abdul-Rahman</surname> <given-names>O. A.</given-names></name> <name><surname>Schlaubitz</surname> <given-names>S.</given-names></name> <etal/></person-group>. (<year>2012a</year>). <article-title>Mutations in KAT6B, encoding a histone acetyltransferase, cause Genitopatellar syndrome</article-title>. <source>Am. J. Hum. Genet.</source> <volume>90</volume>, <fpage>282</fpage>&#x02013;<lpage>289</lpage>. <pub-id pub-id-type="doi">10.1016/j.ajhg.2011.11.023</pub-id><pub-id pub-id-type="pmid">22265014</pub-id></citation></ref>
<ref id="B12"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Campeau</surname> <given-names>P. M.</given-names></name> <name><surname>Lu</surname> <given-names>J. T.</given-names></name> <name><surname>Dawson</surname> <given-names>B. C.</given-names></name> <name><surname>Fokkema</surname> <given-names>I. F.</given-names></name> <name><surname>Robertson</surname> <given-names>S. P.</given-names></name> <name><surname>Gibbs</surname> <given-names>R. A.</given-names></name> <etal/></person-group>. (<year>2012b</year>). <article-title>The KAT6B-related disorders genitopatellar syndrome and Ohdo/SBBYS syndrome have distinct clinical features reflecting distinct molecular mechanisms</article-title>. <source>Hum. Mutat.</source> <volume>33</volume>, <fpage>1520</fpage>&#x02013;<lpage>1525</lpage>. <pub-id pub-id-type="doi">10.1002/humu.22141</pub-id><pub-id pub-id-type="pmid">22715153</pub-id></citation></ref>
<ref id="B13"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Campos</surname> <given-names>A. C.</given-names></name> <name><surname>Molognoni</surname> <given-names>F.</given-names></name> <name><surname>Melo</surname> <given-names>F. H.</given-names></name> <name><surname>Galdieri</surname> <given-names>L. C.</given-names></name> <name><surname>Carneiro</surname> <given-names>C. R.</given-names></name> <name><surname>D&#x02019;almeida</surname> <given-names>V.</given-names></name> <etal/></person-group>. (<year>2007</year>). <article-title>Oxidative stress modulates DNA methylation during melanocyte anchorage blockade associated with malignant transformation</article-title>. <source>Neoplasia</source> <volume>9</volume>, <fpage>1111</fpage>&#x02013;<lpage>1121</lpage>. <pub-id pub-id-type="doi">10.1593/neo.07712</pub-id><pub-id pub-id-type="pmid">18084618</pub-id></citation></ref>
<ref id="B14"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Campos</surname> <given-names>E. I.</given-names></name> <name><surname>Reinberg</surname> <given-names>D.</given-names></name></person-group> (<year>2009</year>). <article-title>Histones: annotating chromatin</article-title>. <source>Annu. Rev. Genet.</source> <volume>43</volume>, <fpage>559</fpage>&#x02013;<lpage>599</lpage>. <pub-id pub-id-type="doi">10.1146/annurev.genet.032608.103928</pub-id><pub-id pub-id-type="pmid">19886812</pub-id></citation></ref>
<ref id="B15"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname> <given-names>F. Q.</given-names></name> <name><surname>Schacht</surname> <given-names>J.</given-names></name> <name><surname>Sha</surname> <given-names>S. H.</given-names></name></person-group> (<year>2009</year>). <article-title>Aminoglycoside-induced histone deacetylation and hair cell death in the mouse cochlea</article-title>. <source>J. Neurochem.</source> <volume>108</volume>, <fpage>1226</fpage>&#x02013;<lpage>1236</lpage>. <pub-id pub-id-type="doi">10.1111/j.1471-4159.2009.05871.x</pub-id><pub-id pub-id-type="pmid">19141081</pub-id></citation></ref>
<ref id="B16"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Cheng</surname> <given-names>A. G.</given-names></name> <name><surname>Cunningham</surname> <given-names>L. L.</given-names></name> <name><surname>Rubel</surname> <given-names>E. W.</given-names></name></person-group> (<year>2005</year>). <article-title>Mechanisms of hair cell death and protection</article-title>. <source>Curr. Opin. Otolaryngol. Head Neck. Surg.</source> <volume>13</volume>, <fpage>343</fpage>&#x02013;<lpage>348</lpage>. <pub-id pub-id-type="doi">10.1097/01.moo.0000186799.45377.63</pub-id><pub-id pub-id-type="pmid">16282762</pub-id></citation></ref>
<ref id="B17"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Cohen</surname> <given-names>D. E.</given-names></name> <name><surname>Melton</surname> <given-names>D.</given-names></name></person-group> (<year>2011</year>). <article-title>Turning straw into gold: directing cell fate for regenerative medicine</article-title>. <source>Nat. Rev. Genet.</source> <volume>12</volume>, <fpage>243</fpage>&#x02013;<lpage>252</lpage>. <pub-id pub-id-type="doi">10.1038/nrg2938</pub-id><pub-id pub-id-type="pmid">21386864</pub-id></citation></ref>
<ref id="B18"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Colbert</surname> <given-names>L. E.</given-names></name> <name><surname>Petrova</surname> <given-names>A. V.</given-names></name> <name><surname>Fisher</surname> <given-names>S. B.</given-names></name> <name><surname>Pantazides</surname> <given-names>B. G.</given-names></name> <name><surname>Madden</surname> <given-names>M. Z.</given-names></name> <name><surname>Hardy</surname> <given-names>C. W.</given-names></name> <etal/></person-group>. (<year>2014</year>). <article-title>CHD7 expression predicts survival outcomes in patients with resected pancreatic cancer</article-title>. <source>Cancer Res.</source> <volume>74</volume>, <fpage>2677</fpage>&#x02013;<lpage>2687</lpage>. <pub-id pub-id-type="doi">10.1158/0008-5472.can-13-1996</pub-id><pub-id pub-id-type="pmid">24626090</pub-id></citation></ref>
<ref id="B19"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Corwin</surname> <given-names>J. T.</given-names></name> <name><surname>Oberholtzer</surname> <given-names>J. C.</given-names></name></person-group> (<year>1997</year>). <article-title>Fish n&#x02019; chicks: model recipes for hair-cell regeneration?</article-title> <source>Neuron</source> <volume>19</volume>, <fpage>951</fpage>&#x02013;<lpage>954</lpage>. <pub-id pub-id-type="doi">10.1016/S0896-6273(00)80386-4</pub-id><pub-id pub-id-type="pmid">9390508</pub-id></citation></ref>
<ref id="B20"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Deaton</surname> <given-names>A. M.</given-names></name> <name><surname>Bird</surname> <given-names>A.</given-names></name></person-group> (<year>2011</year>). <article-title>CpG islands and the regulation of transcription</article-title>. <source>Genes Dev.</source> <volume>25</volume>, <fpage>1010</fpage>&#x02013;<lpage>1022</lpage>. <pub-id pub-id-type="doi">10.1101/gad.2037511</pub-id><pub-id pub-id-type="pmid">21576262</pub-id></citation></ref>
<ref id="B21"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Donkena</surname> <given-names>K. V.</given-names></name> <name><surname>Young</surname> <given-names>C. Y.</given-names></name> <name><surname>Tindall</surname> <given-names>D. J.</given-names></name></person-group> (<year>2010</year>). <article-title>Oxidative stress and DNA methylation in prostate cancer</article-title>. <source>Obstet. Gynecol. Int.</source> <volume>2010</volume>:<fpage>302051</fpage>. <pub-id pub-id-type="doi">10.1155/2010/302051</pub-id><pub-id pub-id-type="pmid">20671914</pub-id></citation></ref>
<ref id="B22"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Drottar</surname> <given-names>M.</given-names></name> <name><surname>Liberman</surname> <given-names>M. C.</given-names></name> <name><surname>Ratan</surname> <given-names>R. R.</given-names></name> <name><surname>Roberson</surname> <given-names>D. W.</given-names></name></person-group> (<year>2006</year>). <article-title>The histone deacetylase inhibitor sodium butyrate protects against cisplatin-induced hearing loss in guinea pigs</article-title>. <source>Laryngoscope</source> <volume>116</volume>, <fpage>292</fpage>&#x02013;<lpage>296</lpage>. <pub-id pub-id-type="doi">10.1097/01.mlg.0000197630.85208.36</pub-id><pub-id pub-id-type="pmid">16467722</pub-id></citation></ref>
<ref id="B23"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Elkan-Miller</surname> <given-names>T.</given-names></name> <name><surname>Ulitsky</surname> <given-names>I.</given-names></name> <name><surname>Hertzano</surname> <given-names>R.</given-names></name> <name><surname>Rudnicki</surname> <given-names>A.</given-names></name> <name><surname>Dror</surname> <given-names>A. A.</given-names></name> <name><surname>Lenz</surname> <given-names>D. R.</given-names></name> <etal/></person-group>. (<year>2011</year>). <article-title>Integration of transcriptomics, proteomics and microRNA analyses reveals novel microRNA regulation of targets in the mammalian inner ear</article-title>. <source>PLoS One</source> <volume>6</volume>:<fpage>e18195</fpage>. <pub-id pub-id-type="doi">10.1371/journal.pone.0018195</pub-id><pub-id pub-id-type="pmid">21483685</pub-id></citation></ref>
<ref id="B24"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Faraco</surname> <given-names>G.</given-names></name> <name><surname>Pittelli</surname> <given-names>M.</given-names></name> <name><surname>Cavone</surname> <given-names>L.</given-names></name> <name><surname>Fossati</surname> <given-names>S.</given-names></name> <name><surname>Porcu</surname> <given-names>M.</given-names></name> <name><surname>Mascagni</surname> <given-names>P.</given-names></name> <etal/></person-group>. (<year>2009</year>). <article-title>Histone deacetylase (HDAC) inhibitors reduce the glial inflammatory response in vitro and in vivo</article-title>. <source>Neurobiol. Dis.</source> <volume>36</volume>, <fpage>269</fpage>&#x02013;<lpage>279</lpage>. <pub-id pub-id-type="doi">10.1016/j.nbd.2009.07.019</pub-id><pub-id pub-id-type="pmid">19635561</pub-id></citation></ref>
<ref id="B25"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Feng</surname> <given-names>S.</given-names></name> <name><surname>Jacobsen</surname> <given-names>S. E.</given-names></name> <name><surname>Reik</surname> <given-names>W.</given-names></name></person-group> (<year>2010</year>). <article-title>Epigenetic reprogramming in plant and animal development</article-title>. <source>Science</source> <volume>330</volume>, <fpage>622</fpage>&#x02013;<lpage>627</lpage>. <pub-id pub-id-type="doi">10.1126/science.1190614</pub-id><pub-id pub-id-type="pmid">21030646</pub-id></citation></ref>
<ref id="B26"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Fuchs</surname> <given-names>G.</given-names></name> <name><surname>Hollander</surname> <given-names>D.</given-names></name> <name><surname>Voichek</surname> <given-names>Y.</given-names></name> <name><surname>Ast</surname> <given-names>G.</given-names></name> <name><surname>Oren</surname> <given-names>M.</given-names></name></person-group> (<year>2014</year>). <article-title>Cotranscriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate</article-title>. <source>Genome Res.</source> <volume>24</volume>, <fpage>1572</fpage>&#x02013;<lpage>1583</lpage>. <pub-id pub-id-type="doi">10.1101/gr.176487.114</pub-id><pub-id pub-id-type="pmid">25049226</pub-id></citation></ref>
