RNA修饰对长链非编码RNA的调控作用
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摘要
长链非编码RNA (lncRNA)能在表观遗传、转录以及转录后水平上调控基因表达,与疾病的发生、发展和防治有着密切的联系。RNA修饰介导的表观转录组学调控是表观遗传的新领域,可以在转录后水平调控基因表达,并且可以作为一种重要的修饰手段对lncRNA进行调控。RNA修饰可以通过对lncRNA表达水平、剪切方式及二级结构的调控,影响各种生物学进程。现回顾和展望RNA修饰对lncRNA的调控作用和其潜在的生物学功能。
With the ability to regulate the gene expression in epigenetic, transcriptional or/and post-transcriptional manners, long non-coding RNA(lncRNA) is closely associated with occurrence, development and treatment of some diseases. As a new field, epigenetic transcriptomics through RNA modification could influence gene expression in post-transcriptional manner, which is an important modification to regulate lncRNA. Through regulating the expression, splicing and secondary structure of lncRNA, RNA modification is capable of affecting various biological processes. In this paper, we will review and prospect the regulatory effects of RNA modification on lncRNA and its potential biological functions.
With the ability to regulate the gene expression in epigenetic, transcriptional or/and post-transcriptional manners, long non-coding RNA(lncRNA) is closely associated with occurrence, development and treatment of some diseases. As a new field, epigenetic transcriptomics through RNA modification could influence gene expression in post-transcriptional manner, which is an important modification to regulate lncRNA. Through regulating the expression, splicing and secondary structure of lncRNA, RNA modification is capable of affecting various biological processes. In this paper, we will review and prospect the regulatory effects of RNA modification on lncRNA and its potential biological functions.
引文
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[43]Zhou KI,Parisien M,Dai Q,et al.N6-methyladenosine modification in a long non-coding RNA hairpin predisposes its conformation to protein binding.J Mol Biol,2016,428:822-33
[44]Dominissini D,Moshitchmoshkovitz S,Schwartz S,et al.Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.Nature,2012,485:201-6
[45]Rinn JL,Kertesz M,Wang JK,et al.Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs.Cell,2007,129:1311-23
[46]Amort T,Soulière MF,Wille A,et al.Long non-coding RNAs as targets for cytosine methylation.RNA Biol,2013,10:1003
[47]Patil DP,Chen CK,Pickering BF,et al.m(6)A RNAmethylation promotes XIST-mediated transcriptional repression.Nature,2016,537:369-73
[48]Huisman B,Manske G,Carney S,et al.Functional dissection of the m6A RNA modification.Trends Biochem Sci,2017,42:85-6
[2]Gibb EA,Brown CJ,Lam WL.The functional role of long non-coding RNA in human carcinomas.Mol Cancer,2011,10:38
[3]Zhang Y,Yang L,Chen LL.Life without A tail:new formats of long noncoding RNAs.Int J Biochem Cell Biol,2014,54:338-49
[4]Rapicavoli NA,Poth EM,Zhu H,et al.The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity.Neural Dev,2011,6:1-15
[5]Yang G,Lu X,Yuan L.LncRNA:a link between RNA and cancer.Biochim Biophys Acta,2014,1839:1097
[6]Zhou J,Yang L,Zhong T,et al.H19 lncRNA alters DNAmethylation genome wide by regulating S-adenosylhomocysteine hydrolase.Nat Commun,2015,6:10221
[7]Desrosiers R,Friderici K,Rottman F.Identification of methylated nucleosides in messenger RNA from Novikoff hepatoma cells.Proc Natl Acad Sci USA,1974,71:3971-5
[8]Molinie B,Wang J,Lim KS,et al.m6A level and isoform characterization sequencing(m6A-LAIC-seq)reveals the census and complexity of the m6A epitranscriptome.Nat Methods,2016,13:692-8
[9]Bokar JA,Shambaugh ME,Polayes D,et al.Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA(N6-adenosine)-methyltransferase.RNA,1997,3:1233-47
[10]Schwartz,Mumbach MR,Jovanovic M,et al.Perturbation of m6A writers reveals two distinct classes of mRNAmethylation at internal and 5′sites.Cell Rep,2014,8:284-96
[11]Horiuchi K,Kawamura T,Iwanari H,et al.Identification of Wilms’tumor 1-associating protein complex and its role in alternative splicing and the cell cycle.J Biol Chem,2013,288:33292-302
[12]Warda AS,Kretschmer J,Hackert P,et al.Human METTL16 is a N6-methyladenosine(m6A)methyltransferase that targets pre-mRNAs and various non-coding RNAs.EMBO Rep,2017,18:2004
[13]Jia G,Fu Y,Zhao X,et al.N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO.Nat Chem Biol,2011,7:885-7
