非编码RNA参与昼夜节律调控研究进展
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摘要
微小RNA(microRNA)、长链非编码RNA(lncRNA)、环状RNA(circRNA)等非编码RNA(noncoding RNAs,ncRNA)属于表观遗传调控因子,通过在染色质水平、转录及转录后水平、翻译水平调控基因表达和功能,进而影响各种细胞生物学过程。在人体生理活动中,昼夜节律受到多种内外因素的调节,包括ncRNA。本文总结了参与调节昼夜节律的ncRNA,并讨论了在钟基因功能中ncRNA的作用机制,为进一步探究ncRNA在昼夜节律调控中的作用提供新的研究思路,为节律相关疾病的研究和诊治提供借鉴。
Non-coding RNAs(ncRNAs),such as microRNAs,long non-coding RNAs(lncRNAs)and circular RNAs(circRNAs),etc,are epigenetic regulatory factors.They regulate gene expression and functions on chromosomal level,transcriptional and post-transcriptional levels,translation level,and then affect various biological processes of cells.In human physiological activities,circadian rhythm is regulated by both internal and external factors,including ncRNAs.Here,we reviewed the studies related to the ncRNAs participating in the regulation of circadian rhythm,and discussed the underlying mechanisms of ncRNAs in the regulation of the expression and functions of clock genes.It is expected to provide a new direction to further explore the roles of ncRNAs in the regulation of circadian rhythms,as well as a reference for the research of diagnosis and treatment of circadian rhythmic related diseases.
Non-coding RNAs(ncRNAs),such as microRNAs,long non-coding RNAs(lncRNAs)and circular RNAs(circRNAs),etc,are epigenetic regulatory factors.They regulate gene expression and functions on chromosomal level,transcriptional and post-transcriptional levels,translation level,and then affect various biological processes of cells.In human physiological activities,circadian rhythm is regulated by both internal and external factors,including ncRNAs.Here,we reviewed the studies related to the ncRNAs participating in the regulation of circadian rhythm,and discussed the underlying mechanisms of ncRNAs in the regulation of the expression and functions of clock genes.It is expected to provide a new direction to further explore the roles of ncRNAs in the regulation of circadian rhythms,as well as a reference for the research of diagnosis and treatment of circadian rhythmic related diseases.
引文
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[30]Vodala S,Pescatore S,Rodriguez J,et al.The oscillating miRNA 959-964cluster impacts Drosophila feeding time and other circadian outputs[J].Cell Metabolism,2012,16(5):601-612.
[31]Yang M,Lee JE,Padgett RW,et al.Circadian regulation of a limited set of conserved microRNAs in Drosophila[J].BMC Genomics,2008,9(1):83.
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[35]Tan X,Zhang P,Zhou L,et al.Clock-controlled mir-142-3p can target its activator,Bmal1[J].BMC Mol Biology,2012,7(13):27.
[36]Zhang W,Wang P,Chen S,et al.Rhythmic expression of miR-27b-3p targets the clock gene Bmal1at the posttranscriptional level in the mouse liver[J].Exprimental Biology,2016,30(6):2151-2160.
[37]Zhao X,Zhu X,Cheng S,et al.MiR-29a/b/c regulate human circadian gene hPER1expression by targeting its 3’UTR[J].Acta Biochim Biophys Sin,2014,46(4):313-317.
[38]Chen R,D’Alessandro M,Lee C.miRNAs are required for generating a time delay critical for the circadian oscillator[J].Current biology CB,2013,23(20):1959-1968.
[39]Panda S,Antoch MP,Miller BH,et al.Coordinated transcription of key pathways in the mouse by the circadian clock[J].Cell,2002,109(3):307-320.
[40]Su AI,Cooke MP,Ching KA,et al.Large-scale analysis of the human and mouse transcriptomes[J].Proceedings of National Academy of Sciences of USA,2002,99(7):4465-4470.