<ref id="B27"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Garzon</surname> <given-names>R.</given-names></name> <name><surname>Liu</surname> <given-names>S.</given-names></name> <name><surname>Fabbri</surname> <given-names>M.</given-names></name> <name><surname>Liu</surname> <given-names>Z.</given-names></name> <name><surname>Heaphy</surname> <given-names>C. E.</given-names></name> <name><surname>Callegari</surname> <given-names>E.</given-names></name> <etal/></person-group>. (<year>2009</year>). <article-title>MicroRNA-29b induces global DNA hypomethylation and tumor suppressor gene reexpression in acute myeloid leukemia by targeting directly DNMT3A and 3B and indirectly DNMT1</article-title>. <source>Blood</source> <volume>113</volume>, <fpage>6411</fpage>&#x02013;<lpage>6418</lpage>. <pub-id pub-id-type="doi">10.1182/blood-2008-07-170589</pub-id><pub-id pub-id-type="pmid">19211935</pub-id></citation></ref>
<ref id="B28"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Grove</surname> <given-names>G. W.</given-names></name> <name><surname>Zweidler</surname> <given-names>A.</given-names></name></person-group> (<year>1984</year>). <article-title>Regulation of nucleosomal core histone variant levels in differentiating murine erythroleukemia cells</article-title>. <source>Biochemistry</source> <volume>23</volume>, <fpage>4436</fpage>&#x02013;<lpage>4443</lpage>. <pub-id pub-id-type="doi">10.1021/bi00314a030</pub-id><pub-id pub-id-type="pmid">6593094</pub-id></citation></ref>
<ref id="B29"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Gubbels</surname> <given-names>S. P.</given-names></name> <name><surname>Woessner</surname> <given-names>D. W.</given-names></name> <name><surname>Mitchell</surname> <given-names>J. C.</given-names></name> <name><surname>Ricci</surname> <given-names>A. J.</given-names></name> <name><surname>Brigande</surname> <given-names>J. V.</given-names></name></person-group> (<year>2008</year>). <article-title>Functional auditory hair cells produced in the mammalian cochlea by in utero gene transfer</article-title>. <source>Nature</source> <volume>455</volume>, <fpage>537</fpage>&#x02013;<lpage>541</lpage>. <pub-id pub-id-type="doi">10.1038/nature07265</pub-id><pub-id pub-id-type="pmid">18754012</pub-id></citation></ref>
<ref id="B30"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hanna</surname> <given-names>J. H.</given-names></name> <name><surname>Saha</surname> <given-names>K.</given-names></name> <name><surname>Jaenisch</surname> <given-names>R.</given-names></name></person-group> (<year>2010</year>). <article-title>Pluripotency and cellular reprogramming: facts, hypotheses, unresolved issues</article-title>. <source>Cell</source> <volume>143</volume>, <fpage>508</fpage>&#x02013;<lpage>525</lpage>. <pub-id pub-id-type="doi">10.1016/j.cell.2010.10.008</pub-id><pub-id pub-id-type="pmid">21074044</pub-id></citation></ref>
<ref id="B31"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hawker</surname> <given-names>K.</given-names></name> <name><surname>Fuchs</surname> <given-names>H.</given-names></name> <name><surname>Angelis</surname> <given-names>M. H.</given-names></name> <name><surname>Steel</surname> <given-names>K. P.</given-names></name></person-group> (<year>2005</year>). <article-title>Two new mouse mutants with vestibular defects that map to the highly mutable locus on chromosome 4</article-title>. <source>Int. J. Audiol.</source> <volume>44</volume>, <fpage>171</fpage>&#x02013;<lpage>177</lpage>. <pub-id pub-id-type="doi">10.1080/14992020500057434</pub-id><pub-id pub-id-type="pmid">15916118</pub-id></citation></ref>
<ref id="B32"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>He</surname> <given-names>Y. F.</given-names></name> <name><surname>Li</surname> <given-names>B. Z.</given-names></name> <name><surname>Li</surname> <given-names>Z.</given-names></name> <name><surname>Liu</surname> <given-names>P.</given-names></name> <name><surname>Wang</surname> <given-names>Y.</given-names></name> <name><surname>Tang</surname> <given-names>Q.</given-names></name> <etal/></person-group>. (<year>2011</year>). <article-title>Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA</article-title>. <source>Science</source> <volume>333</volume>, <fpage>1303</fpage>&#x02013;<lpage>1307</lpage>. <pub-id pub-id-type="doi">10.1126/science.1210944</pub-id><pub-id pub-id-type="pmid">21817016</pub-id></citation></ref>
<ref id="B33"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Helin</surname> <given-names>K.</given-names></name> <name><surname>Dhanak</surname> <given-names>D.</given-names></name></person-group> (<year>2013</year>). <article-title>Chromatin proteins and modifications as drug targets</article-title>. <source>Nature</source> <volume>502</volume>, <fpage>480</fpage>&#x02013;<lpage>488</lpage>. <pub-id pub-id-type="doi">10.1038/nature12751</pub-id><pub-id pub-id-type="pmid">24153301</pub-id></citation></ref>
<ref id="B34"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hojo</surname> <given-names>K.</given-names></name> <name><surname>Imamura</surname> <given-names>T.</given-names></name> <name><surname>Takanashi</surname> <given-names>M.</given-names></name> <name><surname>Ishii</surname> <given-names>K.</given-names></name> <name><surname>Sasaki</surname> <given-names>M.</given-names></name> <name><surname>Imura</surname> <given-names>S.</given-names></name> <etal/></person-group>. (<year>1999</year>). <article-title>Hereditary sensory neuropathy with deafness and dementia: a clinical and neuroimaging study</article-title>. <source>Eur. J. Neurol.</source> <volume>6</volume>, <fpage>357</fpage>&#x02013;<lpage>361</lpage>. <pub-id pub-id-type="doi">10.1046/j.1468-1331.1999.630357.x</pub-id><pub-id pub-id-type="pmid">10210919</pub-id></citation></ref>
<ref id="B35"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Holliday</surname> <given-names>R.</given-names></name> <name><surname>Pugh</surname> <given-names>J. E.</given-names></name></person-group> (<year>1975</year>). <article-title>DNA modification mechanisms and gene activity during development</article-title>. <source>Science</source> <volume>187</volume>, <fpage>226</fpage>&#x02013;<lpage>232</lpage>. <pub-id pub-id-type="doi">10.1126/science.1111098</pub-id><pub-id pub-id-type="pmid">1111098</pub-id></citation></ref>
<ref id="B36"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hon</surname> <given-names>G. C.</given-names></name> <name><surname>Rajagopal</surname> <given-names>N.</given-names></name> <name><surname>Shen</surname> <given-names>Y.</given-names></name> <name><surname>Mccleary</surname> <given-names>D. F.</given-names></name> <name><surname>Yue</surname> <given-names>F.</given-names></name> <name><surname>Dang</surname> <given-names>M. D.</given-names></name> <etal/></person-group>. (<year>2013</year>). <article-title>Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues</article-title>. <source>Nat. Genet.</source> <volume>45</volume>, <fpage>1198</fpage>&#x02013;<lpage>1206</lpage>. <pub-id pub-id-type="doi">10.1038/ng.2746</pub-id><pub-id pub-id-type="pmid">23995138</pub-id></citation></ref>
<ref id="B37"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Huang</surname> <given-names>J.</given-names></name> <name><surname>Sengupta</surname> <given-names>R.</given-names></name> <name><surname>Espejo</surname> <given-names>A. B.</given-names></name> <name><surname>Lee</surname> <given-names>M. G.</given-names></name> <name><surname>Dorsey</surname> <given-names>J. A.</given-names></name> <name><surname>Richter</surname> <given-names>M.</given-names></name> <etal/></person-group>. (<year>2007</year>). <article-title>p53 is regulated by the lysine demethylase LSD1</article-title>. <source>Nature</source> <volume>449</volume>, <fpage>105</fpage>&#x02013;<lpage>108</lpage>. <pub-id pub-id-type="doi">10.1038/nature06092</pub-id><pub-id pub-id-type="pmid">17805299</pub-id></citation></ref>
<ref id="B38"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Huangfu</surname> <given-names>D.</given-names></name> <name><surname>Maehr</surname> <given-names>R.</given-names></name> <name><surname>Guo</surname> <given-names>W.</given-names></name> <name><surname>Eijkelenboom</surname> <given-names>A.</given-names></name> <name><surname>Snitow</surname> <given-names>M.</given-names></name> <name><surname>Chen</surname> <given-names>A. E.</given-names></name> <etal/></person-group>. (<year>2008</year>). <article-title>Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds</article-title>. <source>Nat. Biotechnol.</source> <volume>26</volume>, <fpage>795</fpage>&#x02013;<lpage>797</lpage>. <pub-id pub-id-type="doi">10.1038/nbt1418</pub-id><pub-id pub-id-type="pmid">18568017</pub-id></citation></ref>
<ref id="B39"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hurd</surname> <given-names>E. A.</given-names></name> <name><surname>Capers</surname> <given-names>P. L.</given-names></name> <name><surname>Blauwkamp</surname> <given-names>M. N.</given-names></name> <name><surname>Adams</surname> <given-names>M. E.</given-names></name> <name><surname>Raphael</surname> <given-names>Y.</given-names></name> <name><surname>Poucher</surname> <given-names>H. K.</given-names></name> <etal/></person-group>. (<year>2007</year>). <article-title>Loss of Chd7 function in gene-trapped reporter mice is embryonic lethal and associated with severe defects in multiple developing tissues</article-title>. <source>Mamm. Genome</source> <volume>18</volume>, <fpage>94</fpage>&#x02013;<lpage>104</lpage>. <pub-id pub-id-type="doi">10.1007/s00335-006-0107-6</pub-id><pub-id pub-id-type="pmid">17334657</pub-id></citation></ref>
<ref id="B40"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Hurd</surname> <given-names>E. A.</given-names></name> <name><surname>Poucher</surname> <given-names>H. K.</given-names></name> <name><surname>Cheng</surname> <given-names>K.</given-names></name> <name><surname>Raphael</surname> <given-names>Y.</given-names></name> <name><surname>Martin</surname> <given-names>D. M.</given-names></name></person-group> (<year>2010</year>). <article-title>The ATP-dependent chromatin remodeling enzyme CHD7 regulates pro-neural gene expression and neurogenesis in the inner ear</article-title>. <source>Development</source> <volume>137</volume>, <fpage>3139</fpage>&#x02013;<lpage>3150</lpage>. <pub-id pub-id-type="doi">10.1242/dev.047894</pub-id><pub-id pub-id-type="pmid">20736290</pub-id></citation></ref>
<ref id="B41"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Iorio</surname> <given-names>M. V.</given-names></name> <name><surname>Piovan</surname> <given-names>C.</given-names></name> <name><surname>Croce</surname> <given-names>C. M.</given-names></name></person-group> (<year>2010</year>). <article-title>Interplay between microRNAs and the epigenetic machinery: an intricate network</article-title>. <source>Biochim. Biophys. Acta</source> <volume>1799</volume>, <fpage>694</fpage>&#x02013;<lpage>701</lpage>. <pub-id pub-id-type="doi">10.1016/j.bbagrm.2010.05.005</pub-id><pub-id pub-id-type="pmid">20493980</pub-id></citation></ref>
<ref id="B42"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ito</surname> <given-names>S.</given-names></name> <name><surname>Shen</surname> <given-names>L.</given-names></name> <name><surname>Dai</surname> <given-names>Q.</given-names></name> <name><surname>Wu</surname> <given-names>S. C.</given-names></name> <name><surname>Collins</surname> <given-names>L. B.</given-names></name> <name><surname>Swenberg</surname> <given-names>J. A.</given-names></name> <etal/></person-group>. (<year>2011</year>). <article-title>Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine</article-title>. <source>Science</source> <volume>333</volume>, <fpage>1300</fpage>&#x02013;<lpage>1333</lpage>. <pub-id pub-id-type="doi">10.1126/science.1210597</pub-id><pub-id pub-id-type="pmid">21778364</pub-id></citation></ref>
