哺乳动物生物钟的遗传和表观遗传研究进展

doi:10.16288/j.yczz.17-350

遗传 ›› 2017, Vol. 39 ›› Issue (12): 1122-1137.doi: 10.16288/j.yczz.17-350

哺乳动物生物钟的遗传和表观遗传研究进展

岳敏^1,²(),杨禹¹,郭改丽¹,秦曦明¹()

1. 安徽大学健康科学研究院,合肥 230601
2. 安徽大学生命科学学院,合肥 230601

收稿日期:2017-10-27 修回日期:2017-11-16 出版日期:2017-12-20 发布日期:2017-12-20
作者简介:岳敏,本科,专业方向：生物科学。E-mail: yuemin_ahu@163.com|秦曦明，博士，教授，博士生导师，研究方向：生物钟分子组分的功能及其相互作用参与生物钟调控的分子机制。E-mail: qin.ximing@ahu.edu.cn|秦曦明教授,2010年从美国Vanderbilt大学获得博士学位,现任职于安徽大学健康科学研究院。课题组主要研究方向是生物钟(近日节律)的分子与结构基础、生物钟组分的功能和生物钟调节健康的靶点分子的研究。曾经利用蓝绿细菌作为模式生物,阐述核心振荡器和次级振荡器之间的联系与相互作用,并提出真核生物可能存在不依赖转录翻译环路的核心分子振荡器的假设。通过研究生物钟蛋白分子的相互作用,解析生物钟如何维持稳定的相关机制。相关的研究成果发表在Nature、Proc Natl Acad Sci USA、PLoS Biology、Current Biology、J Biol Rhythms等学术期刊上。目前主持国家自然科学基金面上项目与安徽省自然科学基金项目。
基金资助:
国家自然科学基金项目(31571208);安徽省自然科学基金项目(1608085MH212);安徽大学大学生科研训练计划项目(J10118520418)

Genetic and epigeneticregulations of mammalian circadian rhythms

Yue Min^1,²(),Yang Yu¹,Guo Gaili¹,Qin Ximing¹()

1. Institute of Health Sciences, Anhui University, Hefei 230601, China
2. School of Life Sciences, Anhui University, Hefei 230601, China

Received:2017-10-27 Revised:2017-11-16 Online:2017-12-20 Published:2017-12-20
Supported by:
the National Natural Science Foundation of China(31571208);the Natural Science Foundation of Anhui Province(1608085MH212);Anhui University Undergraduate Student Training Grant(J10118520418)

摘要/Abstract

摘要：

生物钟对生物机体的生存与环境适应具有着重要意义,其相关研究近年来受到人们的广泛关注。生物钟的重要性质之一是内源节律的周期性,当前的研究认为这种周期性是由生物钟相关基因转录翻译的多反馈环路构成核心机制调控着近似24 h的节律振荡。哺乳动物的生物钟系统存在一个多层次的结构,包括位于视交叉上核的主时钟和外周器官和组织的子时钟。虽然主时钟和子时钟存在的组织不同,但是参与调节生物钟的分子机制是一致的。近年来,通过正向、反向遗传学方法和表观遗传学的研究方法,对生物钟的分子机制的解析和认知愈发深入。本文在简单回顾生物钟基因发现历史的基础上,重点从遗传学和表观遗传学两个方面,从振荡周期的角度,对哺乳动物生物钟分子机制的研究进展进行了综述性介绍,以期为靶向调节生物钟来改善机体的稳态系统的研究提供参考,同时希望能促进时间生物学领域与更多其他领域形成交叉研究。

关键词: 生物钟, 近日节律, 生物钟基因, 转录翻译反馈环路, 顺式作用元件, 转录因子, 表观遗传学

Abstract:

The circadian clocks are vital to many organisms for their survival and adaption to the surrounding environment. More and more people are interested in the circadian clock and related researches. One of the key characteristics of this endogenous clock is its periodicity. Mechanisms underlying the mammalian circadian rhythms with ~24 h periodicity involve interlocked transcriptional and translational feedback loops. The circadian clock system in mammals consists of hierarchical structures, with the suprachiasmatic nucleus (SCN) as the central pacemaker and peripheral oscillators in other organs. In spite of the central and peripheral oscillators, the molecular mechanisms are the same within the SCN and peripheral organs. In the past decades, major achievements are accomplished by using forward and reverse genetics, as well as epigenetic approaches. In this review, we recapitulate the history of how clock-related genes were identified, and summarize the main achievements in genetics and epigenetics to understand the molecular underpinnings. We hope it can offer basic knowledge for further researches, a reference for experimental designs aiming to adjust organisms’ homeostasis by modulating the clock, and provide a foundation to build interdisciplinary research networks.

