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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Endocrinol.</journal-id>
<journal-title>Frontiers in Endocrinology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Endocrinol.</abbrev-journal-title>
<issn pub-type="epub">1664-2392</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fendo.2017.00027</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Endocrinology</subject>
<subj-group>
<subject>Mini Review</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Rodent Models for the Analysis of Tissue Clock Function in Metabolic Rhythms Research</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name><surname>Tsang</surname> <given-names>Anthony H.</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<uri xlink:href="http://frontiersin.org/people/u/405907"/>
</contrib>
<contrib contrib-type="author">
<name><surname>Astiz</surname> <given-names>Mariana</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
</contrib>
<contrib contrib-type="author">
<name><surname>Leinweber</surname> <given-names>Brinja</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
</contrib>
<contrib contrib-type="author" corresp="yes">
<name><surname>Oster</surname> <given-names>Henrik</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="corresp" rid="cor1">&#x0002A;</xref>
<uri xlink:href="http://frontiersin.org/people/u/110430"/>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup><institution>Chronophysiology Group, Medical Department I, University of L&#x000FC;beck</institution>, <addr-line>L&#x000FC;beck</addr-line>, <country>Germany</country></aff>
<aff id="aff2"><sup>2</sup><institution>Department of Clinical Biochemistry, Institute of Metabolic Science, University of Cambridge</institution>, <addr-line>Cambridge</addr-line>, <country>UK</country></aff>
<author-notes>
<fn fn-type="edited-by"><p>Edited by: Andries Kalsbeek, Academic Medical Center, Netherlands</p></fn>
<fn fn-type="edited-by"><p>Reviewed by: Michael T. Sellix, University of Rochester School of Medicine and Dentistry, USA; David A. Bechtold, University of Manchester, UK</p></fn>
<corresp content-type="corresp" id="cor1">&#x0002A;Correspondence: Henrik Oster, <email>henrik.oster&#x00040;uni-luebeck.de</email></corresp>
<fn fn-type="other" id="fn002"><p>Specialty section: This article was submitted to Neuroendocrine Science, a section of the journal Frontiers in Endocrinology</p></fn>
</author-notes>
<pub-date pub-type="epub">
<day>13</day>
<month>02</month>
<year>2017</year>
</pub-date>
<pub-date pub-type="collection">
<year>2017</year>
</pub-date>
<volume>8</volume>
<elocation-id>27</elocation-id>
<history>
<date date-type="received">
<day>21</day>
<month>10</month>
<year>2016</year>
</date>
<date date-type="accepted">
<day>30</day>
<month>01</month>
<year>2017</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#x000A9; 2017 Tsang, Astiz, Leinweber and Oster.</copyright-statement>
<copyright-year>2017</copyright-year>
<copyright-holder>Tsang, Astiz, Leinweber and Oster</copyright-holder>
<license 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 or 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 circadian timing system consists on a distributed network of cellular clocks that together coordinate 24-h rhythms of physiology and behavior. Clock function and metabolism are tightly coupled, from the cellular to the organismal level. Genetic and non-genetic approaches in rodents have been employed to study circadian clock function in the living organism. Due to the ubiquitous expression of clock genes and the intricate interaction between the circadian system and energy metabolism, genetic approaches targeting specific tissue clocks have been used to assess their contribution in systemic metabolic processes. However, special requirements regarding specificity and efficiency have to be met to allow for valid conclusions from such studies. In this review, we provide a brief summary of different approaches developed for dissecting tissue clock function in the metabolic context in rodents, compare their strengths and weaknesses, and suggest new strategies in assessing tissue clock output and the consequences of circadian clock disruption <italic>in vivo</italic>.</p>
</abstract>
<kwd-group>
<kwd>clock genes</kwd>
<kwd>metabolism</kwd>
<kwd>gene targeting</kwd>