<ref id="B43"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Izumikawa</surname> <given-names>M.</given-names></name> <name><surname>Minoda</surname> <given-names>R.</given-names></name> <name><surname>Kawamoto</surname> <given-names>K.</given-names></name> <name><surname>Abrashkin</surname> <given-names>K. A.</given-names></name> <name><surname>Swiderski</surname> <given-names>D. L.</given-names></name> <name><surname>Dolan</surname> <given-names>D. F.</given-names></name> <etal/></person-group>. (<year>2005</year>). <article-title>Auditory hair cell replacement and hearing improvement by Atoh1 gene therapy in deaf mammals</article-title>. <source>Nat. Med.</source> <volume>11</volume>, <fpage>271</fpage>&#x02013;<lpage>276</lpage>. <pub-id pub-id-type="doi">10.1038/nm1193</pub-id><pub-id pub-id-type="pmid">15711559</pub-id></citation></ref>
<ref id="B44"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Jackson</surname> <given-names>M.</given-names></name> <name><surname>Krassowska</surname> <given-names>A.</given-names></name> <name><surname>Gilbert</surname> <given-names>N.</given-names></name> <name><surname>Chevassut</surname> <given-names>T.</given-names></name> <name><surname>Forrester</surname> <given-names>L.</given-names></name> <name><surname>Ansell</surname> <given-names>J.</given-names></name> <etal/></person-group>. (<year>2004</year>). <article-title>Severe global DNA hypomethylation blocks differentiation and induces histone hyperacetylation in embryonic stem cells</article-title>. <source>Mol. Cell. Biol.</source> <volume>24</volume>, <fpage>8862</fpage>&#x02013;<lpage>8871</lpage>. <pub-id pub-id-type="doi">10.1128/mcb.24.20.8862-8871.2004</pub-id><pub-id pub-id-type="pmid">15456861</pub-id></citation></ref>
<ref id="B45"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Jiang</surname> <given-names>H.</given-names></name> <name><surname>Sha</surname> <given-names>S. H.</given-names></name> <name><surname>Schacht</surname> <given-names>J.</given-names></name></person-group> (<year>2006</year>). <article-title>Kanamycin alters cytoplasmic and nuclear phosphoinositide signaling in the organ of Corti in vivo</article-title>. <source>J. Neurochem.</source> <volume>99</volume>, <fpage>269</fpage>&#x02013;<lpage>276</lpage>. <pub-id pub-id-type="doi">10.1111/j.1471-4159.2006.04117.x</pub-id><pub-id pub-id-type="pmid">16903869</pub-id></citation></ref>
<ref id="B46"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Jiang</surname> <given-names>W.</given-names></name> <name><surname>Wang</surname> <given-names>J.</given-names></name> <name><surname>Zhang</surname> <given-names>Y.</given-names></name></person-group> (<year>2013</year>). <article-title>Histone H3K27me3 demethylases KDM6A and KDM6B modulate definitive endoderm differentiation from human ESCs by regulating WNT signaling pathway</article-title>. <source>Cell Res.</source> <volume>23</volume>, <fpage>122</fpage>&#x02013;<lpage>130</lpage>. <pub-id pub-id-type="doi">10.1038/cr.2012.119</pub-id><pub-id pub-id-type="pmid">22907667</pub-id></citation></ref>
<ref id="B47"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Jurkowska</surname> <given-names>R. Z.</given-names></name> <name><surname>Jurkowski</surname> <given-names>T. P.</given-names></name> <name><surname>Jeltsch</surname> <given-names>A.</given-names></name></person-group> (<year>2011</year>). <article-title>Structure and function of mammalian DNA methyltransferases</article-title>. <source>Chembiochem</source> <volume>12</volume>, <fpage>206</fpage>&#x02013;<lpage>222</lpage>. <pub-id pub-id-type="doi">10.1002/cbic.201000195</pub-id><pub-id pub-id-type="pmid">21243710</pub-id></citation></ref>
<ref id="B48"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kelly</surname> <given-names>M. C.</given-names></name> <name><surname>Chang</surname> <given-names>Q.</given-names></name> <name><surname>Pan</surname> <given-names>A.</given-names></name> <name><surname>Lin</surname> <given-names>X.</given-names></name> <name><surname>Chen</surname> <given-names>P.</given-names></name></person-group> (<year>2012</year>). <article-title>Atoh1 directs the formation of sensory mosaics and induces cell proliferation in the postnatal mammalian cochlea in vivo</article-title>. <source>J. Neurosci.</source> <volume>32</volume>, <fpage>6699</fpage>&#x02013;<lpage>6710</lpage>. <pub-id pub-id-type="doi">10.1523/jneurosci.5420-11.2012</pub-id><pub-id pub-id-type="pmid">22573692</pub-id></citation></ref>
<ref id="B49"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kiernan</surname> <given-names>A. E.</given-names></name> <name><surname>Erven</surname> <given-names>A.</given-names></name> <name><surname>Voegeling</surname> <given-names>S.</given-names></name> <name><surname>Peters</surname> <given-names>J.</given-names></name> <name><surname>Nolan</surname> <given-names>P.</given-names></name> <name><surname>Hunter</surname> <given-names>J.</given-names></name> <etal/></person-group>. (<year>2002</year>). <article-title>ENU mutagenesis reveals a highly mutable locus on mouse Chromosome 4 that affects ear morphogenesis</article-title>. <source>Mamm. Genome</source> <volume>13</volume>, <fpage>142</fpage>&#x02013;<lpage>148</lpage>. <pub-id pub-id-type="doi">10.1007/bf02684018</pub-id><pub-id pub-id-type="pmid">11919684</pub-id></citation></ref>
<ref id="B50"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kim</surname> <given-names>M. S.</given-names></name> <name><surname>Chung</surname> <given-names>N. G.</given-names></name> <name><surname>Kang</surname> <given-names>M. R.</given-names></name> <name><surname>Yoo</surname> <given-names>N. J.</given-names></name> <name><surname>Lee</surname> <given-names>S. H.</given-names></name></person-group> (<year>2011</year>). <article-title>Genetic and expressional alterations of CHD genes in gastric and colorectal cancers</article-title>. <source>Histopathology</source> <volume>58</volume>, <fpage>660</fpage>&#x02013;<lpage>668</lpage>. <pub-id pub-id-type="doi">10.1111/j.1365-2559.2011.03819.x</pub-id><pub-id pub-id-type="pmid">21447119</pub-id></citation></ref>
<ref id="B51"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kim</surname> <given-names>K.</given-names></name> <name><surname>Doi</surname> <given-names>A.</given-names></name> <name><surname>Wen</surname> <given-names>B.</given-names></name> <name><surname>Ng</surname> <given-names>K.</given-names></name> <name><surname>Zhao</surname> <given-names>R.</given-names></name> <name><surname>Cahan</surname> <given-names>P.</given-names></name> <etal/></person-group>. (<year>2010</year>). <article-title>Epigenetic memory in induced pluripotent stem cells</article-title>. <source>Nature</source> <volume>467</volume>, <fpage>285</fpage>&#x02013;<lpage>290</lpage>. <pub-id pub-id-type="doi">10.1038/nature09342</pub-id><pub-id pub-id-type="pmid">20644535</pub-id></citation></ref>
<ref id="B52"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kleefstra</surname> <given-names>T.</given-names></name> <name><surname>Smidt</surname> <given-names>M.</given-names></name> <name><surname>Banning</surname> <given-names>M. J.</given-names></name> <name><surname>Oudakker</surname> <given-names>A. R.</given-names></name> <name><surname>Van Esch</surname> <given-names>H.</given-names></name> <name><surname>De Brouwer</surname> <given-names>A. P.</given-names></name> <etal/></person-group>. (<year>2005</year>). <article-title>Disruption of the gene Euchromatin Histone Methyl Transferase1 (Eu-HMTase1) is associated with the 9q34 subtelomeric deletion syndrome</article-title>. <source>J. Med. Genet.</source> <volume>42</volume>, <fpage>299</fpage>&#x02013;<lpage>306</lpage>. <pub-id pub-id-type="doi">10.1136/jmg.2004.028464</pub-id><pub-id pub-id-type="pmid">15805155</pub-id></citation></ref>
<ref id="B53"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Klein</surname> <given-names>C. J.</given-names></name> <name><surname>Botuyan</surname> <given-names>M. V.</given-names></name> <name><surname>Wu</surname> <given-names>Y.</given-names></name> <name><surname>Ward</surname> <given-names>C. J.</given-names></name> <name><surname>Nicholson</surname> <given-names>G. A.</given-names></name> <name><surname>Hammans</surname> <given-names>S.</given-names></name> <etal/></person-group>. (<year>2011</year>). <article-title>Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss</article-title>. <source>Nat. Genet.</source> <volume>43</volume>, <fpage>595</fpage>&#x02013;<lpage>600</lpage>. <pub-id pub-id-type="doi">10.1038/ng.830</pub-id><pub-id pub-id-type="pmid">21532572</pub-id></citation></ref>
<ref id="B54"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kolasinska-Zwierz</surname> <given-names>P.</given-names></name> <name><surname>Down</surname> <given-names>T.</given-names></name> <name><surname>Latorre</surname> <given-names>I.</given-names></name> <name><surname>Liu</surname> <given-names>T.</given-names></name> <name><surname>Liu</surname> <given-names>X. S.</given-names></name> <name><surname>Ahringer</surname> <given-names>J.</given-names></name></person-group> (<year>2009</year>). <article-title>Differential chromatin marking of introns and expressed exons by H3K36me3</article-title>. <source>Nat. Genet.</source> <volume>41</volume>, <fpage>376</fpage>&#x02013;<lpage>381</lpage>. <pub-id pub-id-type="doi">10.1038/ng.322</pub-id><pub-id pub-id-type="pmid">19182803</pub-id></citation></ref>
<ref id="B55"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kontaki</surname> <given-names>H.</given-names></name> <name><surname>Talianidis</surname> <given-names>I.</given-names></name></person-group> (<year>2010</year>). <article-title>Lysine methylation regulates E2F1-induced cell death</article-title>. <source>Mol. Cell</source> <volume>39</volume>, <fpage>152</fpage>&#x02013;<lpage>160</lpage>. <pub-id pub-id-type="doi">10.1016/j.molcel.2010.06.006</pub-id><pub-id pub-id-type="pmid">20603083</pub-id></citation></ref>
<ref id="B56"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kooistra</surname> <given-names>S. M.</given-names></name> <name><surname>Helin</surname> <given-names>K.</given-names></name></person-group> (<year>2012</year>). <article-title>Molecular mechanisms and potential functions of histone demethylases</article-title>. <source>Nat. Rev. Mol. Cell Biol.</source> <volume>13</volume>, <fpage>297</fpage>&#x02013;<lpage>311</lpage>. <pub-id pub-id-type="doi">10.1038/nrm3327</pub-id><pub-id pub-id-type="pmid">22473470</pub-id></citation></ref>
<ref id="B57"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kornberg</surname> <given-names>R. D.</given-names></name></person-group> (<year>1974</year>). <article-title>Chromatin structure: a repeating unit of histones and DNA</article-title>. <source>Science</source> <volume>184</volume>, <fpage>868</fpage>&#x02013;<lpage>871</lpage>. <pub-id pub-id-type="doi">10.1126/science.184.4139.868</pub-id><pub-id pub-id-type="pmid">4825889</pub-id></citation></ref>
