RNA结合蛋白与RNA相互作用鉴定技术
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摘要
RNA结合蛋白(RNA binding proteins,RBPs)通过与RNA相互作用,广泛参与到RNA的剪切、转运、编辑、胞内定位及翻译调控等过程中。RNA领域尤其是非编码RNA(non-coding RNA,ncRNA)研究的快速发展,催生了多种RBPs-RNAs相互作用鉴定技术。这些技术反之又推动了RNA领域的研究进程。本文对紫外交联免疫沉淀(ultraviolet crosslinking and immunoprecipitation,CLIP),CLIP cDNA文库高通量测序(high-throughput sequencing of CLIP cDNA library,HITS-CLIP),光活化核苷增强的CLIP(photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation,PAR-CLIP),单核苷酸分离CLIP(individual nucleotide resolution CLIP,i CLIP),TRIBE(targets of RNA-binding protein identified by editing),RNA标记,相互作用组捕获(interactome capture,IC)和Ser IC(serial RNA interactome capture)等RBPs-RNAs相互作用鉴定技术的基本原理和优缺点以及应用进行综述。
RNA binding proteins( RBPs) are widely involved in RNA related processes such as splicing,transport,editing,cellular localization,and translational regulatory via interacting with target RNAs. With the rapid development of RNA research,especially in non-coding RNA( ncRNA),a variety of techniques of RBPs-RNAs interaction identification were created,which in turn contributed to the understanding of molecular mechanisms of RNAs processing and function. Herein,we review the basic principles,advantages and disadvantages,and applications of some important techniques that are mainly used for studying the interactome of RBPs-RNAs, including CLIP( ultraviolet crosslinking and immunoprecipitation),HITS-CLIP( high-throughput sequencing of CLIP) analysis of cDNA library,PAR-CLIP( photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation), i CLIP( individual nucleotide resolution CLIP),TRIBE( targets of RNA-binding protein identified by editing),RNA tagging,IC( interactome capture) and Ser IC( serial RNA interactome capture).
RNA binding proteins( RBPs) are widely involved in RNA related processes such as splicing,transport,editing,cellular localization,and translational regulatory via interacting with target RNAs. With the rapid development of RNA research,especially in non-coding RNA( ncRNA),a variety of techniques of RBPs-RNAs interaction identification were created,which in turn contributed to the understanding of molecular mechanisms of RNAs processing and function. Herein,we review the basic principles,advantages and disadvantages,and applications of some important techniques that are mainly used for studying the interactome of RBPs-RNAs, including CLIP( ultraviolet crosslinking and immunoprecipitation),HITS-CLIP( high-throughput sequencing of CLIP) analysis of cDNA library,PAR-CLIP( photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation), i CLIP( individual nucleotide resolution CLIP),TRIBE( targets of RNA-binding protein identified by editing),RNA tagging,IC( interactome capture) and Ser IC( serial RNA interactome capture).