<kwd><italic>Bmal1</italic></kwd>
<kwd>conditional knockout</kwd>
<kwd>CRE-<italic>loxP</italic> system</kwd>
</kwd-group>
<contract-num rid="cn01">Lichtenberg Fellowship</contract-num>
<contract-num rid="cn02">GRK1957, SFB134, SFB654</contract-num>
<contract-num rid="cn03">Research Fellowship</contract-num>
<contract-sponsor id="cn01">Volkswagen Foundation<named-content content-type="fundref-id">10.13039/501100001663</named-content></contract-sponsor>
<contract-sponsor id="cn02">Deutsche Forschungsgemeinschaft<named-content content-type="fundref-id">10.13039/501100001659</named-content></contract-sponsor>
<contract-sponsor id="cn03">International Brain Research Organization<named-content content-type="fundref-id">10.13039/501100001675</named-content></contract-sponsor>
<counts>
<fig-count count="1"/>
<table-count count="1"/>
<equation-count count="0"/>
<ref-count count="72"/>
<page-count count="7"/>
<word-count count="5487"/>
</counts>
</article-meta>
</front>
<body>
<sec id="S1" sec-type="introduction">
<title>Introduction</title>
<p>A network of cellular clocks adapts physiology and behavior to a 24-h rhythmic environment. Epidemiological evidence suggests a strong association between circadian rhythm disruption&#x02014;e.g., in shift workers&#x02014;and metabolic disorders (<xref ref-type="bibr" rid="B1">1</xref>). The development of genetic rodent models has been essential in deciphering the mechanisms linking clock dysfunction and the pathogenesis of metabolic diseases, highlighting the therapeutic potential of circadian rhythm manipulation in this context. Here, we provide a brief overview of the metabolic consequences of circadian disruption derived from rodent model studies and discuss potential and pitfalls of emerging genetic techniques in studying clock-metabolism crosstalk.</p>
</sec>
<sec id="S2">
<title>Non-Genetic Circadian Disruption Models</title>
<p>Early approaches describing the interplay between circadian clock function and metabolism were based on models of non-genetic circadian disruption (Table <xref ref-type="table" rid="T1">1</xref>). Lesion experiments identified the suprachiasmatic nucleus (SCN) as the central circadian pacemaker (<xref ref-type="bibr" rid="B2">2</xref>, <xref ref-type="bibr" rid="B3">3</xref>). In rats, SCN lesions abolish plasma rhythms of glucose, insulin (<xref ref-type="bibr" rid="B4">4</xref>), and leptin (<xref ref-type="bibr" rid="B5">5</xref>). In terms of general energy homeostasis, there are differences between studies that range from slight weight reductions (<xref ref-type="bibr" rid="B6">6</xref>) to no effect (<xref ref-type="bibr" rid="B5">5</xref>) and marked obesity (<xref ref-type="bibr" rid="B7">7</xref>). In the latter study on mice, increased weight is accompanied by hepatic insulin resistance. In sum, these studies illustrate that the SCN regulates metabolic hormones and tissue physiology either directly or <italic>via</italic> its control on food intake rhythms.</p>
<table-wrap position="float" id="T1">
<label>Table 1</label>
<caption><p><bold>Advantages and disadvantages of different clock targeting approaches in rodents</bold>.</p></caption>
<table frame="hsides" rules="groups">
<thead>
<tr>
<th valign="top" align="left">Paradigm</th>
<th valign="top" align="left">Advantages</th>
<th valign="top" align="left">Disadvantages</th>
</tr>
</thead>
<tbody>
<tr>
<td align="left" valign="top">Non-genetic clock disruption</td>
<td align="left" valign="top"><list list-type="bullet">
<list-item><p>No gene targeting necessary</p></list-item>
<list-item><p>No developmental effects</p></list-item>
<list-item><p>At least partly reversible</p></list-item>
</list>
</td>
<td align="left" valign="top"><list list-type="bullet">
<list-item><p>Non-specific (except for lesioning) and non-targeted (very broad intervention)</p></list-item>
</list>
</td>
</tr><tr><td align="left" valign="top" colspan="3"><hr/></td></tr>
<tr>
<td align="left" valign="top">Classical (global) gene targeting</td>
<td align="left" valign="top"><list list-type="bullet">
<list-item><p>High recombination efficiency</p></list-item>
</list>
</td>
<td align="left" valign="top"><list list-type="bullet">
<list-item><p>No spatio-temporal control</p></list-item>
<list-item><p>Possible developmental effects</p></list-item>