<ref id="B58"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kornberg</surname> <given-names>R. D.</given-names></name> <name><surname>Thomas</surname> <given-names>J. O.</given-names></name></person-group> (<year>1974</year>). <article-title>Chromatin structure; oligomers of the histones</article-title>. <source>Science</source> <volume>184</volume>, <fpage>865</fpage>&#x02013;<lpage>868</lpage>. <pub-id pub-id-type="doi">10.1126/science.184.4139.865</pub-id><pub-id pub-id-type="pmid">4825888</pub-id></citation></ref>
<ref id="B59"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kriaucionis</surname> <given-names>S.</given-names></name> <name><surname>Heintz</surname> <given-names>N.</given-names></name></person-group> (<year>2009</year>). <article-title>The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain</article-title>. <source>Science</source> <volume>324</volume>, <fpage>929</fpage>&#x02013;<lpage>930</lpage>. <pub-id pub-id-type="doi">10.1126/science.1169786</pub-id><pub-id pub-id-type="pmid">19372393</pub-id></citation></ref>
<ref id="B60"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Kunej</surname> <given-names>T.</given-names></name> <name><surname>Godnic</surname> <given-names>I.</given-names></name> <name><surname>Ferdin</surname> <given-names>J.</given-names></name> <name><surname>Horvat</surname> <given-names>S.</given-names></name> <name><surname>Dovc</surname> <given-names>P.</given-names></name> <name><surname>Calin</surname> <given-names>G. A.</given-names></name></person-group> (<year>2011</year>). <article-title>Epigenetic regulation of microRNAs in cancer: an integrated review of literature</article-title>. <source>Mutat. Res.</source> <volume>717</volume>, <fpage>77</fpage>&#x02013;<lpage>84</lpage>. <pub-id pub-id-type="doi">10.1016/j.mrfmmm.2011.03.008</pub-id><pub-id pub-id-type="pmid">21420983</pub-id></citation></ref>
<ref id="B61"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Layman</surname> <given-names>W. S.</given-names></name> <name><surname>Hurd</surname> <given-names>E. A.</given-names></name> <name><surname>Martin</surname> <given-names>D. M.</given-names></name></person-group> (<year>2010</year>). <article-title>Chromodomain proteins in development: lessons from CHARGE syndrome</article-title>. <source>Clin. Genet.</source> <volume>78</volume>, <fpage>11</fpage>&#x02013;<lpage>20</lpage>. <pub-id pub-id-type="doi">10.1111/j.1399-0004.2010.01446.x</pub-id><pub-id pub-id-type="pmid">20507341</pub-id></citation></ref>
<ref id="B62"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Layman</surname> <given-names>W. S.</given-names></name> <name><surname>Sauceda</surname> <given-names>M. A.</given-names></name> <name><surname>Zuo</surname> <given-names>J.</given-names></name></person-group> (<year>2013</year>). <article-title>Epigenetic alterations by NuRD and PRC2 in the neonatal mouse cochlea</article-title>. <source>Hear. Res.</source> <volume>304</volume>, <fpage>167</fpage>&#x02013;<lpage>178</lpage>. <pub-id pub-id-type="doi">10.1016/j.heares.2013.07.017</pub-id><pub-id pub-id-type="pmid">23911933</pub-id></citation></ref>
<ref id="B63"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Lee</surname> <given-names>J. E.</given-names></name> <name><surname>Wang</surname> <given-names>C.</given-names></name> <name><surname>Xu</surname> <given-names>S.</given-names></name> <name><surname>Cho</surname> <given-names>Y. W.</given-names></name> <name><surname>Wang</surname> <given-names>L.</given-names></name> <name><surname>Feng</surname> <given-names>X.</given-names></name> <etal/></person-group>. (<year>2013</year>). <article-title>H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation</article-title>. <source>Elife</source> <volume>2</volume>:<fpage>e01503</fpage>. <pub-id pub-id-type="doi">10.3410/f.718218082.793490513</pub-id><pub-id pub-id-type="pmid">24368734</pub-id></citation></ref>
<ref id="B64"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Li</surname> <given-names>E.</given-names></name> <name><surname>Bestor</surname> <given-names>T. H.</given-names></name> <name><surname>Jaenisch</surname> <given-names>R.</given-names></name></person-group> (<year>1992</year>). <article-title>Targeted mutation of the DNA methyltransferase gene results in embryonic lethality</article-title>. <source>Cell</source> <volume>69</volume>, <fpage>915</fpage>&#x02013;<lpage>926</lpage>. <pub-id pub-id-type="doi">10.1016/0092-8674(92)90611-f</pub-id><pub-id pub-id-type="pmid">1606615</pub-id></citation></ref>
<ref id="B65"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Li</surname> <given-names>H.</given-names></name> <name><surname>Collado</surname> <given-names>M.</given-names></name> <name><surname>Villasante</surname> <given-names>A.</given-names></name> <name><surname>Strati</surname> <given-names>K.</given-names></name> <name><surname>Ortega</surname> <given-names>S.</given-names></name> <name><surname>Canamero</surname> <given-names>M.</given-names></name> <etal/></person-group>. (<year>2009</year>). <article-title>The Ink4/Arf locus is a barrier for iPS cell reprogramming</article-title>. <source>Nature</source> <volume>460</volume>, <fpage>1136</fpage>&#x02013;<lpage>1139</lpage>. <pub-id pub-id-type="doi">10.1038/nature08290</pub-id><pub-id pub-id-type="pmid">19668188</pub-id></citation></ref>
<ref id="B66"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Lim</surname> <given-names>S. O.</given-names></name> <name><surname>Gu</surname> <given-names>J. M.</given-names></name> <name><surname>Kim</surname> <given-names>M. S.</given-names></name> <name><surname>Kim</surname> <given-names>H. S.</given-names></name> <name><surname>Park</surname> <given-names>Y. N.</given-names></name> <name><surname>Park</surname> <given-names>C. K.</given-names></name> <etal/></person-group>. (<year>2008</year>). <article-title>Epigenetic changes induced by reactive oxygen species in hepatocellular carcinoma: methylation of the E-cadherin promoter</article-title>. <source>Gastroenterology</source> <volume>135</volume>, <fpage>2128</fpage>&#x02013;<lpage>2140</lpage>, <fpage>2140.e1</fpage>&#x02013;<lpage>2148.e2</lpage>. <pub-id pub-id-type="doi">10.1053/j.gastro.2008.07.027</pub-id><pub-id pub-id-type="pmid">18801366</pub-id></citation></ref>
<ref id="B67"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Lister</surname> <given-names>R.</given-names></name> <name><surname>Pelizzola</surname> <given-names>M.</given-names></name> <name><surname>Dowen</surname> <given-names>R. H.</given-names></name> <name><surname>Hawkins</surname> <given-names>R. D.</given-names></name> <name><surname>Hon</surname> <given-names>G.</given-names></name> <name><surname>Tonti-Filippini</surname> <given-names>J.</given-names></name> <etal/></person-group>. (<year>2009</year>). <article-title>Human DNA methylomes at base resolution show widespread epigenomic differences</article-title>. <source>Nature</source> <volume>462</volume>, <fpage>315</fpage>&#x02013;<lpage>322</lpage>. <pub-id pub-id-type="doi">10.1038/nature08514</pub-id><pub-id pub-id-type="pmid">19829295</pub-id></citation></ref>
<ref id="B68"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Lister</surname> <given-names>R.</given-names></name> <name><surname>Pelizzola</surname> <given-names>M.</given-names></name> <name><surname>Kida</surname> <given-names>Y. S.</given-names></name> <name><surname>Hawkins</surname> <given-names>R. D.</given-names></name> <name><surname>Nery</surname> <given-names>J. R.</given-names></name> <name><surname>Hon</surname> <given-names>G.</given-names></name> <etal/></person-group>. (<year>2011</year>). <article-title>Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells</article-title>. <source>Nature</source> <volume>471</volume>, <fpage>68</fpage>&#x02013;<lpage>73</lpage>. <pub-id pub-id-type="doi">10.1038/nature09798</pub-id><pub-id pub-id-type="pmid">21289626</pub-id></citation></ref>
<ref id="B69"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname> <given-names>X. S.</given-names></name> <name><surname>Chopp</surname> <given-names>M.</given-names></name> <name><surname>Kassis</surname> <given-names>H.</given-names></name> <name><surname>Jia</surname> <given-names>L. F.</given-names></name> <name><surname>Hozeska-Solgot</surname> <given-names>A.</given-names></name> <name><surname>Zhang</surname> <given-names>R. L.</given-names></name> <etal/></person-group>. (<year>2012a</year>). <article-title>Valproic acid increases white matter repair and neurogenesis after stroke</article-title>. <source>Neuroscience</source> <volume>220</volume>, <fpage>313</fpage>&#x02013;<lpage>321</lpage>. <pub-id pub-id-type="doi">10.1016/j.neuroscience.2012.06.012</pub-id><pub-id pub-id-type="pmid">22704966</pub-id></citation></ref>
<ref id="B70"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname> <given-names>Z.</given-names></name> <name><surname>Dearman</surname> <given-names>J. A.</given-names></name> <name><surname>Cox</surname> <given-names>B. C.</given-names></name> <name><surname>Walters</surname> <given-names>B. J.</given-names></name> <name><surname>Zhang</surname> <given-names>L.</given-names></name> <name><surname>Ayrault</surname> <given-names>O.</given-names></name> <etal/></person-group>. (<year>2012b</year>). <article-title>Age-dependent in vivo conversion of mouse cochlear pillar and Deiters&#x02019; cells to immature hair cells by Atoh1 ectopic expression</article-title>. <source>J. Neurosci.</source> <volume>32</volume>, <fpage>6600</fpage>&#x02013;<lpage>6610</lpage>. <pub-id pub-id-type="doi">10.1523/JNEUROSCI.0818-12.2012</pub-id><pub-id pub-id-type="pmid">22573682</pub-id></citation></ref>
<ref id="B71"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Luger</surname> <given-names>K.</given-names></name> <name><surname>Mader</surname> <given-names>A. W.</given-names></name> <name><surname>Richmond</surname> <given-names>R. K.</given-names></name> <name><surname>Sargent</surname> <given-names>D. F.</given-names></name> <name><surname>Richmond</surname> <given-names>T. J.</given-names></name></person-group> (<year>1997</year>). <article-title>Crystal structure of the nucleosome core particle at 2.8 A resolution</article-title>. <source>Nature</source> <volume>389</volume>, <fpage>251</fpage>&#x02013;<lpage>260</lpage>. <pub-id pub-id-type="doi">10.1038/38444</pub-id><pub-id pub-id-type="pmid">9305837</pub-id></citation></ref>
<ref id="B72"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Maze</surname> <given-names>I.</given-names></name> <name><surname>Noh</surname> <given-names>K. M.</given-names></name> <name><surname>Soshnev</surname> <given-names>A. A.</given-names></name> <name><surname>Allis</surname> <given-names>C. D.</given-names></name></person-group> (<year>2014</year>). <article-title>Every amino acid matters: essential contributions of histone variants to mammalian development and disease</article-title>. <source>Nat. Rev. Genet.</source> <volume>15</volume>, <fpage>259</fpage>&#x02013;<lpage>271</lpage>. <pub-id pub-id-type="doi">10.1038/nrg3673</pub-id><pub-id pub-id-type="pmid">24614311</pub-id></citation></ref>