Key words: Circadian clock, circadian rhythm, clock genes, transcriptional and translational feedback loop, cis-regulating elements, transcription factors, epigenetics

岳敏, 杨禹, 郭改丽, 秦曦明. 哺乳动物生物钟的遗传和表观遗传研究进展[J]. 遗传, 2017, 39(12): 1122-1137.

Yue Min, Yang Yu, Guo Gaili, Qin Ximing. Genetic and epigeneticregulations of mammalian circadian rhythms[J]. Hereditas(Beijing), 2017, 39(12): 1122-1137.

参考文献

[1]	Dunlap JC, Loros JJ, DeCoursey PJ. Chronobiology: Biological Timekeeping. Sunderland: Sinauer Associates, Inc. Publishers, 2004.
[2]	Czeisler CA, Duffy JF, Shanahan TL, Brown EN, Mitchell JF, Rimmer DW, Ronda JM, Silva EJ, Allan JS, Emens JS, Dijk DJ, Kronauer RE. Stability, precision, and near-24-hour period of the human circadian pacemaker. Science, 1999, 284(5423): 2177-2181.
[3]	Duffy JF, Wright KP Jr. Entrainment of the human circadian system by light. J Biol Rhythms, 2005, 20(4): 326-338.
[4]	Qin XM, Guo JH. Synchronization of the mammalian central and peripheral circadian clocks. Chin Sci Bull, 2017, 62(25): 2849-2856.
[4]	秦曦明, 郭金虎. 哺乳动物生物钟同步化的研究进展. 科学通报, 2017, 62(25): 2849-2856.
[5]	Ouyang Y, Andersson CR, Kondo T, Golden SS, Johnson CH. Resonating circadian clocks enhance fitness in cyanobacteria. Proc Natl Acad Sci USA, 1998, 95(15): 8660-8664.
[6]	Spoelstra K, Wikelski M, Daan S, Loudon ASI, Hau M. Natural selection against a circadian clock gene mutation in mice. Proc Natl Acad Sci USA, 2016, 113(3): 686-691.
[7]	Takahashi JS Molecular components of the circadian clock in mammals. Diabetes Obes Metab, 2015, 17(Suppl 1): 6-11.
[8]	Takahashi JS. Transcriptional architecture of the mammalian circadian clock. Nat Rev Genet, 2017, 18(3): 164-179.
[9]	Schibler U, Gotic I, Saini C, Gos P, Curie T, Emmenegger Y, Sinturel F, Gosselin P, Gerber A, Fleury-Olela F, Rando G, Demarque M, Franken P. Clock-Talk: Interactions between central and peripheral circadian oscillators in mammals. Cold Spring Harb Symp Quant Biol, 2015, 80: 223-232.
[10]	Buijs RM, Hermes MHLJ, Kalsbeek A. The suprachiasmatic nucleus—paraventricular nucleus interactions: a bridge to the neuroendocrine and autonomic nervous system. Prog Brain Res, 1998, 119: 365-382.
[11]	Balsalobre A, Damiola F, Schibler U. A serum shock induces circadian gene expression in mammalian tissue culture cells. Cell, 1998, 93(6): 929-937.
[12]	An Y, Xu Y. The mechanism of mammalian circadian rhythms. Chin Bull Life Sci, 2015, 27(11): 1372-1379.
[12]	安扬, 徐璎. 哺乳动物昼夜节律机制研究进展. 生命科学, 2015, 27(11): 1372-1379.
[13]	Pittendrigh CS. Circadian rhythms and the circadian organization of living systems. Cold Spring Harb Symp Quant Biol, 1960, 25: 159-184.
[14]	Aschoff J. Exogenous and endogenous components in circadian rhythms. Cold Spring Harb Symp Quant Biol, 1960, 25: 11-28.
[15]	Konopka RJ, Benzer S. Clock mutants of Drosophila melanogaster. Proc Natl Acad Sci USA, 1971, 68(9): 2112-2116.
[16]	Reddy P, Zehring WA, Wheeler DA, Pirrotta V, Hadfield C, Hall JC, Rosbash M. Molecular analysis of the period locus in Drosophila melanogaster and identification of a transcript involved in biological rhythms. Cell, 1984, 38(3): 701-710.
[17]	Bargiello TA, Jackson FR, Young MW. Restoration of circadian behavioural rhythms by gene transfer in. Drosophila. Nature, 1984, 312(5996): 752-754.
[18]	Sehgal A, Price JL, Man B, Young MW. Loss of circadian behavioral rhythms and per RNA oscillations in the Drosophila mutant timeless. Science, 1994, 263(5153): 1603-1606.