<list-item><p>Irreversible and non-tunable</p></list-item>
</list>
</td>
</tr><tr><td align="left" valign="top" colspan="3"><hr/></td></tr>
<tr>
<td align="left" valign="top">Conventional CRE-<italic>loxP</italic> gene targeting</td>
<td align="left" valign="top"><list list-type="bullet">
<list-item><p>Relatively high recombination efficiency</p></list-item>
</list>
</td>
<td align="left" valign="top"><list list-type="bullet">
<list-item><p>Relative tissue specificity</p></list-item>
<list-item><p>Possible developmental effects</p></list-item>
<list-item><p>Irreversible and non-tunable</p></list-item>
</list>
</td>
</tr><tr><td align="left" valign="top" colspan="3"><hr/></td></tr>
<tr>
<td align="left" valign="top">Inducible CRE-<italic>loxP</italic> gene targeting</td>
<td align="left" valign="top"><list list-type="bullet">
<list-item><p>Exclude developmental effects</p></list-item>
</list>
</td>
<td align="left" valign="top"><list list-type="bullet">
<list-item><p>Relative tissue specificity</p></list-item>
<list-item><p>Irreversible and non-tunable</p></list-item>
<list-item><p>Reduced recombination efficiency</p></list-item>
</list>
</td>
</tr><tr><td align="left" valign="top" colspan="3"><hr/></td></tr>
<tr>
<td align="left" valign="top">Chemogenetics</td>
<td align="left" valign="top"><list list-type="bullet">
<list-item><p>Reversible, tunable, and good temporal control (depending on the pharmacokinetics of the drug used)</p></list-item>
</list>
</td>
<td align="left" valign="top"><list list-type="bullet">
<list-item><p>Drug administration can interfere with the experiment</p></list-item>
<list-item><p>Poor tissue specificity (unless combined with the use of CRE-driver mice and/or viral transgene delivery)</p></list-item>
</list>
</td>
</tr><tr><td align="left" valign="top" colspan="3"><hr/></td></tr>
<tr>
<td align="left" valign="top">Optogenetics</td>
<td align="left" valign="top"><list list-type="bullet">
<list-item><p>Very good tissue specificity with implantation of light sources (when combined with the use of CRE-driver mice and/or viral transgene delivery)</p></list-item>
<list-item><p>Reversible, tunable, and excellent temporal resolution</p></list-item>
</list>
</td>
<td align="left" valign="top"><list list-type="bullet">
<list-item><p>Phototoxicity for extended activation</p></list-item>
<list-item><p>Technically demanding and only few (mainly CNS) tissues are applicable in mammals</p></list-item>
</list>
</td>
</tr>
</tbody>
</table>
</table-wrap>
<p>In an alternative paradigm, exposure to altered light regimens leads to disruption of behavioral circadian rhythms and energy metabolism. Mice exposed to bright day/dim night illumination lose their feeding rhythm along with reduced glucose tolerance and increased body weight (<xref ref-type="bibr" rid="B8">8</xref>). Constant light (LL)-exposed mice develop a higher body weight together with a profound loss in insulin sensitivity (<xref ref-type="bibr" rid="B7">7</xref>). In rats, LL exposure disrupts pancreatic beta cell clocks, correlating with reduced glucose-stimulated insulin secretion (<xref ref-type="bibr" rid="B9">9</xref>). In type-2 diabetes-prone rats, LL accelerates disease development due to a 50% reduction in beta cell mass (<xref ref-type="bibr" rid="B10">10</xref>). Most of these studies interpret their findings as a consequence of the disruptive effects of abnormal light exposure on SCN function. However, light can alter various centrally controlled functions such as mood and appetite independent of a clock effect (<xref ref-type="bibr" rid="B11">11</xref>, <xref ref-type="bibr" rid="B12">12</xref>). Moreover, even though irregular light regimens are common for many animals and humans, there are only very few occasions where continuous light exposure above a certain threshold level may occur, making LL a highly artificial paradigm.</p>