<ref id="B73"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Melberg</surname> <given-names>A.</given-names></name> <name><surname>Hetta</surname> <given-names>J.</given-names></name> <name><surname>Dahl</surname> <given-names>N.</given-names></name> <name><surname>Nennesmo</surname> <given-names>I.</given-names></name> <name><surname>Bengtsson</surname> <given-names>M.</given-names></name> <name><surname>Wibom</surname> <given-names>R.</given-names></name> <etal/></person-group>. (<year>1995</year>). <article-title>Autosomal dominant cerebellar ataxia deafness and narcolepsy</article-title>. <source>J. Neurol. Sci.</source> <volume>134</volume>, <fpage>119</fpage>&#x02013;<lpage>129</lpage>. <pub-id pub-id-type="doi">10.1016/0022-510X(95)00228-0</pub-id><pub-id pub-id-type="pmid">8747854</pub-id></citation></ref>
<ref id="B74"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Micucci</surname> <given-names>J. A.</given-names></name> <name><surname>Layman</surname> <given-names>W. S.</given-names></name> <name><surname>Hurd</surname> <given-names>E. A.</given-names></name> <name><surname>Sperry</surname> <given-names>E. D.</given-names></name> <name><surname>Frank</surname> <given-names>S. F.</given-names></name> <name><surname>Durham</surname> <given-names>M. A.</given-names></name> <etal/></person-group>. (<year>2014</year>). <article-title>CHD7 and retinoic acid signaling cooperate to regulate neural stem cell and inner ear development in mouse models of CHARGE syndrome</article-title>. <source>Hum. Mol. Genet.</source> <volume>23</volume>, <fpage>434</fpage>&#x02013;<lpage>448</lpage>. <pub-id pub-id-type="doi">10.1093/hmg/ddt435</pub-id><pub-id pub-id-type="pmid">24026680</pub-id></citation></ref>
<ref id="B75"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Mikkelsen</surname> <given-names>T. S.</given-names></name> <name><surname>Hanna</surname> <given-names>J.</given-names></name> <name><surname>Zhang</surname> <given-names>X.</given-names></name> <name><surname>Ku</surname> <given-names>M.</given-names></name> <name><surname>Wernig</surname> <given-names>M.</given-names></name> <name><surname>Schorderet</surname> <given-names>P.</given-names></name> <etal/></person-group>. (<year>2008</year>). <article-title>Dissecting direct reprogramming through integrative genomic analysis</article-title>. <source>Nature</source> <volume>454</volume>, <fpage>49</fpage>&#x02013;<lpage>55</lpage>. <pub-id pub-id-type="doi">10.1038/nature07056</pub-id><pub-id pub-id-type="pmid">18509334</pub-id></citation></ref>
<ref id="B76"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Mikkelsen</surname> <given-names>T. S.</given-names></name> <name><surname>Ku</surname> <given-names>M.</given-names></name> <name><surname>Jaffe</surname> <given-names>D. B.</given-names></name> <name><surname>Issac</surname> <given-names>B.</given-names></name> <name><surname>Lieberman</surname> <given-names>E.</given-names></name> <name><surname>Giannoukos</surname> <given-names>G.</given-names></name> <etal/></person-group>. (<year>2007</year>). <article-title>Genome-wide maps of chromatin state in pluripotent and lineage-committed cells</article-title>. <source>Nature</source> <volume>448</volume>, <fpage>553</fpage>&#x02013;<lpage>560</lpage>. <pub-id pub-id-type="doi">10.1038/nature06008</pub-id><pub-id pub-id-type="pmid">17603471</pub-id></citation></ref>
<ref id="B77"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Mosammaparast</surname> <given-names>N.</given-names></name> <name><surname>Kim</surname> <given-names>H.</given-names></name> <name><surname>Laurent</surname> <given-names>B.</given-names></name> <name><surname>Zhao</surname> <given-names>Y.</given-names></name> <name><surname>Lim</surname> <given-names>H. J.</given-names></name> <name><surname>Majid</surname> <given-names>M. C.</given-names></name> <etal/></person-group>. (<year>2013</year>). <article-title>The histone demethylase LSD1/KDM1A promotes the DNA damage response</article-title>. <source>J. Cell. Biol.</source> <volume>203</volume>, <fpage>457</fpage>&#x02013;<lpage>470</lpage>. <pub-id pub-id-type="doi">10.1084/jem.21012oia55</pub-id><pub-id pub-id-type="pmid">24217620</pub-id></citation></ref>
<ref id="B78"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Mutai</surname> <given-names>H.</given-names></name> <name><surname>Nagashima</surname> <given-names>R.</given-names></name> <name><surname>Sugitani</surname> <given-names>Y.</given-names></name> <name><surname>Noda</surname> <given-names>T.</given-names></name> <name><surname>Fujii</surname> <given-names>M.</given-names></name> <name><surname>Matsunaga</surname> <given-names>T.</given-names></name></person-group> (<year>2009</year>). <article-title>Expression of Pou3f3/Brn-1 and its genomic methylation in developing auditory epithelium</article-title>. <source>Dev. Neurobiol.</source> <volume>69</volume>, <fpage>913</fpage>&#x02013;<lpage>930</lpage>. <pub-id pub-id-type="doi">10.1002/dneu.20746</pub-id><pub-id pub-id-type="pmid">19743445</pub-id></citation></ref>
<ref id="B79"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ng</surname> <given-names>S. B.</given-names></name> <name><surname>Bigham</surname> <given-names>A. W.</given-names></name> <name><surname>Buckingham</surname> <given-names>K. J.</given-names></name> <name><surname>Hannibal</surname> <given-names>M. C.</given-names></name> <name><surname>Mcmillin</surname> <given-names>M. J.</given-names></name> <name><surname>Gildersleeve</surname> <given-names>H. I.</given-names></name> <etal/></person-group>. (<year>2010</year>). <article-title>Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome</article-title>. <source>Nat. Genet.</source> <volume>42</volume>, <fpage>790</fpage>&#x02013;<lpage>793</lpage>. <pub-id pub-id-type="doi">10.1038/ng.646</pub-id><pub-id pub-id-type="pmid">20711175</pub-id></citation></ref>
<ref id="B80"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Okano</surname> <given-names>M.</given-names></name> <name><surname>Bell</surname> <given-names>D. W.</given-names></name> <name><surname>Haber</surname> <given-names>D. A.</given-names></name> <name><surname>Li</surname> <given-names>E.</given-names></name></person-group> (<year>1999</year>). <article-title>DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development</article-title>. <source>Cell</source> <volume>99</volume>, <fpage>247</fpage>&#x02013;<lpage>257</lpage>. <pub-id pub-id-type="doi">10.1016/s0092-8674(00)81656-6</pub-id><pub-id pub-id-type="pmid">10555141</pub-id></citation></ref>
<ref id="B81"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Onder</surname> <given-names>T. T.</given-names></name> <name><surname>Kara</surname> <given-names>N.</given-names></name> <name><surname>Cherry</surname> <given-names>A.</given-names></name> <name><surname>Sinha</surname> <given-names>A. U.</given-names></name> <name><surname>Zhu</surname> <given-names>N.</given-names></name> <name><surname>Bernt</surname> <given-names>K. M.</given-names></name> <etal/></person-group>. (<year>2012</year>). <article-title>Chromatin-modifying enzymes as modulators of reprogramming</article-title>. <source>Nature</source> <volume>483</volume>, <fpage>598</fpage>&#x02013;<lpage>602</lpage>. <pub-id pub-id-type="doi">10.1038/nature10953</pub-id><pub-id pub-id-type="pmid">22388813</pub-id></citation></ref>
<ref id="B82"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Pina</surname> <given-names>B.</given-names></name> <name><surname>Suau</surname> <given-names>P.</given-names></name></person-group> (<year>1987</year>). <article-title>Changes in histones H2A and H3 variant composition in differentiating and mature rat brain cortical neurons</article-title>. <source>Dev. Biol.</source> <volume>123</volume>, <fpage>51</fpage>&#x02013;<lpage>58</lpage>. <pub-id pub-id-type="doi">10.1016/0012-1606(87)90426-x</pub-id><pub-id pub-id-type="pmid">3622934</pub-id></citation></ref>
<ref id="B83"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Pleasance</surname> <given-names>E. D.</given-names></name> <name><surname>Stephens</surname> <given-names>P. J.</given-names></name> <name><surname>O&#x02019;meara</surname> <given-names>S.</given-names></name> <name><surname>Mcbride</surname> <given-names>D. J.</given-names></name> <name><surname>Meynert</surname> <given-names>A.</given-names></name> <name><surname>Jones</surname> <given-names>D.</given-names></name> <etal/></person-group>. (<year>2010</year>). <article-title>A small-cell lung cancer genome with complex signatures of tobacco exposure</article-title>. <source>Nature</source> <volume>463</volume>, <fpage>184</fpage>&#x02013;<lpage>190</lpage>. <pub-id pub-id-type="doi">10.1038/nature08629</pub-id><pub-id pub-id-type="pmid">20016488</pub-id></citation></ref>
<ref id="B84"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Qiao</surname> <given-names>Q.</given-names></name> <name><surname>Li</surname> <given-names>Y.</given-names></name> <name><surname>Chen</surname> <given-names>Z.</given-names></name> <name><surname>Wang</surname> <given-names>M.</given-names></name> <name><surname>Reinberg</surname> <given-names>D.</given-names></name> <name><surname>Xu</surname> <given-names>R. M.</given-names></name></person-group> (<year>2011</year>). <article-title>The structure of NSD1 reveals an autoregulatory mechanism underlying histone H3K36 methylation</article-title>. <source>J. Biol. Chem.</source> <volume>286</volume>, <fpage>8361</fpage>&#x02013;<lpage>8368</lpage>. <pub-id pub-id-type="doi">10.1074/jbc.m110.204115</pub-id><pub-id pub-id-type="pmid">21196496</pub-id></citation></ref>
<ref id="B85"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Raphael</surname> <given-names>Y.</given-names></name></person-group> (<year>1992</year>). <article-title>Evidence for supporting cell mitosis in response to acoustic trauma in the avian inner ear</article-title>. <source>J. Neurocytol.</source> <volume>21</volume>, <fpage>663</fpage>&#x02013;<lpage>671</lpage>. <pub-id pub-id-type="doi">10.1007/bf01191727</pub-id><pub-id pub-id-type="pmid">1403011</pub-id></citation></ref>
<ref id="B86"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Riggs</surname> <given-names>A. D.</given-names></name></person-group> (<year>1975</year>). <article-title>X inactivation, differentiation and DNA methylation</article-title>. <source>Cytogenet. Cell Genet.</source> <volume>14</volume>, <fpage>9</fpage>&#x02013;<lpage>25</lpage>. <pub-id pub-id-type="doi">10.1159/000130315</pub-id><pub-id pub-id-type="pmid">1093816</pub-id></citation></ref>
<ref id="B87"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Roberson</surname> <given-names>D. W.</given-names></name> <name><surname>Alosi</surname> <given-names>J. A.</given-names></name> <name><surname>Cotanche</surname> <given-names>D. A.</given-names></name></person-group> (<year>2004</year>). <article-title>Direct transdifferentiation gives rise to the earliest new hair cells in regenerating avian auditory epithelium</article-title>. <source>J. Neurosci. Res.</source> <volume>78</volume>, <fpage>461</fpage>&#x02013;<lpage>471</lpage>. <pub-id pub-id-type="doi">10.1002/jnr.20271</pub-id><pub-id pub-id-type="pmid">15372572</pub-id></citation></ref>