[19]	Myers MP, Wager-Smith K, Wesley CS, Young MW, Sehgal A. Positional cloning and sequence analysis of the Drosophila clock gene, timeless. Science, 1995, 270(5237): 805-808.
[20]	Gekakis N, Saez L, Delahaye-Brown AM, Myers MP, Sehgal A, Young MW, Weitz CJ. Isolation of timeless by PER protein interaction: defective interaction between timeless protein and long-period mutant PERL. Science , 1995, 270(5237): 811-815.
[21]	Allada R, White NE, So WV, Hall JC, Rosbash M. A mutant Drosophila homolog of mammalian Clock disrupts circadian rhythms and transcription of period and timeless. Cell, 1998, 93(5): 791-804.
[22]	Rutila JE, Suri V, Le M, So WV, Rosbash M, Hall JC. CYCLE is a second bHLH-PAS clock protein essential for circadian rhythmicity and transcription of Drosophila period and timeless. Cell, 1998, 93(5): 805-814.
[23]	Price JL, Blau J, Rothenfluh A, Abodeely M, Kloss B, Young MW. double-time is a novel Drosophila clock gene that regulates PERIOD protein accumulation. Cell, 1998, 94(1): 83-95.
[24]	Vitaterna MH, King DP, Chang AM, Kornhauser JM, Lowrey PL, McDonald JD, Dove WF, Pinto LH, Turek FW, Takahashi JS. Mutagenesis and mapping of a mouse gene, Clock, essential for circadian behavior. Science, 1994, 264(5159): 719-725.
[25]	Gekakis N, Staknis D, Nguyen HB, Davis FC, Wilsbacher LD, King DP, Takahashi JS, Weitz CJ. Role of the CLOCK protein in the mammalian circadian mechanism. Science, 1998, 280(5369): 1564-1569.
[26]	Bunger MK, Wilsbacher LD, Moran SM, Clendenin C, Radcliffe LA, Hogenesch JB, Simon MC, Takahashi JS, Bradfield CA. Mop3 is an essential component of the master circadian pacemaker in mammals. Cell, 2000, 103(7): 1009-1017.
[27]	Tei H, Okamura H, Shigeyoshi Y, Fukuhara C, Ozawa R, Hirose M, Sakaki Y. Circadian oscillation of a mammalian homologue of the Drosophila period gene. Nature, 1997, 389(6650): 512-516.
[28]	Sun ZS, Albrecht U, Zhuchenko O, Bailey J, Eichele G, Lee CC. RIGUI, a putative mammalian ortholog of the Drosophila period gene. Cell, 1997, 90(6): 1003-1011.
[29]	Albrecht U, Sun ZS, Eichele G, Lee CC. A differential response of two putative mammalian circadian regulators, mper1 and mper2, to light. Cell, 1997, 91(7): 1055-1064.
[30]	Shearman LP, Zylka MJ, Weaver DR, Kolakowski LF Jr, Reppert SM. Two period homologs: circadian expression and photic regulation in the suprachiasmatic nuclei. Neuron, 1997, 19(6): 1261-1269.
[31]	Takumi T, Taguchi K, Miyake S, Sakakida Y, Takashima N, Matsubara C, Maebayashi Y, Okumura K, Takekida S, Yamamoto S, Yagita K, Yan L, Young MW, Okamura H. A light-independent oscillatory gene mPer3 in mouse SCN and OVLT. EMBO J, 1998, 17(16): 4753-4759.
[32]	van der Horst GT, Muijtjens M, Kobayashi K, Takano R, Kanno S, Takao M, de Wit J, Verkerk A, Eker AP, van Leenen D, Buijs R, Bootsma D, Hoeijmakers JH, Yasui A. Mammalian Cry1 and Cry2 are essential for maintenance of circadian rhythms. Nature, 1999, 398(6728): 627-630.
[33]	Vitaterna MH, Selby CP, Todo T, Niwa H, Thompson C, Fruechte EM, Hitomi K, Thresher RJ, Ishikawa T, Miyazaki J, Takahashi JS, Sancar A. Differential regulation of mammalian period genes and circadian rhythmicity by cryptochromes 1 and 2. Proc Natl Acad Sci USA, 1999, 96(21): 12114-12119.
[34]	Lowrey PL, Shimomura K, Antoch MP, Yamazaki S, Zemenides PD, Ralph MR, Menaker M, Takahashi JS. Positional syntenic cloning and functional characterization of the mammalian circadian mutation tau. Science, 2000, 288(5465): 483-491.