[41]Ueda HR,Hayashi S,Chen W,et al.System-level identification of transcriptional circuits underlying mammalian circadian clocks[J].Nature Genetics,2005,37(2):187-192.
[42]Hangauer MJ,Vaughn IW,McManus MT.Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs[J].PloS One,2013,9(6):e1003569.
[43]Guttman M,Amit I,Garber M,et al.Chromatin signature reveals over a thousand highly conserved large noncoding RNAs in mammals[J].Nature,2009,458(7235):223-227.
[44]Cabili MN,Trapnell C,Goff L,et al.Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses[J].Gene&Development,2011,25(18):1915-1927.
[45]Ulitsky I,Shkumatava A,Jan CH,et al.Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution[J].Cell,2011,147(7):1537-1550.
[46]Ulitsky I,Bartel DP.lincRNAs:genomics,evolution,and mechanisms[J].Cell,2013,154(1):26-46.
[47]Koike N,Yoo SH,Huang HC,et al.Transcriptional architecture and chromatin landscape of the core circadian clock in mammals[J].Science,2012,338(6105):349-354.
[48]Fang B,Everett LJ,Jager J,et al.Circadian enhancers coordinate multiple phases of rhythmic gene transcription in vivo[J].Cell,2014,159(5):1140-1152.
[49]Fan Z,Zhao M,Joshi PD,et al.A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation[J].Nucleic Acids Research,2017,45(10):5720-5738.
[50]Coon SL,Munson PJ,Cherukuri PF,et al.Circadian changes in long noncoding RNAs in the pineal gland[J].Proceedings of the National Academy of Sciences of the USA,2012,109(33):13319-13324.
[51]Vollmers C,Schmitz RJ,Nathanson J,et al.Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome[J].Cell Metabolism,2012,16(6):833-845.
[52]Aitken S,Semple CA.The circadian dynamics of small nucleolar RNA in the mouse liver[J].Journal of the Royal Society,2017,14(130):20170034.
[53]Li JB,Church GM.Deciphering the functions and regulation of brain-enriched A-to-I RNA editing[J].Nature Neutroscience,2013,16(11):1518-1522.
[54]Hazen SP,Naef F,Quisel T,et al.Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays[J].Genome Biology,2009,10(2):R17.
[2]陈海龙,吕柯,曲丽娜.航天飞行对人体睡眠-觉醒节律的影响研究进展[J].航天医学与医学工程,2017,30(4):308-312Chen HL,LüK,Qu LN.Research progress in effects of spaceflight on sleep-wake pattern[J].Space Medicine&Medical Engineering,2017,30(4):308-312
[3]Fabbri M,Garzon R,Andreeff M,et al.MicroRNAs and noncoding RNAs in hematological malignancies:molecular,clinical and therapeutic implications[J].Leukemia,2008,22(6):1095-1105.
[4]Guo M,Lo PC,Mount SM.Species-specific signals for the splicing of a short Drosophila intron in vitro[J].Molecular and Cellular Biology,1993,13(2):1104-1118.
[5]Valadkhan S,Gunawardane LS.Role of small nuclear RNAs in eukaryotic gene expression[J].Essays in Biochemistry,2013,54(1):79-90.
[6]Chen XS,White WT,Collins LJ,et al.Computational identification of four spliceosomal snRNAs from the deepbranching eukaryote Giardia intestinalis[J].PloS One,2008,3(8):e3106.
[7]Bartel DP.MicroRNAs:genomics,biogenesis,mechanism,and function[J].Cell,2004,116(2):281-297.
[8]Wu S,Fesler A,Ju J.Implications of circadian rhythm regulation by microRNAs in colorectal cancer[J].Cancer Translational Medicine,2016,2(1):1-6.
[9]Li W,Wang R,Ma JY,et al.A Human long non-coding RNA ALT1controls the cell cycle of vascular endothelial cells via ACE2and cyclin D1pathway[J].Cellular Physiology and Biochemistry,2017,43(3):1152-1167.