<ref id="B88"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Robert</surname> <given-names>C.</given-names></name> <name><surname>Rassool</surname> <given-names>F. V.</given-names></name></person-group> (<year>2012</year>). <article-title>HDAC inhibitors: roles of DNA damage and repair</article-title>. <source>Adv. Cancer Res.</source> <volume>116</volume>, <fpage>87</fpage>&#x02013;<lpage>129</lpage>. <pub-id pub-id-type="doi">10.1016/B978-0-12-394387-3.00003-3</pub-id><pub-id pub-id-type="pmid">23088869</pub-id></citation></ref>
<ref id="B89"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Robertson</surname> <given-names>K. D.</given-names></name> <name><surname>Ait-Si-Ali</surname> <given-names>S.</given-names></name> <name><surname>Yokochi</surname> <given-names>T.</given-names></name> <name><surname>Wade</surname> <given-names>P. A.</given-names></name> <name><surname>Jones</surname> <given-names>P. L.</given-names></name> <name><surname>Wolffe</surname> <given-names>A. P.</given-names></name></person-group> (<year>2000</year>). <article-title>DNMT1 forms a complex with Rb, E2F1 and HDAC1 and represses transcription from E2F-responsive promoters</article-title>. <source>Nat. Genet.</source> <volume>25</volume>, <fpage>338</fpage>&#x02013;<lpage>342</lpage>. <pub-id pub-id-type="doi">10.1038/77124</pub-id><pub-id pub-id-type="pmid">10888886</pub-id></citation></ref>
<ref id="B90"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Rudnicki</surname> <given-names>A.</given-names></name> <name><surname>Isakov</surname> <given-names>O.</given-names></name> <name><surname>Ushakov</surname> <given-names>K.</given-names></name> <name><surname>Shivatzki</surname> <given-names>S.</given-names></name> <name><surname>Weiss</surname> <given-names>I.</given-names></name> <name><surname>Friedman</surname> <given-names>L. M.</given-names></name> <etal/></person-group>. (<year>2014</year>). <article-title>Next-generation sequencing of small RNAs from inner ear sensory epithelium identifies microRNAs and defines regulatory pathways</article-title>. <source>BMC Genomics</source> <volume>15</volume>:<fpage>484</fpage>. <pub-id pub-id-type="doi">10.1186/1471-2164-15-484</pub-id><pub-id pub-id-type="pmid">24942165</pub-id></citation></ref>
<ref id="B91"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Rugg-Gunn</surname> <given-names>P. J.</given-names></name> <name><surname>Cox</surname> <given-names>B. J.</given-names></name> <name><surname>Ralston</surname> <given-names>A.</given-names></name> <name><surname>Rossant</surname> <given-names>J.</given-names></name></person-group> (<year>2010</year>). <article-title>Distinct histone modifications in stem cell lines and tissue lineages from the early mouse embryo</article-title>. <source>Proc. Natl. Acad. Sci. U S A</source> <volume>107</volume>, <fpage>10783</fpage>&#x02013;<lpage>10790</lpage>. <pub-id pub-id-type="doi">10.1073/pnas.0914507107</pub-id><pub-id pub-id-type="pmid">20479220</pub-id></citation></ref>
<ref id="B92"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ryu</surname> <given-names>H.</given-names></name> <name><surname>Lee</surname> <given-names>J.</given-names></name> <name><surname>Olofsson</surname> <given-names>B. A.</given-names></name> <name><surname>Mwidau</surname> <given-names>A.</given-names></name> <name><surname>Dedeoglu</surname> <given-names>A.</given-names></name> <name><surname>Escudero</surname> <given-names>M.</given-names></name> <etal/></person-group>. (<year>2003</year>). <article-title>Histone deacetylase inhibitors prevent oxidative neuronal death independent of expanded polyglutamine repeats via an Sp1-dependent pathway</article-title>. <source>Proc. Natl. Acad. Sci. U S A</source> <volume>100</volume>, <fpage>4281</fpage>&#x02013;<lpage>4286</lpage>. <pub-id pub-id-type="doi">10.1073/pnas.0737363100</pub-id><pub-id pub-id-type="pmid">12640146</pub-id></citation></ref>
<ref id="B93"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Saito</surname> <given-names>Y.</given-names></name> <name><surname>Liang</surname> <given-names>G.</given-names></name> <name><surname>Egger</surname> <given-names>G.</given-names></name> <name><surname>Friedman</surname> <given-names>J. M.</given-names></name> <name><surname>Chuang</surname> <given-names>J. C.</given-names></name> <name><surname>Coetzee</surname> <given-names>G. A.</given-names></name> <etal/></person-group>. (<year>2006</year>). <article-title>Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells</article-title>. <source>Cancer Cell</source> <volume>9</volume>, <fpage>435</fpage>&#x02013;<lpage>443</lpage>. <pub-id pub-id-type="doi">10.1016/j.ccr.2006.04.020</pub-id><pub-id pub-id-type="pmid">16766263</pub-id></citation></ref>
<ref id="B94"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Schacht</surname> <given-names>J.</given-names></name> <name><surname>Talaska</surname> <given-names>A. E.</given-names></name> <name><surname>Rybak</surname> <given-names>L. P.</given-names></name></person-group> (<year>2012</year>). <article-title>Cisplatin and aminoglycoside antibiotics: hearing loss and its prevention</article-title>. <source>Anat. Rec. (Hoboken)</source> <volume>295</volume>, <fpage>1837</fpage>&#x02013;<lpage>1850</lpage>. <pub-id pub-id-type="doi">10.1002/ar.22578</pub-id><pub-id pub-id-type="pmid">23045231</pub-id></citation></ref>
<ref id="B95"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Shen</surname> <given-names>L.</given-names></name> <name><surname>Zhang</surname> <given-names>Y.</given-names></name></person-group> (<year>2013</year>). <article-title>5-Hydroxymethylcytosine: generation, fate and genomic distribution</article-title>. <source>Curr. Opin. Cell Biol.</source> <volume>25</volume>, <fpage>289</fpage>&#x02013;<lpage>296</lpage>. <pub-id pub-id-type="doi">10.1016/j.ceb.2013.02.017</pub-id><pub-id pub-id-type="pmid">23498661</pub-id></citation></ref>
<ref id="B96"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Simpson</surname> <given-names>M. A.</given-names></name> <name><surname>Deshpande</surname> <given-names>C.</given-names></name> <name><surname>Dafou</surname> <given-names>D.</given-names></name> <name><surname>Vissers</surname> <given-names>L. E.</given-names></name> <name><surname>Woollard</surname> <given-names>W. J.</given-names></name> <name><surname>Holder</surname> <given-names>S. E.</given-names></name> <etal/></person-group>. (<year>2012</year>). <article-title>De novo mutations of the gene encoding the histone acetyltransferase KAT6B cause Genitopatellar syndrome</article-title>. <source>Am. J. Hum. Genet.</source> <volume>90</volume>, <fpage>290</fpage>&#x02013;<lpage>294</lpage>. <pub-id pub-id-type="doi">10.1016/j.ajhg.2011.11.024</pub-id><pub-id pub-id-type="pmid">22265017</pub-id></citation></ref>
<ref id="B97"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Slattery</surname> <given-names>E. L.</given-names></name> <name><surname>Speck</surname> <given-names>J. D.</given-names></name> <name><surname>Warchol</surname> <given-names>M. E.</given-names></name></person-group> (<year>2009</year>). <article-title>Epigenetic influences on sensory regeneration: histone deacetylases regulate supporting cell proliferation in the avian utricle</article-title>. <source>J. Assoc. Res. Otolaryngol.</source> <volume>10</volume>, <fpage>341</fpage>&#x02013;<lpage>353</lpage>. <pub-id pub-id-type="doi">10.1007/s10162-009-0166-y</pub-id><pub-id pub-id-type="pmid">19340485</pub-id></citation></ref>
<ref id="B98"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Smeti</surname> <given-names>I.</given-names></name> <name><surname>Assou</surname> <given-names>S.</given-names></name> <name><surname>Savary</surname> <given-names>E.</given-names></name> <name><surname>Masmoudi</surname> <given-names>S.</given-names></name> <name><surname>Zine</surname> <given-names>A.</given-names></name></person-group> (<year>2012</year>). <article-title>Transcriptomic analysis of the developing and adult mouse cochlear sensory epithelia</article-title>. <source>PLoS One</source> <volume>7</volume>:<fpage>e42987</fpage>. <pub-id pub-id-type="doi">10.1371/journal.pone.0042987</pub-id><pub-id pub-id-type="pmid">22900075</pub-id></citation></ref>
<ref id="B99"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Smith</surname> <given-names>Z. D.</given-names></name> <name><surname>Meissner</surname> <given-names>A.</given-names></name></person-group> (<year>2013</year>). <article-title>DNA methylation: roles in mammalian development</article-title>. <source>Nat. Rev. Genet.</source> <volume>14</volume>, <fpage>204</fpage>&#x02013;<lpage>220</lpage>. <pub-id pub-id-type="doi">10.1038/nrg3354</pub-id><pub-id pub-id-type="pmid">23400093</pub-id></citation></ref>
<ref id="B100"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Stadler</surname> <given-names>M. B.</given-names></name> <name><surname>Murr</surname> <given-names>R.</given-names></name> <name><surname>Burger</surname> <given-names>L.</given-names></name> <name><surname>Ivanek</surname> <given-names>R.</given-names></name> <name><surname>Lienert</surname> <given-names>F.</given-names></name> <name><surname>Scholer</surname> <given-names>A.</given-names></name> <etal/></person-group>. (<year>2011</year>). <article-title>DNA-binding factors shape the mouse methylome at distal regulatory regions</article-title>. <source>Nature</source> <volume>480</volume>, <fpage>490</fpage>&#x02013;<lpage>495</lpage>. <pub-id pub-id-type="doi">10.1038/nature10716</pub-id><pub-id pub-id-type="pmid">22170606</pub-id></citation></ref>
<ref id="B101"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Stroud</surname> <given-names>H.</given-names></name> <name><surname>Feng</surname> <given-names>S.</given-names></name> <name><surname>Morey Kinney</surname> <given-names>S.</given-names></name> <name><surname>Pradhan</surname> <given-names>S.</given-names></name> <name><surname>Jacobsen</surname> <given-names>S. E.</given-names></name></person-group> (<year>2011</year>). <article-title>5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells</article-title>. <source>Genome Biol.</source> <volume>12</volume>:<fpage>R54</fpage>. <pub-id pub-id-type="doi">10.1186/gb-2011-12-6-r54</pub-id><pub-id pub-id-type="pmid">21689397</pub-id></citation></ref>
<ref id="B102"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Sun</surname> <given-names>Z.</given-names></name> <name><surname>Wu</surname> <given-names>Y.</given-names></name> <name><surname>Ordog</surname> <given-names>T.</given-names></name> <name><surname>Baheti</surname> <given-names>S.</given-names></name> <name><surname>Nie</surname> <given-names>J.</given-names></name> <name><surname>Duan</surname> <given-names>X.</given-names></name> <etal/></person-group>. (<year>2014</year>). <article-title>Aberrant signature methylome by DNMT1 hot spot mutation in hereditary sensory and autonomic neuropathy 1E</article-title>. <source>Epigenetics</source> <volume>9</volume>, <fpage>1184</fpage>&#x02013;<lpage>1193</lpage>. <pub-id pub-id-type="doi">10.4161/epi.29676</pub-id><pub-id pub-id-type="pmid">25033457</pub-id></citation></ref>