[35]	Siepka SM, Yoo SH, Park J, Song WM, Kumar V, Hu YN, Lee C, Takahashi JS. Circadian mutant Overtime reveals F-box protein FBXL3 regulation of Cryptochrome and Period gene expression. Cell, 2007, 129(5): 1011-1023.
[36]	Hirano A, Yumimoto K, Tsunematsu R, Matsumoto M, Oyama M, Kozuka-Hata H, Nakagawa T, Lanjakornsiripan D, Nakayama KI, Fukada Y. FBXL21 regulates oscillation of the circadian clock through ubiquitination and stabilization of cryptochromes. Cell, 2013, 152(5): 1106-1118.
[37]	Shirogane T, Jin JP, Ang XL, Harper JW. SCFβ-TRCP controls clock-dependent transcription via casein kinase 1-dependent degradation of the mammalian period-1 (Per1) proteinm. . J Biol Chem, 2005, 280(29): 26863-26872.
[38]	Sato TK, Panda S, Miraglia LJ, Reyes TM, Rudic RD, McNamara P, Naik KA, FitzGerald GA, Kay SA, Hogenesch JB. A functional genomics strategy reveals Rora as a component of the mammalian circadian clock. Neuron, 2004, 43(4): 527-537.
[39]	Preitner N, Damiola F, Lopez-Molina L, Zakany J, Duboule D, Albrecht U, Schibler U. The orphan nuclear receptor REV-ERBα controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell, 2002, 110(2): 251-260.
[40]	Yamaguchi S, Mitsui S, Yan L, Yagita K, Miyake S, Okamura H. Role of DBP in the circadian oscillatory mechanism. Mol Cell Biol, 2000, 20(13): 4773-4781.
[41]	Oishi K, Miyazaki K, Kadota K, Kikuno R, Nagase T, Atsumi GI, Ohkura N, Azama T, Mesaki M, Yukimasa S, Kobayashi H, Iitaka C, Umehara T, Horikoshi M, Kudo T, Shimizu Y, Yano M, Monden M, Machida K, Matsuda J, Horie S, Todo T, Ishida N. Genome-wide expression analysis of mouse liver reveals CLOCK-regulated circadian output genes. J Biol Chem, 2003, 278(42): 41519-41527.
[42]	Hardin PE, Hall JC, Rosbash M. Feedback of the. Drosophila period gene product on circadian cycling of its messenger RNA levels. Nature, 1990, 343(6258): 536-540.
[43]	Panda S, Antoch MP, Miller BH, Su AI, Schook AB, Straume M, Schultz PG, Kay SA, Takahashi JS, Hogenesch JB. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell, 2002, 109(3): 307-320.
[44]	Mosko SS, Moore RY. Neonatal suprachiasmatic nucleus lesions: effects on the development of circadian rhythms in the rat. Brain Res, 1979, 164(1-2): 17-38.
[45]	Kafka MS, Marangos PJ, Moore RY. Suprachiasmatic nucleus ablation abolishes circadian rhythms in rat brain neurotransmitter receptors. Brain Res, 1985, 327(1-2): 344-347.
[46]	Ralph MR, Foster RG, Davis FC, Menaker M. Transplanted suprachiasmatic nucleus determines circadian period. Science, 1990, 247(4945): 975-978.
[47]	Sujino M, Masumoto KH, Yamaguchi S, Van Der Horst GTJ, Okamura H, Inouye SIT. Suprachiasmatic nucleus grafts restore circadian behavioral rhythms of genetically arrhythmic mice. Curr Biol, 2003, 13(8): 664-668.
[48]	DeBruyne JP, Weaver DR, Reppert SM. CLOCK and NPAS2 have overlapping roles in the suprachiasmatic circadian clock. Nat Neurosci, 2007, 10(5): 543-545.
[49]	DeBruyne JP, Weaver DR, Reppert SM. Peripheral circadian oscillators require CLOCK. Curr Biol, 2007, 17(14): R538-R539.
[50]	Kondratov RV, Chernov MV, Kondratova AA, Gorbacheva VY, Gudkov AV, Antoch MP. BMAL1-dependent circadian oscillation of nuclear CLOCK: posttranslational events induced by dimerization of transcriptional activators of the mammalian clock system. Genes Dev, 2003, 17(15): 1921-1932.
[51]	Lee C, Etchegaray JP, Cagampang FRA, Loudon ASI, Reppert SM. Posttranslational mechanisms regulate the mammalian circadian clock. Cell, 2001, 107(7): 855-867.