<p>Several studies have outlined shift-working as a risk factor for the development of metabolic diseases (<xref ref-type="bibr" rid="B13">13</xref>), and various animal models have been developed to mimic this condition. Mice exposed to repeated 6-h advances of the light/dark (LD) cycle gain significantly more body weight than stable-LD controls (<xref ref-type="bibr" rid="B14">14</xref>). Interestingly, when mice are exposed to paradigms mimicking even more rapidly rotating weekly shift-work patterns, there is no or only a moderate effect on body weight (<xref ref-type="bibr" rid="B15">15</xref>). Sleep-restricting mice during their normal rest phase for 2&#x02009;weeks leads to significant alterations in liver clock gene expression rhythms associated impaired pyruvate-stimulated gluconeogenesis, but no significant alterations in body weight (<xref ref-type="bibr" rid="B16">16</xref>). A similar approach in rats further yielded body weight increases and impaired glucose tolerance (<xref ref-type="bibr" rid="B17">17</xref>).</p>
<p>The mixed metabolic outcomes in the mentioned shift-work studies are likely directly related to the ability of the chosen paradigms to provoke food intake during the normal rest phase. Rest phase-restricted food access in mice promotes weight gain without increased energy intake (<xref ref-type="bibr" rid="B18">18</xref>). In line with that, while both the rapid-shift (<xref ref-type="bibr" rid="B15">15</xref>) and our sleep-restriction study in mice (<xref ref-type="bibr" rid="B16">16</xref>) showed no change in food intake rhythms, the 6-h shift model (<xref ref-type="bibr" rid="B14">14</xref>) and the rat sleep-restriction study (<xref ref-type="bibr" rid="B17">17</xref>) reported misaligned food intake. Considering the reciprocal interaction between energy intake and clock function, it has been speculated that epigenetic programming may be an important mechanism in the circadian regulation of energy metabolism&#x02014;even across generations [reviewed in Ref. (<xref ref-type="bibr" rid="B19">19</xref>, <xref ref-type="bibr" rid="B20">20</xref>)].</p>
</sec>
<sec id="S3">
<title>Metabolic Alterations in Conventional Clock Gene Mutant Mice</title>
<p>The development of clock gene mutant mouse models has provided a substantial tool to understand clock-metabolism interaction at the molecular level. Following the identification of <italic>circadian locomotor output cycles kaput</italic> (<italic>Clock</italic>) (<xref ref-type="bibr" rid="B21">21</xref>), further mammalian <italic>clock genes</italic> have been cloned and functionally characterized in corresponding mouse mutants (<xref ref-type="bibr" rid="B22">22</xref>&#x02013;<xref ref-type="bibr" rid="B25">25</xref>). So far, brain and muscle ARNT-like 1 (BMAL1) has been identified as the only essential component of the molecular clockwork in mammals. Deletion of <italic>Bmal1</italic> in mice abolishes behavioral circadian rhythms in constant environmental conditions (<xref ref-type="bibr" rid="B25">25</xref>). Gene expression profiling experiments show that the rate-limiting steps of various metabolic pathways are subject to circadian regulation (<xref ref-type="bibr" rid="B26">26</xref>). <italic>Bmal1</italic> knockout (KO) mice show impaired glucose metabolism and insulin hypersensitivity (<xref ref-type="bibr" rid="B27">27</xref>, <xref ref-type="bibr" rid="B28">28</xref>). At young age, they also gain weight more rapidly than wild-type littermates (<xref ref-type="bibr" rid="B28">28</xref>). Recently, an inducible global <italic>Bmal1</italic> KO mouse model has been developed. Unexpectedly, adult-onset <italic>Bmal1</italic> KOs do not suffer from many metabolic abnormalities described in the standard <italic>Bmal1</italic> KOs (<xref ref-type="bibr" rid="B29">29</xref>).</p>
<p>Mice expressing a dominant-negative CLOCK variant (CLOCK-&#x00394;19) on a C57BL/6J genetic background display altered 24-h feeding patterns (<xref ref-type="bibr" rid="B30">30</xref>). <italic>Clock-&#x00394;19</italic> mice are hyperphagic and show reduced energy expenditure. They also develop hyperglycemia, hyperlipidemia, hyperleptinemia, hypoinsulinemia, and increase in body weight and visceral adiposity under different diet conditions. These phenotypes may be partly explained by a reduced lipolytic capacity of white adipose tissue (<xref ref-type="bibr" rid="B31">31</xref>). By contrast, on an ICR genetic background, the same <italic>Clock-&#x00394;19</italic> mutation leads to a reduction in body weight and impaired dietary lipid absorption, suggesting that the genetic background influences clock-metabolism interaction (<xref ref-type="bibr" rid="B32">32</xref>).</p>