<ref id="B103"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Suzuki</surname> <given-names>H.</given-names></name> <name><surname>Takatsuka</surname> <given-names>S.</given-names></name> <name><surname>Akashi</surname> <given-names>H.</given-names></name> <name><surname>Yamamoto</surname> <given-names>E.</given-names></name> <name><surname>Nojima</surname> <given-names>M.</given-names></name> <name><surname>Maruyama</surname> <given-names>R.</given-names></name> <etal/></person-group>. (<year>2011</year>). <article-title>Genome-wide profiling of chromatin signatures reveals epigenetic regulation of MicroRNA genes in colorectal cancer</article-title>. <source>Cancer Res.</source> <volume>71</volume>, <fpage>5646</fpage>&#x02013;<lpage>5658</lpage>. <pub-id pub-id-type="doi">10.1158/0008-5472.can-11-1076</pub-id><pub-id pub-id-type="pmid">21734013</pub-id></citation></ref>
<ref id="B104"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Szulwach</surname> <given-names>K. E.</given-names></name> <name><surname>Li</surname> <given-names>X.</given-names></name> <name><surname>Li</surname> <given-names>Y.</given-names></name> <name><surname>Song</surname> <given-names>C. X.</given-names></name> <name><surname>Han</surname> <given-names>J. W.</given-names></name> <name><surname>Kim</surname> <given-names>S.</given-names></name> <etal/></person-group>. (<year>2011</year>). <article-title>Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells</article-title>. <source>PLoS Genet.</source> <volume>7</volume>:<fpage>e1002154</fpage>. <pub-id pub-id-type="doi">10.1371/journal.pgen.1002154</pub-id><pub-id pub-id-type="pmid">21731508</pub-id></citation></ref>
<ref id="B105"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tachibana</surname> <given-names>M.</given-names></name> <name><surname>Ueda</surname> <given-names>J.</given-names></name> <name><surname>Fukuda</surname> <given-names>M.</given-names></name> <name><surname>Takeda</surname> <given-names>N.</given-names></name> <name><surname>Ohta</surname> <given-names>T.</given-names></name> <name><surname>Iwanari</surname> <given-names>H.</given-names></name> <etal/></person-group>. (<year>2005</year>). <article-title>Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3&#x02013;K9</article-title>. <source>Genes Dev.</source> <volume>19</volume>, <fpage>815</fpage>&#x02013;<lpage>826</lpage>. <pub-id pub-id-type="doi">10.1101/gad.1284005</pub-id><pub-id pub-id-type="pmid">15774718</pub-id></citation></ref>
<ref id="B106"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tahara</surname> <given-names>T.</given-names></name> <name><surname>Yamamoto</surname> <given-names>E.</given-names></name> <name><surname>Madireddi</surname> <given-names>P.</given-names></name> <name><surname>Suzuki</surname> <given-names>H.</given-names></name> <name><surname>Maruyama</surname> <given-names>R.</given-names></name> <name><surname>Chung</surname> <given-names>W.</given-names></name> <etal/></person-group>. (<year>2014</year>). <article-title>Colorectal carcinomas with CpG island methylator phenotype 1 frequently contain mutations in chromatin regulators</article-title>. <source>Gastroenterology</source> <volume>146</volume>, <fpage>530</fpage>&#x02013;<lpage>538.e5</lpage>. <pub-id pub-id-type="doi">10.1053/j.gastro.2013.10.060</pub-id><pub-id pub-id-type="pmid">24211491</pub-id></citation></ref>
<ref id="B107"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tahiliani</surname> <given-names>M.</given-names></name> <name><surname>Koh</surname> <given-names>K. P.</given-names></name> <name><surname>Shen</surname> <given-names>Y.</given-names></name> <name><surname>Pastor</surname> <given-names>W. A.</given-names></name> <name><surname>Bandukwala</surname> <given-names>H.</given-names></name> <name><surname>Brudno</surname> <given-names>Y.</given-names></name> <etal/></person-group>. (<year>2009</year>). <article-title>Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1</article-title>. <source>Science</source> <volume>324</volume>, <fpage>930</fpage>&#x02013;<lpage>935</lpage>. <pub-id pub-id-type="doi">10.1126/science.1170116</pub-id><pub-id pub-id-type="pmid">19372391</pub-id></citation></ref>
<ref id="B109"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tatton-Brown</surname> <given-names>K.</given-names></name> <name><surname>Murray</surname> <given-names>A.</given-names></name> <name><surname>Hanks</surname> <given-names>S.</given-names></name> <name><surname>Douglas</surname> <given-names>J.</given-names></name> <name><surname>Armstrong</surname> <given-names>R.</given-names></name> <name><surname>Banka</surname> <given-names>S.</given-names></name> <etal/></person-group>. (<year>2013</year>). <article-title>Weaver syndrome and EZH2 mutations: clarifying the clinical phenotype</article-title>. <source>Am. J. Med. Genet. A</source> <volume>161A</volume>, <fpage>2972</fpage>&#x02013;<lpage>2980</lpage>. <pub-id pub-id-type="doi">10.1002/ajmg.a.36229</pub-id><pub-id pub-id-type="pmid">24214728</pub-id></citation></ref>
<ref id="B108"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tatton-Brown</surname> <given-names>K.</given-names></name> <name><surname>Rahman</surname> <given-names>N.</given-names></name></person-group> (<year>2013</year>). <article-title>The NSD1 and EZH2 overgrowth genes, similarities and differences</article-title>. <source>Am. J. Med. Genet. C Semin. Med. Genet.</source> <volume>163C</volume>, <fpage>86</fpage>&#x02013;<lpage>91</lpage>. <pub-id pub-id-type="doi">10.1002/ajmg.c.31359</pub-id><pub-id pub-id-type="pmid">23592277</pub-id></citation></ref>
<ref id="B110"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Tsumura</surname> <given-names>A.</given-names></name> <name><surname>Hayakawa</surname> <given-names>T.</given-names></name> <name><surname>Kumaki</surname> <given-names>Y.</given-names></name> <name><surname>Takebayashi</surname> <given-names>S.</given-names></name> <name><surname>Sakaue</surname> <given-names>M.</given-names></name> <name><surname>Matsuoka</surname> <given-names>C.</given-names></name> <etal/></person-group>. (<year>2006</year>). <article-title>Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b</article-title>. <source>Genes Cells</source> <volume>11</volume>, <fpage>805</fpage>&#x02013;<lpage>814</lpage>. <pub-id pub-id-type="doi">10.1111/j.1365-2443.2006.00984.x</pub-id><pub-id pub-id-type="pmid">16824199</pub-id></citation></ref>
<ref id="B111"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Valinluck</surname> <given-names>V.</given-names></name> <name><surname>Tsai</surname> <given-names>H. H.</given-names></name> <name><surname>Rogstad</surname> <given-names>D. K.</given-names></name> <name><surname>Burdzy</surname> <given-names>A.</given-names></name> <name><surname>Bird</surname> <given-names>A.</given-names></name> <name><surname>Sowers</surname> <given-names>L. C.</given-names></name></person-group> (<year>2004</year>). <article-title>Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2)</article-title>. <source>Nucleic Acids Res.</source> <volume>32</volume>, <fpage>4100</fpage>&#x02013;<lpage>4108</lpage>. <pub-id pub-id-type="doi">10.1093/nar/gkh739</pub-id><pub-id pub-id-type="pmid">15302911</pub-id></citation></ref>
<ref id="B112"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Van Nostrand</surname> <given-names>J. L.</given-names></name> <name><surname>Brady</surname> <given-names>C. A.</given-names></name> <name><surname>Jung</surname> <given-names>H.</given-names></name> <name><surname>Fuentes</surname> <given-names>D. R.</given-names></name> <name><surname>Kozak</surname> <given-names>M. M.</given-names></name> <name><surname>Johnson</surname> <given-names>T. M.</given-names></name> <etal/></person-group>. (<year>2014</year>). <article-title>Inappropriate p53 activation during development induces features of CHARGE syndrome</article-title>. <source>Nature</source> <volume>514</volume>, <fpage>228</fpage>&#x02013;<lpage>232</lpage>. <pub-id pub-id-type="doi">10.1038/nature13585</pub-id><pub-id pub-id-type="pmid">25119037</pub-id></citation></ref>
<ref id="B113"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Vaquero</surname> <given-names>A.</given-names></name> <name><surname>Loyola</surname> <given-names>A.</given-names></name> <name><surname>Reinberg</surname> <given-names>D.</given-names></name></person-group> (<year>2003</year>). <article-title>The constantly changing face of chromatin</article-title>. <source>Sci. Aging Knowledge Environ.</source> <volume>2003</volume>:<fpage>RE4</fpage>. <pub-id pub-id-type="doi">10.1126/sageke.2003.14.re4</pub-id><pub-id pub-id-type="pmid">12844523</pub-id></citation></ref>
<ref id="B114"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Velasco</surname> <given-names>G.</given-names></name> <name><surname>Hube</surname> <given-names>F.</given-names></name> <name><surname>Rollin</surname> <given-names>J.</given-names></name> <name><surname>Neuillet</surname> <given-names>D.</given-names></name> <name><surname>Philippe</surname> <given-names>C.</given-names></name> <name><surname>Bouzinba-Segard</surname> <given-names>H.</given-names></name> <etal/></person-group>. (<year>2010</year>). <article-title>Dnmt3b recruitment through E2F6 transcriptional repressor mediates germ-line gene silencing in murine somatic tissues</article-title>. <source>Proc. Natl. Acad. Sci. U S A</source> <volume>107</volume>, <fpage>9281</fpage>&#x02013;<lpage>9286</lpage>. <pub-id pub-id-type="doi">10.1073/pnas.1000473107</pub-id><pub-id pub-id-type="pmid">20439742</pub-id></citation></ref>
<ref id="B115"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Voigt</surname> <given-names>P.</given-names></name> <name><surname>Tee</surname> <given-names>W. W.</given-names></name> <name><surname>Reinberg</surname> <given-names>D.</given-names></name></person-group> (<year>2013</year>). <article-title>A double take on bivalent promoters</article-title>. <source>Genes Dev.</source> <volume>27</volume>, <fpage>1318</fpage>&#x02013;<lpage>1338</lpage>. <pub-id pub-id-type="doi">10.1101/gad.219626.113</pub-id><pub-id pub-id-type="pmid">23788621</pub-id></citation></ref>
<ref id="B116"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Waddington</surname> <given-names>C. H.</given-names></name></person-group> (<year>2012</year>). <article-title>The epigenotype. 1942</article-title>. <source>Int. J. Epidemiol.</source> <volume>41</volume>, <fpage>10</fpage>&#x02013;<lpage>13</lpage>. <pub-id pub-id-type="doi">10.1093/ije/dyr184</pub-id><pub-id pub-id-type="pmid">22186258</pub-id></citation></ref>
<ref id="B117"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Wang</surname> <given-names>J.</given-names></name> <name><surname>Hevi</surname> <given-names>S.</given-names></name> <name><surname>Kurash</surname> <given-names>J. K.</given-names></name> <name><surname>Lei</surname> <given-names>H.</given-names></name> <name><surname>Gay</surname> <given-names>F.</given-names></name> <name><surname>Bajko</surname> <given-names>J.</given-names></name> <etal/></person-group>. (<year>2009</year>). <article-title>The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation</article-title>. <source>Nat. Genet.</source> <volume>41</volume>, <fpage>125</fpage>&#x02013;<lpage>129</lpage>. <pub-id pub-id-type="doi">10.1038/ng.268</pub-id><pub-id pub-id-type="pmid">19098913</pub-id></citation></ref>