[52]	Shearman LP, Sriram S, Weaver DR, Maywood ES, Chaves I, Zheng BH, Kume K, Lee CC, Van Der Horst GTJ, Hastings MH, Reppert SM. Interacting molecular loops in the mammalian circadian clock. Science, 2000, 288(5468): 1013-1019.
[53]	Marcheva B, Ramsey KM, Buhr ED, Kobayashi Y, Su H, Ko CH, Ivanova G, Omura C, Mo S, Vitaterna MH, Lopez JP, Philipson LH, Bradfield CA, Crosby SD, JeBailey L, Wang XZ, Takahashi JS, Bass J. Disruption of the clock components CLOCK and BMAL1 leads to hypoinsulinaemia and diabetes. Nature, 2010, 466(7306): 627-631.
[54]	Janich P, Pascual G, Merlos-Suárez A, Batlle E, Ripperger J, Albrecht U, Cheng HYM, Obrietan K, Di Croce L, Benitah SA. The circadian molecular clock creates epidermal stem cell heterogeneity. Nature, 2011, 480(7376): 209-214.
[55]	Nam D, Yechoor VK, Ma K. Molecular clock integration of brown adipose tissue formation and function. Adipocyte, 2015, 5(2): 243-250.
[56]	Vielhaber E, Eide E, Rivers A, Gao ZH, Virshup DM. Nuclear entry of the circadian regulator mPER1 is controlled by mammalian casein kinase I ?. Mol Cell Biol, 2000, 20(13): 4888-4899.
[57]	Yagita K, Tamanini F, Yasuda M, Hoeijmakers JHJ, Van Der Horst GTJ, Okamura H. Nucleocytoplasmic shuttling and mCRY-dependent inhibition of ubiquitylation of the mPER2 clock protein. EMBO J, 2002, 21(6): 1301-1314.
[58]	Yang Y, Xu TT, Zhang YF, Qin XM. Molecular basis for the regulation of the circadian clock kinases CK1δ and CK1ε. Cell Signal, 2017, 31: 58-65.
[59]	Tamaru T, Hirayama J, Isojima Y, Nagai K, Norioka S, Takamatsu K, Sassone-Corsi P. CK2α phosphorylates BMAL1 to regulate the mammalian clock. Nat Struct Mol Biol, 2009, 16(4): 446-448.
[60]	Lamia KA, Sachdeva UM, DiTacchio L, Williams EC, Alvarez JG, Egan DF, Vasquez DS, Juguilon H, Panda S, Shaw RJ, Thompson CB, Evans RM. AMPK regulates the circadian clock by cryptochrome phosphorylation and degradation. Science, 2009, 326(5951): 437-440.
[61]	Sahar S, Zocchi L, Kinoshita C, Borrelli E, Sassone-Corsi P. Regulation of BMAL1 protein stability and circadian function by GSK3β-mediated phosphorylation. PLoS One, 2010, 5(1): e8561.
[62]	Yu B, Wu T, Ni YH, Zhou JL, Zhuge F, Sun L, Fu ZW. Posttranscriptional and posttranslational regulation of circadian clock. Chin Bull Life Sci, 2011, 23(5): 470-476.
[62]	俞波, 吴涛, 倪银华, 周静露, 诸葛芬, 孙璐, 傅正伟. 生物钟的转录后与翻译后水平调控进展. 生命科学, 2011, 23(5): 470-476.
[63]	Kim EY, Jeong EH, Park S, Jeong HJ, Edery I, Cho JW. A role for O-GlcNAcylation in setting circadian clock speed. Genes Dev, 2012, 26(5): 490-502.
[64]	Church GM, Ephrussi A, Gilbert W, Tonegawa S. Cell-type-specific contacts to immunoglobulin enhancers in nuclei. Nature, 1985, 313(6005): 798-801.
[65]	Mu?oz E, Brewer M, Baler R. Circadian transcription thinking outside the E-Box. J Biol Chem, 2002, 277(39): 36009-36017.
[66]	Gordan R, Shen N, Dror I, Zhou TY, Horton J, Rohs R, Bulyk ML. Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Rep, 2013, 3(4): 1093-1104.
[67]	Hao H, Allen DL, Hardin PE. A circadian enhancer mediates PER-dependent mRNA cycling in Drosophila melanogaster. Mol Cell Biol, 1997, 17(7): 3687-3693.
[68]	Hogenesch JB, Gu YZ, Jain S, Bradfield CA. The basic-helix-loop-helix-PAS orphan MOP3 forms transcriptionally active complexes with circadian and hypoxia factors. Proc Natl Acad Sci USA, 1998, 95(10): 5474-5479.
[69]	Rey G, Cesbron F, Rougemont J, Reinke H, Brunner M, Naef F. Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver. PLoS Biol, 2011, 9(2): e1000595.