<p>Inconsistent findings were also reported for the metabolic consequences of mutations in another clock gene, <italic>Period (Per) 2</italic>. <italic>Per2<sup>Brdm1</sup></italic> mutant mice (<xref ref-type="bibr" rid="B24">24</xref>) show hyperphagy, diet-induced obesity (<xref ref-type="bibr" rid="B33">33</xref>), hyperinsulinemia with altered insulin sensitivity, hypoglycemia, and low fasting hepatic glycogen content (<xref ref-type="bibr" rid="B34">34</xref>). By contrast, <italic>Per2<sup>ldc</sup></italic> mutants (<xref ref-type="bibr" rid="B35">35</xref>) show reduced adiposity, increased fatty acid oxidation, and hypotriglyceridemia (<xref ref-type="bibr" rid="B36">36</xref>), but are normoglycemic with improved clearance after glucose challenge (<xref ref-type="bibr" rid="B37">37</xref>). Of note, while genetic background may also play a role here, residual protein-coding transcripts have been detected in both mutants that may yield biologically active peptides (<xref ref-type="bibr" rid="B35">35</xref>, <xref ref-type="bibr" rid="B38">38</xref>). Male, but not female, <italic>Per1/2/3</italic> triple mutants become obese under an HFD (<xref ref-type="bibr" rid="B39">39</xref>). A <italic>Per3</italic> KO alone has even stronger effects on male diet-induced weight gain, suggesting a genetic interaction of different <italic>Per</italic> genes in metabolic regulation (<xref ref-type="bibr" rid="B39">39</xref>).</p>
<p>Liver transcriptomic analyses from mice carrying <italic>Rev-Erb&#x003B1;</italic> loss- or gain-of-function alleles have identified it as a circadian regulator of cholesterol/lipid and bile acid homeostasis (<xref ref-type="bibr" rid="B40">40</xref>). In line with this, mice with adult-onset global loss of <italic>Rev-Erb&#x003B1;/&#x003B2;</italic> show deregulated glucose and lipid metabolism (<xref ref-type="bibr" rid="B41">41</xref>). Moreover, administration of REV-ERB agonists in mice induces body weight loss and decreased lipogenesis in liver and white adipose tissue, increased lipid and glucose oxidation in skeletal muscle, and elevated energy expenditure (<xref ref-type="bibr" rid="B42">42</xref>).</p>
<p>Together, these studies provide evidence that the circadian clock plays a fundamental role in energy homeostasis and that different clock components have specific functions in this context. However, because the mice used in these studies carry clock gene mutations in all tissues including the SCN, much like the non-genetic models discussed above, metabolic phenotypes may be confounded by systemic abnormalities such as altered sleep patterns, activity and feeding behaviors, or counteractive consequences of clock disruption in different tissues.</p>
</sec>
<sec id="S4">
<title>Tissue Clock Function in Metabolic Regulation</title>
<p>Several techniques have been developed to study the physiology of tissue circadian clocks (Table <xref ref-type="table" rid="T1">1</xref>). <italic>In vitro</italic> experiments allow the study of tissue rhythms in the absence of external influences (<xref ref-type="bibr" rid="B43">43</xref>). However, such approaches have only limited potential for predicting the impact of tissue clock disruption on complex physiological processes such as energy metabolism. Transplantations have been used to study tissue clock function (<xref ref-type="bibr" rid="B44">44</xref>, <xref ref-type="bibr" rid="B45">45</xref>). However, such techniques are highly invasive and only applicable for few tissues. Instead, conditional CRE-<italic>loxP</italic>-based gene targeting has been widely used for tissue-specific deletion of clock function <italic>in vivo</italic> (in most cases by targeting <italic>Bmal1</italic>) (<xref ref-type="bibr" rid="B46">46</xref>, <xref ref-type="bibr" rid="B47">47</xref>). Here, we highlight some studies which have provided important insights into the contribution of different tissue clocks to metabolism.</p>