<ref id="B118"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Wang</surname> <given-names>T.</given-names></name> <name><surname>Pan</surname> <given-names>Q.</given-names></name> <name><surname>Lin</surname> <given-names>L.</given-names></name> <name><surname>Szulwach</surname> <given-names>K. E.</given-names></name> <name><surname>Song</surname> <given-names>C. X.</given-names></name> <name><surname>He</surname> <given-names>C.</given-names></name> <etal/></person-group>. (<year>2012</year>). <article-title>Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human cerebellum</article-title>. <source>Hum. Mol. Genet.</source> <volume>21</volume>, <fpage>5500</fpage>&#x02013;<lpage>5510</lpage>. <pub-id pub-id-type="doi">10.1093/hmg/dds394</pub-id><pub-id pub-id-type="pmid">23042784</pub-id></citation></ref>
<ref id="B119"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Weisleder</surname> <given-names>P.</given-names></name> <name><surname>Rubel</surname> <given-names>E. W.</given-names></name></person-group> (<year>1993</year>). <article-title>Hair cell regeneration after streptomycin toxicity in the avian vestibular epithelium</article-title>. <source>J. Comp. Neurol.</source> <volume>331</volume>, <fpage>97</fpage>&#x02013;<lpage>110</lpage>. <pub-id pub-id-type="doi">10.1002/cne.903310106</pub-id><pub-id pub-id-type="pmid">8320350</pub-id></citation></ref>
<ref id="B120"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Winkelmann</surname> <given-names>J.</given-names></name> <name><surname>Lin</surname> <given-names>L.</given-names></name> <name><surname>Schormair</surname> <given-names>B.</given-names></name> <name><surname>Kornum</surname> <given-names>B. R.</given-names></name> <name><surname>Faraco</surname> <given-names>J.</given-names></name> <name><surname>Plazzi</surname> <given-names>G.</given-names></name> <etal/></person-group>. (<year>2012</year>). <article-title>Mutations in DNMT1 cause autosomal dominant cerebellar ataxia, deafness and narcolepsy</article-title>. <source>Hum. Mol. Genet.</source> <volume>21</volume>, <fpage>2205</fpage>&#x02013;<lpage>2210</lpage>. <pub-id pub-id-type="doi">10.1093/hmg/dds035</pub-id><pub-id pub-id-type="pmid">22328086</pub-id></citation></ref>
<ref id="B121"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Wright</surname> <given-names>A.</given-names></name> <name><surname>Dyck</surname> <given-names>P. J.</given-names></name></person-group> (<year>1995</year>). <article-title>Hereditary sensory neuropathy with sensorineural deafness and early-onset dementia</article-title>. <source>Neurology</source> <volume>45</volume>, <fpage>560</fpage>&#x02013;<lpage>562</lpage>. <pub-id pub-id-type="doi">10.1212/wnl.45.3.560</pub-id><pub-id pub-id-type="pmid">7898717</pub-id></citation></ref>
<ref id="B122"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Wu</surname> <given-names>S. C.</given-names></name> <name><surname>Zhang</surname> <given-names>Y.</given-names></name></person-group> (<year>2009</year>). <article-title>Minireview: role of protein methylation and demethylation in nuclear hormone signaling</article-title>. <source>Mol. Endocrinol.</source> <volume>23</volume>, <fpage>1323</fpage>&#x02013;<lpage>1334</lpage>. <pub-id pub-id-type="doi">10.1210/me.2009-0131</pub-id><pub-id pub-id-type="pmid">19407220</pub-id></citation></ref>
<ref id="B123"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Wunsch</surname> <given-names>A. M.</given-names></name> <name><surname>Reinhardt</surname> <given-names>K.</given-names></name> <name><surname>Lough</surname> <given-names>J.</given-names></name></person-group> (<year>1991</year>). <article-title>Normal transitions in synthesis of replacement histones H2A.Z and H3.3 during differentiation of dystrophic myotube cells. A brief note</article-title>. <source>Mech. Ageing Dev.</source> <volume>59</volume>, <fpage>299</fpage>&#x02013;<lpage>305</lpage>. <pub-id pub-id-type="doi">10.1016/0047-6374(91)90140-u</pub-id><pub-id pub-id-type="pmid">1921519</pub-id></citation></ref>
<ref id="B124"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Yildirim</surname> <given-names>O.</given-names></name> <name><surname>Li</surname> <given-names>R.</given-names></name> <name><surname>Hung</surname> <given-names>J. H.</given-names></name> <name><surname>Chen</surname> <given-names>P. B.</given-names></name> <name><surname>Dong</surname> <given-names>X.</given-names></name> <name><surname>Ee</surname> <given-names>L. S.</given-names></name> <etal/></person-group>. (<year>2011</year>). <article-title>Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells</article-title>. <source>Cell</source> <volume>147</volume>, <fpage>1498</fpage>&#x02013;<lpage>1510</lpage>. <pub-id pub-id-type="doi">10.1016/j.cell.2011.11.054</pub-id><pub-id pub-id-type="pmid">22196727</pub-id></citation></ref>
<ref id="B126"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Yu</surname> <given-names>X.</given-names></name> <name><surname>Guo</surname> <given-names>Z. S.</given-names></name> <name><surname>Marcu</surname> <given-names>M. G.</given-names></name> <name><surname>Neckers</surname> <given-names>L.</given-names></name> <name><surname>Nguyen</surname> <given-names>D. M.</given-names></name> <name><surname>Chen</surname> <given-names>G. A.</given-names></name> <etal/></person-group>. (<year>2002</year>). <article-title>Modulation of p53, ErbB1, ErbB2 and Raf-1 expression in lung cancer cells by depsipeptide FR901228</article-title>. <source>J. Natl. Cancer Inst.</source> <volume>94</volume>, <fpage>504</fpage>&#x02013;<lpage>513</lpage>. <pub-id pub-id-type="doi">10.1093/jnci/94.7.504</pub-id><pub-id pub-id-type="pmid">11929951</pub-id></citation></ref>
<ref id="B125"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Yu</surname> <given-names>M.</given-names></name> <name><surname>Hon</surname> <given-names>G. C.</given-names></name> <name><surname>Szulwach</surname> <given-names>K. E.</given-names></name> <name><surname>Song</surname> <given-names>C. X.</given-names></name> <name><surname>Zhang</surname> <given-names>L.</given-names></name> <name><surname>Kim</surname> <given-names>A.</given-names></name> <etal/></person-group>. (<year>2012</year>). <article-title>Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome</article-title>. <source>Cell</source> <volume>149</volume>, <fpage>1368</fpage>&#x02013;<lpage>1380</lpage>. <pub-id pub-id-type="doi">10.1016/j.cell.2012.04.027</pub-id><pub-id pub-id-type="pmid">22608086</pub-id></citation></ref>
<ref id="B127"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zeng</surname> <given-names>L.</given-names></name> <name><surname>Zhou</surname> <given-names>M. M.</given-names></name></person-group> (<year>2002</year>). <article-title>Bromodomain: an acetyl-lysine binding domain</article-title>. <source>FEBS Lett.</source> <volume>513</volume>, <fpage>124</fpage>&#x02013;<lpage>128</lpage>. <pub-id pub-id-type="doi">10.1016/s0014-5793(01)03309-9</pub-id><pub-id pub-id-type="pmid">11911891</pub-id></citation></ref>
<ref id="B128"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zentner</surname> <given-names>G. E.</given-names></name> <name><surname>Layman</surname> <given-names>W. S.</given-names></name> <name><surname>Martin</surname> <given-names>D. M.</given-names></name> <name><surname>Scacheri</surname> <given-names>P. C.</given-names></name></person-group> (<year>2010</year>). <article-title>Molecular and phenotypic aspects of CHD7 mutation in CHARGE syndrome</article-title>. <source>Am. J. Med. Genet. A</source> <volume>152A</volume>, <fpage>674</fpage>&#x02013;<lpage>686</lpage>. <pub-id pub-id-type="doi">10.1002/ajmg.a.33323</pub-id><pub-id pub-id-type="pmid">20186815</pub-id></citation></ref>
<ref id="B129"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zhang</surname> <given-names>K.</given-names></name> <name><surname>Dent</surname> <given-names>S. Y.</given-names></name></person-group> (<year>2005</year>). <article-title>Histone modifying enzymes and cancer: going beyond histones</article-title>. <source>J. Cell. Biochem.</source> <volume>96</volume>, <fpage>1137</fpage>&#x02013;<lpage>1148</lpage>. <pub-id pub-id-type="doi">10.1002/jcb.20615</pub-id><pub-id pub-id-type="pmid">16173079</pub-id></citation></ref>
<ref id="B130"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Zheng</surname> <given-names>J. L.</given-names></name> <name><surname>Gao</surname> <given-names>W. Q.</given-names></name></person-group> (<year>2000</year>). <article-title>Overexpression of Math1 induces robust production of extra hair cells in postnatal rat inner ears</article-title>. <source>Nat. Neurosci.</source> <volume>3</volume>, <fpage>580</fpage>&#x02013;<lpage>586</lpage>. <pub-id pub-id-type="doi">10.1038/75753</pub-id><pub-id pub-id-type="pmid">10816314</pub-id></citation></ref>
<ref id="B132"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ziech</surname> <given-names>D.</given-names></name> <name><surname>Franco</surname> <given-names>R.</given-names></name> <name><surname>Pappa</surname> <given-names>A.</given-names></name> <name><surname>Malamou-Mitsi</surname> <given-names>V.</given-names></name> <name><surname>Georgakila</surname> <given-names>S.</given-names></name> <name><surname>Georgakilas</surname> <given-names>A. G.</given-names></name> <etal/></person-group>. (<year>2010</year>). <article-title>The role of epigenetics in environmental and occupational carcinogenesis</article-title>. <source>Chem. Biol. Interact.</source> <volume>188</volume>, <fpage>340</fpage>&#x02013;<lpage>349</lpage>. <pub-id pub-id-type="doi">10.1016/j.cbi.2010.06.012</pub-id><pub-id pub-id-type="pmid">20599843</pub-id></citation></ref>
<ref id="B131"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ziech</surname> <given-names>D.</given-names></name> <name><surname>Franco</surname> <given-names>R.</given-names></name> <name><surname>Pappa</surname> <given-names>A.</given-names></name> <name><surname>Panayiotidis</surname> <given-names>M. I.</given-names></name></person-group> (<year>2011</year>). <article-title>Reactive oxygen species (ROS)&#x02013;induced genetic and epigenetic alterations in human carcinogenesis</article-title>. <source>Mutat. Res.</source> <volume>711</volume>, <fpage>167</fpage>&#x02013;<lpage>173</lpage>. <pub-id pub-id-type="doi">10.1016/j.mrfmmm.2011.02.015</pub-id><pub-id pub-id-type="pmid">21419141</pub-id></citation></ref>
<ref id="B133"><citation citation-type="journal"><person-group person-group-type="author"><name><surname>Ziller</surname> <given-names>M. J.</given-names></name> <name><surname>Gu</surname> <given-names>H.</given-names></name> <name><surname>Muller</surname> <given-names>F.</given-names></name> <name><surname>Donaghey</surname> <given-names>J.</given-names></name> <name><surname>Tsai</surname> <given-names>L. T.</given-names></name> <name><surname>Kohlbacher</surname> <given-names>O.</given-names></name> <etal/></person-group>. (<year>2013</year>). <article-title>Charting a dynamic DNA methylation landscape of the human genome</article-title>. <source>Nature</source> <volume>500</volume>, <fpage>477</fpage>&#x02013;<lpage>481</lpage>. <pub-id pub-id-type="doi">10.1038/nature12433</pub-id><pub-id pub-id-type="pmid">23925113</pub-id></citation></ref>
</ref-list>
</back>
</article>