[70]	Koike N, Yoo SH, Huang HC, Kumar V, Lee C, Kim TK, Takahashi JS. Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science, 2012, 338(6105): 349-354.
[71]	Wu YL, Tang DB, Liu N, Xiong W, Huang HW, Li Y, Ma ZX, Zhao HJ, Chen PH, Qi XB, Zhang EE. Reciprocal regulation between the circadian clock and hypoxia signaling at the genome level in mammals. Cell Metab, 2017, 25(1): 73-85.
[72]	Altman BJ, Hsieh AL, Sengupta A, Krishnanaiah SY, Stine ZE, Walton ZE, Gouw AM, Venkataraman A, Li B, Goraksha-Hicks P, Diskin SJ, Bellovin DI, Simon MC, Rathmell JC, Lazar MA, Maris JM, Felsher DW, Hogenesch JB, Weljie AM, Dang CV. MYC disrupts the circadian clock and metabolism in cancer cells. Cell Metab, 2015, 22(6): 1009-1019.
[73]	Shimomura K, Kumar V, Koike N, Kim TK, Chong J, Buhr ED, Whiteley AR, Low SS, Omura C, Fenner D, Owens JR, Richards M, Yoo SH, Hong HK, Vitaterna MH, Bass J, Pletcher MT, Wiltshire T, Hogenesch J, Lowrey PL, Takahashi JS. Usf1, a suppressor of the circadian Clock mutant, reveals the nature of the DNA-binding of the CLOCK: BMAL1 complex in mice. eLife, 2013, 2: e00426.
[74]	Giguère V, Tini M, Flock G, Ong E, Evans RM, Otulakowski G. Isoform-specific amino-terminal domains dictate DNA-binding properties of RORα, a novel family of orphan hormone nuclear receptors. Genes Dev, 1994, 8(5): 538-553.
[75]	Giguère V, McBroom LD, Flock G. Determinants of target gene specificity for RORα1: monomeric DNA binding by an orphan nuclear receptor. Mol Cell Biol, 1995, 15(5): 2517-2526.
[76]	Harding HP, Lazar MA. The orphan receptor Rev-ErbAα activates transcription via a novel response element. Mol Cell Biol, 1993, 13(5): 3113-3121.
[77]	Baes M, Gulick T, Choi HS, Martinoli MG, Simha D, Moore DD. A new orphan member of the nuclear hormone receptor superfamily that interacts with a subset of retinoic acid response elements. Mol Cell Biol, 1994, 14(3): 1544-1552.
[78]	Ueda HR, Chen WB, Adachi A, Wakamatsu H, Hayashi S, Takasugi T, Nagano M, Nakahama K, Suzuki Y, Sugano S, Iino M, Shigeyoshi Y, Hashimoto S. A transcription factor response element for gene expression during circadian night. Nature, 2002, 418(6897): 534-539.
[79]	Solt LA, Burris TP. Action of RORs and their ligands in (patho)physiology. Trends Endocrinol Metab, 2012, 23(12): 619-627.
[80]	Zhang Y, Luo XY, Wu DH, Xu Y. ROR nuclear receptors: structures, related diseases, and drug discovery. Acta Pharmacol Sin, 2015, 36(1): 71-87.
[81]	Stehlin-Gaon C, Willmann D, Zeyer D, Sanglier S, Van Dorsselaer A, Renaud JP, Moras D, Schüle R. All-trans retinoic acid is a ligand for the orphan nuclear receptor RORβ. Nat Struct Biol, 2003, 10(10): 820-825.
[82]	Gachon F. Physiological function of PARbZip circadian clock-controlled transcription factors. Ann Med, 2007, 39(8): 562-571.
[83]	Fang B, Everett LJ, Jager J, Briggs E, Armour SM, Feng D, Roy A, Gerhart-Hines Z, Sun Z, Lazar MA. Circadian enhancers coordinate multiple phases of rhythmic gene transcription in vivo. Cell, 2014, 159(5): 1140-1152.
[84]	Huang ZJ, Edery I, Rosbash M. PAS is a dimerization domain common to Drosophila period and several transcription factors. Nature, 1993, 364(6434): 259-262.
[85]	Huang N, Chelliah Y, Shan YL, Taylor CA, Yoo SH, Partch C, Green CB, Zhang H, Takahashi JS. Crystal structure of the heterodimeric CLOCK: BMAL1 transcriptional activator complex. Science, 2012, 337(6091): 189-194.