<p>Hepatocyte-specific deletion of <italic>Bmal1</italic> (L-Bmal1 KO) improves glucose tolerance&#x02014;the opposite effect of a global <italic>Bmal1</italic> KO&#x02014;which was attributed to reduced hepatic glucose export during the fasting phase <italic>via</italic> glucose transporter 2 (<xref ref-type="bibr" rid="B28">28</xref>). By contrast, mice with pancreatic beta cell-specific <italic>Bmal1</italic> deletion (P-Bmal1 KOs) show hyperglycemia and impaired glucose tolerance (<xref ref-type="bibr" rid="B48">48</xref>) due to decreased insulin exocytosis (<xref ref-type="bibr" rid="B49">49</xref>). Further, while mice with muscle-specific deletion of <italic>Bmal1</italic> (M-Bmal1 KO) show no significant change in systemic glucose regulation, impaired myocyte glucose uptake, and metabolism have been reported (<xref ref-type="bibr" rid="B50">50</xref>). Finally&#x02014;and similar to global <italic>Bmal1</italic> KOs and <italic>Clock-&#x00394;19</italic> mutants&#x02014;mice with adipocyte-specific <italic>Bmal1</italic> deletion (A-<italic>Bmal1</italic> KOs) become obese (<italic>ca</italic>. 20% body weight) under HFD but not normal chow conditions. This phenotype correlates with misaligned food intake and blunted secretion rhythms of appetite-regulating polyunsaturated fatty acids from adipocytes (<xref ref-type="bibr" rid="B51">51</xref>).</p>
<p>Clock gene rhythms have been reported in central energy regulatory circuits (<xref ref-type="bibr" rid="B52">52</xref>). So far, few studies have addressed the biological function of specific brain clocks. With regard to metabolism, deletion of <italic>Bmal1</italic> in steroidogenic neurons of the ventromedial hypothalamus reduces sympathetic activation of thermogenesis in brown adipose tissue (<xref ref-type="bibr" rid="B53">53</xref>).</p>
<p>These few examples make clear that tissue-specific dissection of clock gene function has provided a much more detailed picture on how circadian clocks affect energy metabolism <italic>in vivo</italic>. Nevertheless, conclusions drawn from these experiments are often confounded by intrinsic drawbacks of the classical CRE<italic>-loxP</italic> system which novel genetic tools may help to overcome.</p>
</sec>
<sec id="S5">
<title>Limitations of Classical Genetic Models in Chronobiology Research</title>
<sec id="S5-1">
<title>Poor Specificity of the CRE Driver</title>
<p>In CRE<italic>-loxP</italic>-based gene targeting, the tissue-specific mutation is determined by the transcription dynamics of the CRE-expressing promoter. While this may not be such an issue for processes confined to specific tissues, for the ubiquitously active circadian system, this poses an important limitation: many allegedly <italic>tissue-specific</italic> promoters show varying amounts of off-target activity. For example, for two of the studies mentioned above, CRE drivers with off-target activities have been employed, namely <italic>Fabp4-Cre</italic> for A-<italic>Bmal1</italic> and <italic>Pdx1-Cre</italic> for P-<italic>Bmal1</italic> KOs. Critically, their expression in several metabolism-regulating circuits in the brain has been documented (<xref ref-type="bibr" rid="B54">54</xref>). Though the authors of these studies used different approaches to address this problem (such as supplementing <italic>in vitro</italic>/<italic>ex vivo</italic> data or repeating key experiments with another CRE driver), certain conclusions drawn from the <italic>in vivo</italic> metabolic experiments may still be ambiguous. Similarly, in the hypothalamic steroidogenic neuron <italic>Bmal1</italic> KO study, the <italic>Sf1-Cre</italic> line used may very likely affect steroidogenic cells in other tissues (<xref ref-type="bibr" rid="B53">53</xref>).</p>
</sec>
<sec id="S5-2">
<title>Developmental Compensation</title>
<p>Some CRE drivers are developmentally active and clock genes are known to be involved in early developmental processes (<xref ref-type="bibr" rid="B55">55</xref>). Therefore, some phenotypes observed in adult mice might reflect changes in developmental programs while others may be masked by compensatory responses. A strategy circumventing this issue is to employ an inducible version of CRE (T2-CRE), which is activated only when animals receive tamoxifen (<xref ref-type="bibr" rid="B56">56</xref>). This approach has been used to globally delete <italic>Bmal1</italic> and <italic>Rev-erb&#x003B1;/&#x003B2;</italic> (<xref ref-type="bibr" rid="B29">29</xref>, <xref ref-type="bibr" rid="B41">41</xref>). In the M-<italic>Bmal1</italic> KO study discussed above, a muscle strength phenotype was only observed in mutants with conventional, but not inducible CRE deletion (<xref ref-type="bibr" rid="B50">50</xref>).</p>
</sec>
<sec id="S5-3">
<title>Incomplete Recombination</title>