[10]Wang L,He Y,Liu W,et al.Non-coding RNALINC00857is predictive of poor patient survival and promotes tumor progression via cell cycle regulation in lung cancer[J].Oncotarget,2016,7(10):11487-11499.
[11]Cheng HY,Papp JW,Varlamova O,et al.microRNAmodulation of circadian-clock period and entrainment[J].Neuron,2007,54(5):813-829.
[12]Cui M,Zheng M,Sun B,et al.A long noncoding RNAperturbs the circadian rhythm of hepatoma cells to facilitate hepatocarcinogenesis[J].Neoplasia,2015,17(1):79-88.
[13]Allada R,Emery P,Takahashi JS,et al.Stopping time:the genetics of fly and mouse circadian clocks[J].Annual Review of Neuroscience,2001,24:1091-1119.
[14]Yu W.Hardin PE.Circadian oscillators of Drosophila and mammals[J].Journal of Cell Science,2006,119(Pt23):4793-4795.
[15]Hardin PE,Hall JC,Rosbash M,et al.Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels[J].Nature,1990,343(6258):536-540.
[16]Ye R,Selby CP,Ozturk N,et al.Biochemical analysis of the canonical model for the mammalian circadian clock[J].The Journal of Biological Chemistry,2011,286(29):25891-25902.
[17]Reppert SM,Weaver DR.Coordination of circadian timing in mammals[J].Nature,2002,418(6901):935-941.
[18]Schibler U.The daily rhythms of genes,cells and organs.Biological clocks and circadian timing in cells[J].EMBOReports,2005,6(S1):S9-S13.
[19]Chen R,Schirmer A,Lee Y,et al.Rhythmic PER abundance defines a critical nodal point for negative feedback within the circadian clock mechanism[J].Molecular Cell,2009,36(3):417-430.
[20]Lee C,Weaver DR,Reppert SM.Direct association between mouse PERIOD and CKIepsilon is critical for a functioning circadian clock[J].Molecular and Cellular Biology,2004,24(2):584-594.
[21]Mohawk JA,Green CB,Takahashi JS.Central and peripheral circadian clocks in mammals[J].Annual Review of Neuroscience,2012,35:445-462.
[22]Welsh DK,Yoo SH,Liu AC,et al.Bioluminescence imaging of individual fibroblasts reveals persistent,independently phased circadian rhythms of clock gene expression[J].Current Biology,2004,14(24):2289-2295.
[23]Liu AC,Welsh DK,Ko CH,et al.Intercellular coupling confers robustness against mutations in the SCN circadian clock network[J].Cell,2007,129(3):605-616.
[24]Carthew RW,Sontheimer EJ.Origins and mechanisms of miRNAs and siRNAs[J].Cell,2009,136(4):642-655.
[25]Stefani G,Slack FJ.Small non-coding RNAs in animal development[J].Molecular Cell Biology,2008,9(3):219-230.
[26]Shende VR,Goldrick MM,Ramani S,et al.Expression and rhythmic modulation of circulating microRNAs targeting the clock gene Bmal1in mice[J].Plos One,2011,6(7):e22586.
[27]Kadener S,Menet JS,Sugino K,et al.A role for microR-NAs in the Drosophila circadian clock[J].Gene&Development,2009,23(18):2179-2191.
[28]Liu K,Wang R.MicroRNA-mediated regulation in the mammalian circadian rhythm[J].Journal of Theoretial Biology,2012,304:103-110.
[29]Kojima S,Green CB.Circadian genomics reveal a role for post-transcriptional regulation in mammals[J].Biolochemistry,2015,54(2):124-133.
[30]Vodala S,Pescatore S,Rodriguez J,et al.The oscillating miRNA 959-964cluster impacts Drosophila feeding time and other circadian outputs[J].Cell Metabolism,2012,16(5):601-612.
[31]Yang M,Lee JE,Padgett RW,et al.Circadian regulation of a limited set of conserved microRNAs in Drosophila[J].BMC Genomics,2008,9(1):83.