[86]	Xu HY, Gustafson CL, Sammons PJ, Khan SK, Parsley NC, Ramanathan C, Lee HW, Liu AC, Partch CL. Cryptochrome 1 regulates the circadian clock through dynamic interactions with the BMAL1 C terminus. Nat Struct Mol Biol, 2015, 22(6): 476-484.
[87]	Menet JS, Pescatore S, Rosbash M. CLOCK: BMAL1 is a pioneer-like transcription factor. Genes Dev, 2014, 28(1): 8-13.
[88]	Zhang YX, Fang B, Emmett MJ, Damle M, Sun Z, Feng D, Armour SM, Remsberg JR, Jager J, Soccio RE, Steger DJ, Lazar MA. Discrete functions of nuclear receptor Rev-erbα couple metabolism to the clock. Science, 2015, 348(6242): 1488-1492.
[89]	Duong HA, Weitz CJ. Temporal orchestration of repressive chromatin modifiers by circadian clock Period complexes. Nat Struct Mol Biol, 2014, 21(2): 126-132.
[90]	Ye R, Selby CP, Ozturk N, Annayev Y, Sancar A. Biochemical analysis of the canonical model for the mammalian circadian clock. J Biol Chem, 2011, 286(29): 25891-25902.
[91]	Kiyohara YB, Tagao S, Tamanini F, Morita A, Sugisawa Y, Yasuda M, Yamanaka I, Ueda HR, Van Der Horst GTJ, Kondo T, Yagita K. The BMAL1 C terminus regulates the circadian transcription feedback loop. Proc Natl Acad Sci USA, 2006, 103(26): 10074-10079.
[92]	Honma S, Kawamoto T, Takagi Y, Fujimoto K, Sato F, Noshiro M, Kato Y, Honma K. Dec1 and Dec2 are regulators of the mammalian molecular clock. Nature, 2002, 419(6909): 841-844.
[93]	Jenuwein T, Allis CD. Translating the histone code. Science, 2001, 293(5532): 1074-1080.
[94]	Soshnev AA, Josefowicz SZ, Allis CD. Greater than the sum of parts: complexity of the dynamic epigenome. Mol Cell, 2016, 62(5): 681-694.
[95]	Vollmers C, Schmitz RJ, Nathanson J, Yeo G, Ecker JR, Panda S. Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome. Cell Metab, 2012, 16(6): 833-845.
[96]	Ripperger JA, Schibler U. Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions. Nat Genet, 2006, 38(3): 369-374.
[97]	Feng D, Liu T, Sun Z, Bugge A, Mullican SE, Alenghat T, Liu XS, Lazar MA. A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism. Science, 2011, 331(6022): 1315-1319.
[98]	Etchegaray JP, Lee C, Wade PA, Reppert SM. Rhythmic histone acetylation underlies transcription in the mammalian circadian clock. Nature, 2003, 421(6919): 177-182.
[99]	Lee Y, Lee J, Kwon I, Nakajima Y, Ohmiya Y, Son GH, Lee KH, Kim K. Coactivation of the CLOCK-BMAL1 complex by CBP mediates resetting of the circadian clock. J Cell Sci, 2010, 123(Pt 20): 3547-3557.
[100]	Nakahata Y, Kaluzova M, Grimaldi B, Sahar S, Hirayama J, Chen D, Guarente LP, Sassone-Corsi P. The NAD +-dependent deacetylase SIRT1 modulates CLOCK- mediated chromatin remodeling and circadian control. . Cell, 2008, 134(2): 329-340.
[101]	Asher G, Gatfield D, Stratmann M, Reinke H, Dibner C, Kreppel F, Mostoslavsky R, Alt FW, Schibler U. SIRT1 regulates circadian clock gene expression through PER2 deacetylation. Cell, 2008, 134(2): 317-328.
[102]	Nakahata Y, Sahar S, Astarita G, Kaluzova M, Sassone-Corsi P. Circadian control of the NAD + salvage pathway by CLOCK-SIRT1. . Science, 2009, 324(5927): 654-657.
[103]	Ramsey KM, Yoshino J, Brace CS, Abrassart D, Kobayashi Y, Marcheva B, Hong HK, Chong JLC, Buhr ED, Lee C, Takahashi JS, Imai SI, Bass J. Circadian clock feedback cycle through NAMPT-mediated NAD + biosynthesis. . Science, 2009, 324(5927): 651-654.
[104]	Le Martelot G, Canella D, Symul L, Migliavacca E, Gilardi F, Liechti R, Martin O, Harshman K, Delorenzi M, Desvergne B, Herr W, Deplancke B, Schibler U, Rougemont J, Guex N, Hernandez N, Naef F, CycliX Consortium. Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biol, 2012, 10(11): e1001442.