<p>Due to variations in expression levels or epigenetic effects, CRE-mediated recombination frequently does not occur in all cells of the same tissue. This issue is further exaggerated with the T2-CRE system. Thus, the lack of certain phenotypes in tissue-specific mutants may stem from non-recombined cells sufficient to maintain tissue function. In the circadian clock context, this issue becomes critical in tissues of strong intercellular coupling such as the SCN. Our own approach to target SCN pacemaker function using a Syt10-Cre-driver line revealed that only with the highest CRE dosage (<italic>Syt10<sup>Cre/Cre</sup></italic>) and on a <italic>Bmal1<sup>flox/del</sup></italic> background, recombination was sufficient to ablate behavioral rhythmicity (<xref ref-type="bibr" rid="B57">57</xref>).</p>
</sec>
<sec id="S5-4">
<title>The Non-Circadian Role of Individual Clock Genes</title>
<p>Many clock gene mutant studies fail to discern whether a phenotype is caused by altered clock rhythmicity or by loss of a specific clock component. For example, in the L-<italic>Bmal1</italic> KO study, the mutation not only abolishes the transcription rhythm of <italic>Glut2</italic>, but also dramatically downregulates its overall expression (<xref ref-type="bibr" rid="B28">28</xref>). The multifaceted phenotype of <italic>Bmal1</italic> KO mice suggests that this gene has important functions outside the circadian timekeeping system (<xref ref-type="bibr" rid="B58">58</xref>). Along this line, the monopolized use of <italic>Bmal1</italic> targeting for tissue-specific clock deletion further exacerbates this issue since some of the reported phenotypes may be caused by a loss of <italic>Bmal1</italic> rather than of the clockwork.</p>
</sec>
</sec>
<sec id="S6">
<title>Emerging Genetic Techniques for Chronobiology Research</title>
<p>Some of the emerging novel genetic techniques may help to overcome the issues discussed above. Below we will highlight some methodologies that may help improving our understanding of the role of tissue clocks in complex physiological contexts.</p>
<sec id="S6-1">
<title>Improving the Spatio-Temporal Resolution of Clock Gene Manipulation</title>
<p>Though pharmacologically inducible CRE systems bypass developmental effects, this strategy often compromises the recombination efficiency and complicates experimental designs (<xref ref-type="bibr" rid="B56">56</xref>). Moreover, the manipulation is irreversible, rendering it unsuitable for certain biological questions. As an alternative approach, chemogenetic manipulations such as tetracycline-based (i.e., Tet-ON/OFF) systems achieve anatomical specificity by expressing effectors under tissue-specific promoters, the activity of which depends on the presence/absence of an otherwise inert chemical (<xref ref-type="bibr" rid="B59">59</xref>, <xref ref-type="bibr" rid="B60">60</xref>). These systems are reversible and have a very flexible space-time window for manipulations. For example, two complementary studies have established mouse lines expressing <italic>Clock-&#x00394;19</italic> and <italic>Rev-erb&#x003B1;</italic> as clock disruptors in brain and liver, respectively, in a tetracycline-dependent manner, to elucidate the relative contribution of central and peripheral clocks to physiological rhythms (<xref ref-type="bibr" rid="B61">61</xref>, <xref ref-type="bibr" rid="B62">62</xref>). This revealed that circadian expression rhythms of most rhythmic transcripts in the liver depend on local oscillators whereas 10% of the rhythmic transcripts (including <italic>Per2</italic>) are sustained by systemic signals.</p>
<p>Optogenetic techniques have recently been introduced in chronobiology research. Photic stimulation on channelrhodopsin-2-expressing SCN neurons results in phase-resetting of SCN firing and behavioral rhythms (<xref ref-type="bibr" rid="B63">63</xref>). Other optogenetic systems allow for photo-switchable control of specific cellular and molecular processes (<xref ref-type="bibr" rid="B64">64</xref>). Of note, one strategy employs modified photo-sensitive plant cryptochrome 2 clock proteins from <italic>Arabidopsis</italic> (<xref ref-type="bibr" rid="B64">64</xref>), which would allow to directly affect molecular clock function by light. In addition to high spatial control (by directing light exposure), optogenetics may benefit chronobiology research because of their supreme temporal resolution, e.g., in phase-resetting experiments.</p>