[32]Zhou W,Li Y,Wang X,et al.MiR-206-mediated dynamic mechanism of the mammalian circadian clock[J].BMCSystem Biology,2011,5(1):141.
[33]Hansen KF,Sakamoto K,Obrietan K.MicroRNAs:apotential interface between the circadian clock and human health[J].Genomo Medicine,2011,3(2):10.
[34]Shende VR,Neuendorff N,Earnest DJ.Role of miR-142-3p in the post-transcriptional regulation of the clock gene Bmal1in the mouse SCN[J].PloS One,2013,8(6):e65300.
[35]Tan X,Zhang P,Zhou L,et al.Clock-controlled mir-142-3p can target its activator,Bmal1[J].BMC Mol Biology,2012,7(13):27.
[36]Zhang W,Wang P,Chen S,et al.Rhythmic expression of miR-27b-3p targets the clock gene Bmal1at the posttranscriptional level in the mouse liver[J].Exprimental Biology,2016,30(6):2151-2160.
[37]Zhao X,Zhu X,Cheng S,et al.MiR-29a/b/c regulate human circadian gene hPER1expression by targeting its 3’UTR[J].Acta Biochim Biophys Sin,2014,46(4):313-317.
[38]Chen R,D’Alessandro M,Lee C.miRNAs are required for generating a time delay critical for the circadian oscillator[J].Current biology CB,2013,23(20):1959-1968.
[39]Panda S,Antoch MP,Miller BH,et al.Coordinated transcription of key pathways in the mouse by the circadian clock[J].Cell,2002,109(3):307-320.
[40]Su AI,Cooke MP,Ching KA,et al.Large-scale analysis of the human and mouse transcriptomes[J].Proceedings of National Academy of Sciences of USA,2002,99(7):4465-4470.
[41]Ueda HR,Hayashi S,Chen W,et al.System-level identification of transcriptional circuits underlying mammalian circadian clocks[J].Nature Genetics,2005,37(2):187-192.
[42]Hangauer MJ,Vaughn IW,McManus MT.Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs[J].PloS One,2013,9(6):e1003569.
[43]Guttman M,Amit I,Garber M,et al.Chromatin signature reveals over a thousand highly conserved large noncoding RNAs in mammals[J].Nature,2009,458(7235):223-227.
[44]Cabili MN,Trapnell C,Goff L,et al.Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses[J].Gene&Development,2011,25(18):1915-1927.
[45]Ulitsky I,Shkumatava A,Jan CH,et al.Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution[J].Cell,2011,147(7):1537-1550.
[46]Ulitsky I,Bartel DP.lincRNAs:genomics,evolution,and mechanisms[J].Cell,2013,154(1):26-46.
[47]Koike N,Yoo SH,Huang HC,et al.Transcriptional architecture and chromatin landscape of the core circadian clock in mammals[J].Science,2012,338(6105):349-354.
[48]Fang B,Everett LJ,Jager J,et al.Circadian enhancers coordinate multiple phases of rhythmic gene transcription in vivo[J].Cell,2014,159(5):1140-1152.
[49]Fan Z,Zhao M,Joshi PD,et al.A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation[J].Nucleic Acids Research,2017,45(10):5720-5738.
[50]Coon SL,Munson PJ,Cherukuri PF,et al.Circadian changes in long noncoding RNAs in the pineal gland[J].Proceedings of the National Academy of Sciences of the USA,2012,109(33):13319-13324.
[51]Vollmers C,Schmitz RJ,Nathanson J,et al.Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome[J].Cell Metabolism,2012,16(6):833-845.
[52]Aitken S,Semple CA.The circadian dynamics of small nucleolar RNA in the mouse liver[J].Journal of the Royal Society,2017,14(130):20170034.
[53]Li JB,Church GM.Deciphering the functions and regulation of brain-enriched A-to-I RNA editing[J].Nature Neutroscience,2013,16(11):1518-1522.
[54]Hazen SP,Naef F,Quisel T,et al.Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays[J].Genome Biology,2009,10(2):R17.