microRNA靶基因鉴定方法研究进展
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摘要
microRNA(miRNA)是由21～23个核苷酸组成的小单链非编码RNA分子,通过结合到靶基因上降解靶mRNA或抑制其翻译,在转录后水平调控基因表达,是许多生理学和病理学过程的主要参与者。miRNA靶标通常通过miRNA种子序列和靶标mRNA内的互补位点之间的配对来识别,但并不是所有的结合位点都是起作用的关键位点。因此,miRNA靶标相互作用的识别和验证对于研究生物过程的调控网络至关重要。文章综述了传统的miRNA鉴定方法,及近年来新发现的miRNA与其靶基因鉴定方法,并对各种方法的优劣进行了分析,为促进对miRNA作用机制的认识,进一步利用miRNA进行发育、生理、病理等研究提供参考。
引文
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[2] 李超,杜志游,陈集双.解读AGO蛋白结构及其功能[J].中国生物化学与分子生物学报,2009,25(11):969 -976.
[3] 敖金霞,高学军,仇有文,等.实时荧光定量PCR技术在转基因检测中的应用[J]. 东北农业大学学报,2009,40(6): 141-144.
[4] ULE J, JENSEN K, MELE A,et al. CLIP: a method for identifying protein-RNA interaction sites in living cells[J]. Methods, 2005, 37(4): 376-386.
[5] GRANNEMAN S, PETFALSKI E, SWIATKOWSKA A,et al. Cracking pre-40S ribosomal subunit structure by systematic analyses of RNA-protein cross-linking[J].EMBO J,2010, 29(12): 2026-2036.
[6] CHI S W,ZHANG J B,MELE A,et al.Argonaute hits-clip decodes microRNA-mRNA interaction maps[J].Nature,2009,460(7254):479-486.
[7] ZISOULIS D G.Comprehensive discovery of endogenous argonaute binding sites in Caenorhabditis elegans[J]. Nat Struct Mol Biol,2010,17(2):173-179.
[8] ZHANG C,DARNELL R B.Mapping in vivo protein-RNA interactions at single-nucleotide resolution from hits-clip data[J].Nat Biotechnol,2011, 29(7):607-614.
[9] HAFNER M,LANDTHALER M,BURGER L,et al.PAR-CliP-a method to identify transcriptome-wide the binding sites of RNA binding proteins[J].J Vis Exp,2010,41:2034.
[10] HAFNER M, LIANOGLOU S,TUSCHL T,et al.Genome-wide identification of mirna targets by par-clip[J]. Methods,2012, 58(2):94-105.
[11] K?NIG J,ZARNACK K, ROT G,et al. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution[J]. Nat Struct Mol Biol,2010, 17(7):909-915.
[12] GRANNEMAN S, KUDLA G, PETFALSKI E, et al. Identifcation of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs[J]. Proc Natl Acad Sci USA, 2009, 106(24): 9613-9618.
[13] EASOW G, TELEMAN A A, COHEN S M. Isolation of microRNA targets by miRNP immunopurification[J].RNA, 2007,13(8):1198-1204.
[14] PICKL J M,TICHY D,KURYSHEV V Y,et al.Ago-RIP-Seq identifes polycomb repressive complex imember CBX7 as a major target of miR-375 in prostate cancer progression[J].Oncotarget,2016,7(37):59589-59603.
[15] MALMEVIK J,PETRI R,KLUSSENDORF T,et al.Identifcation of the miRNA targetome in hippocampal neurons using RIP-seq[J].Sci Rep, 2015,5:12609.
[16] OROM U A,LUND A H.Isolation of microRNA targets using biotinylated synthetic microRNAs[J].Methods,2007,43(2):162-165.
[17] TAN S M,KIRCHNER R,JIN J,et al.Sequencing of captive target transcripts identifies the network of regulated genes and functions of primate-specific miR-522[J].Cell Rep,2014,8(4):1225-1239.
[18] TAN S M,LIEBERMAN J.Capture and identification of miRNA targets by biotin pulldown and RNA-seq[J].Methods Mol Biol,2016,1358:221-228.
[19] KUDLA G,GRANNEMAN S,HAHN D,et al.Crosslinking,ligation,and sequencing of hybrids reveals RNA-RNA interactions in yeast[J].Proc Natl Acad USA,2011,108(24):10010-10015.
[20] HELWAK A,KUDLA G,DUDNAKOVA T,et al.Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding[J]. Cell,2013,153(3):654-665.
[21] TRAVIS A J, MOODY J,HELWAK A, et al. A bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data[J].Methods,2014,65(3): 263-273.
[22] LI Y, ZHANG M,CHEN H,et al.Ratio of miR-196s to HOXC8 messenger RNA correlates with breast cancer cell migration and metastasis[J]. Cancer Res,2010,70(20):7894-7904.
[23] HELWAK A, TOLLERVEY D.Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH)[J].Nat Protoc,2014,9(3):711-728.