[105]	Malapeira J, Khaitova LC, Mas P. Ordered changes in histone modifications at the core of the Arabidopsis circadian clock. Proc Natl Acad Sci USA, 2012, 109(52): 21540-21545.
[106]	Valekunja UK, Edgar RS, Oklejewicz M, Van Der Horst GTJ, O'Neill JS, Tamanini F, Turner DJ, Reddy AB. Histone methyltransferase MLL3 contributes to genome-scale circadian transcription. Proc Natl Acad Sci USA, 2013, 110(4): 1554-1559.
[107]	Katada S, Sassone-Corsi P. The histone methyltransferase MLL1 permits the oscillation of circadian gene expression. Nat Struct Mol Biol, 2010, 17(12): 1414-1421.
[108]	Kim DH, Rhee JC, Yeo S, Shen RK, Lee SK, Lee JW, Lee S. Crucial roles of mixed-lineage leukemia 3 and 4 as epigenetic switches of the hepatic circadian clock controlling bile acid homeostasis in mice. Hepatology, 2015, 61(3): 1012-1023.
[109]	DiTacchio L, Le HD, Vollmers C, Hatori M, Witcher M, Secombe J, Panda S. Histone lysine demethylase JARID1a activates CLOCK-BMAL1 and influences the circadian clock. Science, 2011, 333(6051): 1881-1885.
[110]	Nam HJ, Boo K, Kim D, Han DH, Choe HK, Kim CR, Sun W, Kim H, Kim K, Lee H, Metzger E, Schuele R, Yoo SH, Takahashi JS, Cho S, Son GH, Baek SH. Phosphorylation of LSD1 by PKCα is crucial for circadian rhythmicity and phase resetting. Mol Cell, 2014, 53(5): 791-805.
[111]	Tamayo AG, Duong HA, Robles MS, Mann M, Weitz CJ. Histone monoubiquitination by Clock-BMAL1 complex marks Per1 and Per2 genes for circadian feedback. Nat Struct Mol Biol, 2015, 22(10): 759-766.
[112]	Kim JY, Kwak PB, Weitz CJ. Specificity in circadian clock feedback from targeted reconstitution of the NuRD corepressor. Mol Cell, 2014, 56(6): 738-748.
[113]	Etchegaray JP, Yang XM, DeBruyne JP, Peters AHFM, Weaver DR, Jenuwein T, Reppert SM. The polycomb group protein EZH2 is required for mammalian circadian clock function. J Biol Chem, 2006, 281(30): 21209-21215.
[114]	Nguyen KD, Fentress SJ, Qiu YF, Yun KR, Cox JS, Chawla A. Circadian gene Bmal1 regulates diurnal oscillations of Ly6Chi inflammatory monocytes. Science , 2013, 341(6153): 1483-1488.
[115]	Bannister AJ, Zegerman P, Partridge JF, Miska EA, Thomas JO, Allshire RC, Kouzarides T. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature, 2001, 410(6824): 120-124.
[116]	Lachner M, O'Carroll D, Rea S, Mechtler K, Jenuwein T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature, 2001, 410(6824): 116-120.
[117]	Maekawa F, Shimba S, Takumi S, Sano T, Suzuki T, Bao JH, Ohwada M, Ehara T, Ogawa Y, Nohara K. Diurnal expression of Dnmt3b mRNA in mouse liver is regulated by feeding and hepatic clockwork. Epigenetics, 2012, 7(9): 1046-1056.
[118]	Xia L, Ma SH, Zhang Y, Wang T, Zhou MY, Wang ZQ, Zhang JF. Daily variation in global and local DNA methylation in mouse livers. PLoS One, 2015, 10(2): e0118101.
[119]	Hu SH, Wan J, Su YJ, Song QF, Zeng YX, Nguyen HN, Shin J, Cox E, Rho HS, Woodard C, Xia SL, Liu S, Lyu HB, Ming GL, Wade H, Song HJ, Qian J, Zhu H. DNA methylation presents distinct binding sites for human transcription factors. eLife, 2013, 2: e00726.
[120]	Nakajima M, Imai K, Ito H, Nishiwaki T, Murayama Y, Iwasaki H, Oyama T, Kondo T. Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. Science, 2005, 308(5720): 414-415.

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哺乳动物生物钟的遗传和表观遗传研究进展

Genetic and epigeneticregulations of mammalian circadian rhythms

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