[14]Fu Y,Jia G,Pang X,et al.FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA.Nat Commun,2013,4:1798
[15]Lu H,Samanta D,Xiang L,et al.Chemotherapy triggers HIF-1-dependent glutathione synthesis and copper chelation that induces the breast cancer stem cell phenotype.Proc Natl Acad Sci USA,2015,112:4600-9
[16]Wang X,Lu Z,Gomez A,et al.m6A-dependent regulation of messenger RNA stability.Nature,2014,505:117-20
[17]Meyer K,Patil D,Zhou J,et al.5′UTR m6A promotes cap-independent translation.Cell,2015,163:999-1010
[18]He Y,Hu H,Wang Y,et al.ALKBH5 inhibits pancreatic cancer motility by decreasing long non-coding RNAKCNK15-AS1 methylation.Cell Physiol Biochem,2018,48:838-46
[19]Liu N,Parisien M,Dai Q,et al.Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA.RNA,2013,19:1848-56
[20]Amort T,Rieder D,Wille A,et al.Distinct 5-methylcytosine profiles in poly(A)RNA from mouse embryonic stem cells and brain.Genome Biol,2017,18:1
[21]Squires JE,Patel HR,Marco N,et al.Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA.Nucleic Acids Res,2012,40:5023-33
[22]Kaiser S,Jurkowski TP,Kellner S,et al.The RNA methyltransferase Dnmt2 methylates DNA in the structural context of a tRNA.RNA Biol,2016,14:1
[23]Yang X,Yang Y,Sun BF,et al.5-methylcytosine promotes mRNA export-NSUN2 as the methyltransferase and ALYREF as an m5C reader.Cell Res,2017,27:606-25
[24]孙振,崔恒宓.长链非编码RNAH195-甲基胞嘧啶修饰的精确定位定量分析[A]//遗传多样性:前沿与挑战--中国的遗传学研究(2013-2015).北京:中国遗传学会大会论文摘要汇编[C]
[25]Baer M,Nilsen TW,Costigan C,et al.Structure and transcription of a human gene for H1 RNA,the RNAcomponent of human RNase P.Nucleic Acids Res,1990,18:97-103
[26]Cohn WE,Volkin E.Nucleoside-5′-phosphates from ribonucleic acid.Nature,1951,167:483-4
[27]Li X,Ma S,Yi C.Pseudouridine:the fifth RNA nucleotide with renewed interests.Cur Opin Chem Biol,2016,33:108-16
[28]Charette M,Gray MW.Pseudouridine in RNA:what,where,how,and why.IUBMB Life,2000,49:341-51
[29]Carlile TM,Rojasduran MF,Zinshteyn B,et al.Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells.Nature,2014,515:143-6
[30]Li X,Zhu P,Ma S,et al.Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome.Nat Chem Biol,2015,11:592-7
[31]Shafik A,Schumann U,Evers M,et al.The emerging epitranscriptomics of long noncoding RNAs.Biochim Biophys Acta,2015,1859:59-70
[32]Liu N,Dai Q,Zheng G,et al.N6-methyladenosinedependent RNA structural switches regulate RNA-protein interactions.Nature,2015,518:560-4
[33]Alexandrov A,Chernyakov I,Gu W,et al.Rapid tRNAdecay can result from lack of nonessential modifications.Mol Cell,2006,21:87-96
[34]Chen M,Jiang QX,Li JX,et al.Honokiol inhibiting proliferation of vascular smooth muscle cells by targeting lncRNA(BC033150)via FTO.Int J Clin Exp Med,2018,11:201-8
[35]Kasowitz SD,Ma J,Anderson S J,et al.Nuclear m6Areader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development.PLoS Genet,2018,14:e1007412
[36]孙慧颖.RNA m6A甲基化调控lncRNA选择性剪接[D].合肥:中国科学院大学,2016
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[40]Yang D,Qiao J,Wang G,et al.N6-methyladenosine modification of lincRNA 1281 is critically required for mESCdifferentiation potential.Nucleic Acids Res,2018,46:3906-20
[41]Tripathi V,Ellis JD,Shen Z,et al.The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation.Mol Cell,2010,39:925-38
[42]Moritz E,Tony G,Monika H,et al.Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development.RNA Biol,2012,9:1076
[43]Zhou KI,Parisien M,Dai Q,et al.N6-methyladenosine modification in a long non-coding RNA hairpin predisposes its conformation to protein binding.J Mol Biol,2016,428:822-33
[44]Dominissini D,Moshitchmoshkovitz S,Schwartz S,et al.Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.Nature,2012,485:201-6
[45]Rinn JL,Kertesz M,Wang JK,et al.Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs.Cell,2007,129:1311-23
[46]Amort T,Soulière MF,Wille A,et al.Long non-coding RNAs as targets for cytosine methylation.RNA Biol,2013,10:1003
[47]Patil DP,Chen CK,Pickering BF,et al.m(6)A RNAmethylation promotes XIST-mediated transcriptional repression.Nature,2016,537:369-73
[48]Huisman B,Manske G,Carney S,et al.Functional dissection of the m6A RNA modification.Trends Biochem Sci,2017,42:85-6