<p>While standard viral transgene delivery approaches using short tissue-specific promoters often fall short to confer sufficient specificity (<xref ref-type="bibr" rid="B65">65</xref>), this is circumvented by combining virus injections with CRE-driver mouse lines targeting transgene expression to specific cells and tissues (<xref ref-type="bibr" rid="B66">66</xref>). Viral approaches further benefit from high spatio-temporal control through injection time/sites and viral capsid serotypes. They, however, often suffer from somewhat reduced penetrance and technical variability (<xref ref-type="bibr" rid="B67">67</xref>). Viruses can be used in conjugation with chemogenetic or optogenetic manipulations to interrogate the role of circadian clock in metabolic regulation and other physiological systems with unprecedented spatio-temporal resolution.</p>
</sec>
<sec id="S6-2">
<title>Perspectives for Developing Animal Models That Can Dissociate Circadian and Non-Circadian Functions of Clock Genes</title>
<p>Clock gene knockdown/KO experiments often cannot distinguish between circadian (i.e., timing related) and non-circadian effects of a given mutation. This may to some extent be addressed by comparing phenotypes between mutants of different clock genes. However, because of the interactive nature of clock genes this may often not yield further insights. As an alternative approach, the direct modulation of circadian period length without abolishing clock function itself in a tissue-specific manner is achievable <italic>via</italic> manipulating period-determining genes such as casein kinase I &#x003F5; (<xref ref-type="bibr" rid="B44">44</xref>). To some extent, this and other similar approaches still inevitably change clock protein levels and, thus, pleiotropic clock gene output.</p>
<p>An ideal animal model would be one with altered phasing of clock gene expression rhythms but unaffected overall clock protein abundance. Generating such model has become possible with recent developments in genome editing such as CRISPR and TALEN (<xref ref-type="bibr" rid="B68">68</xref>, <xref ref-type="bibr" rid="B69">69</xref>). CRISPR techniques have been used to &#x0201C;cure&#x0201D; retinal degeneration models in rats (<xref ref-type="bibr" rid="B70">70</xref>, <xref ref-type="bibr" rid="B71">71</xref>). Together with the expanding knowledge of the role of the cis-regulatory elements of clock genes in determining the phase of expression rhythms, such as the identification of the phase-determining intronic enhancer of <italic>Cry1</italic> (<xref ref-type="bibr" rid="B72">72</xref>), <italic>in vivo</italic> genome editing may allow to selectively manipulate clock gene phasing.</p>
</sec>
</sec>
<sec id="S7">
<title>Conclusion</title>
<p>In the last decades, the tools for studying the mechanisms underlying organismal circadian timekeeping and its role in metabolic regulation have been constantly refined (Figure <xref ref-type="fig" rid="F1">1</xref>). The network structure of the circadian system represents an important challenge in this context, posing high demands on both tempo-spatial control and recombination efficiency in genetic experiments. Novel genetic approaches may help to overcome these issues and provide a clearer picture of the complex interaction of different tissue clocks in the regulation of energy metabolism.</p>
<fig id="F1" position="float">
<label>Figure 1</label>
<caption><p><bold>Timeline of the development of experimental rodent models and corresponding milestone papers in circadian tissue clock research</bold>.</p></caption>
<graphic xlink:href="fendo-08-00027-g001.tif"/>
</fig>
</sec>
<sec id="S8" sec-type="author-contributor">
<title>Author Contributions</title>
<p>AT, MA, BL, and HO discussed the concept, complied the literature, and wrote the paper.</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>
<sec id="S10">
<title>Funding</title>
<p>This work was supported by grants from the Volkswagen Foundation (Lichtenberg Fellowship to HO), the German Research Association (DFG; GRK 1957 and SFBs 134 and 654), and an International Brain Research Organization (IBRO) fellowship to MA.</p>
</sec>
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