引文
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[2]Hasan A,Cotobal C,Duncan CD,et al.Systematic analysis of the role of RNA-binding proteins in the regulation of RNA stability[J].PLo S Genet,2014,10(11):e1004684
[3]Chai Y,Liu J,Zhang Z,et al.HuR-regulated lncRNA NEAT1stability in tumorigenesis and progression of ovarian cancer[J].Cancer Med,2016,5(7):1588-1598
[4]Galbán S,Kuwano Y,Pullmann R Jr,et al.RNA-binding proteins HuR and PTB promote the translation of hypoxiainducible factor 1alpha[J].Mol Cell Biol,2008,28(1):93-107
[5]Goodarzi H,Zhang S,Buss CG,et al.Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins[J].Nature,2014,513(7517):256-260
[6]Zagore LL,Grabinski SE,Sweet TJ,et al.RNA binding protein Ptbp2 is essential for male germ cell development[J].Mol Cell Biol,2015,35(23):4030-4042
[7]Wang F,Tidei JJ,Polich ED,et al.Positive feedback between RNA-binding protein Hu D and transcription factor SATB1promotes neurogenesis[J].Proc Natl Acad Sci U S A,2015,112(36):E4995-E5004
[8]Klattenhoff CA,Scheuermann JC,Surface LE,et al.Braveheart,a long noncoding RNA required for cardiovascular lineage commitment[J].Cell,2013,152(3):570-583
[9]Lukong KE,Chang KW,Khandjian EW,et al.RNA-binding proteins in human genetic disease[J].Trends Genet,2008,24(8):416-425
[10]Hsu KF,Shen MR,Huang YF,et al.Overexpression of the RNA-binding proteins Lin28B and IGF2BP3(IMP3)is associated with chemoresistance and poor disease outcome in ovarian cancer[J].Br J Cancer,2015,113(3):414-424
[11]Stoiber MH,Olson S,May GE,et al.Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila[J].Genome Res,2015,25(11):1692-1702
[12]Blech-Hermoni Y,Ladd AN.RNA binding proteins in the regulation of heart development[J].Int J Biochem Cell Biol,2013,45(11):2467-2478
[13]Tenenbaum SA,Carson CC,Lager PJ,et al.Identifying mRNA subsets in messenger ribonucleoprotein complexes by using c DNA arrays[J].Proc Natl Acad Sci U S A,2000,97(26):14085-14090
[14]Dahm GM,Gubin MM,Magee JD,et al.Method for the isolation and identification of mRNAs,microRNAs and protein components of ribonucleoprotein complexes from cell extracts using RIP-chip[J].J Vis Exp,2012,2012(67):3851
[15]Ule J,Jensen KB,Ruggiu M,et al.CLIP identifies Novaregulated RNA networks in the brain[J].Science,2003,302(5648):1212-1215
[16]Fecko CJ,Munson KM,Saunders A,et al.Comparison of femtosecond laser and continuous wave UV sources for proteinnucleic acid crosslinking[J].Photochem Photobiol,2007,83(6):1394-1404
[17]Licatalosi DD,Mele A,Fak JJ,et al.HITS-CLIP yields genome-wide insights into brain alternative RNA processing[J].Nature,2008,456(7221):464-469
[18]Xue Y,Ouyang K,Huang J,et al.Direct conversion of fibroblasts to neurons by reprogramming PTB-regulated microRNA circuits[J].Cell,2013,152(1-2):82-96
[19]Guil S,Cáceres JF.The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a[J].Nat Struct Mol Biol,2007,14(7):591-596
[20]Wang ET,Cody NA,Jog S,et al.Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins[J].Cell,2012,150(4):710-724
[21]Guil S,Soler M,Portela A,et al.Intronic RNAs mediate EZH2regulation of epigenetic targets[J].Nat Struct Mol Biol,2012,19(7):664-670
[22]Kaneko S,Son J,Shen SS,et al.PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells[J].Nat Struct Mol Biol,2013,20(11):1258-1264
[23]Memczak S,Jens M,Elefsinioti A,et al.Circular RNAs are a large class of animal RNAs with regulatory potency[J].Nature,2013,495(7441):333-338
[24]Hafner M,Landthaler M,Burger L,et al.Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP[J].Cell,2010,141(1):129-141
[25]Saldaa-Meyer R,González-Buendía E,Guerrero G,et al.CTCF regulates the human p53 gene through direct interaction with its natural antisense transcript,Wrap53[J].Genes Dev,2014,28(7):723-734
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[27]Knig J,Zarnack K,Rot G,et al.i CLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution[J].Nat Struct Mol Biol,2010,17(7):909-915
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[35]Kwon SC,Yi H,Eichelbaum K,et al.The RNA-binding protein repertoire of embryonic stem cells[J].Nat Struct Mol Biol,2013,20(9):1122-1130
[36]Conrad T,Albrecht AS,de Melo Costa VR,et al.Serial interactome capture of the human cell nucleus[J].Nat Commun,2016,7:11212
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