Pairing beyond the Seed Supports MicroRNA Targeting Specificity

被引：314

作者：

Broughton, James P. ^{[1
]}

Lovci, Michael T. ^{[2
]}

Huang, Jessica L. ^{[1
]}

Yeo, Gene W. ^{[2
]}

Pasquinelli, Amy E. ^{[1
]}

机构：

[1] Univ Calif San Diego, Div Biol, La Jolla, CA 92093 USA

[2] Univ Calif San Diego, Dept Cellular & Mol Med, Inst Genom Med, Stem Cell Program,Sanford Consortium Regenerat Me, 2880 Torrey Pines Scen Dr, La Jolla, CA 92037 USA

来源：

MOLECULAR CELL | 2016年 / 64卷 / 02期

基金：

美国国家科学基金会; 美国国家卫生研究院;

关键词：

MAMMALIAN MESSENGER-RNAS; ARGONAUTE BINDING-SITES; CAENORHABDITIS-ELEGANS; C; ELEGANS; CIRCULAR RNAS; LET-7; REVEALS; MIRNA; RECOGNITION; CLIP;

D O I：

10.1016/j.molcel.2016.09.004

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

To identify endogenous miRNA-target sites, we isolated AGO-bound RNAs from Caenorhabditis elegans by individual-nucleotide resolution cross-linking immunoprecipitation (iCLIP), which fortuitously also produced miRNA-target chimeric reads. Through the analysis of thousands of reproducible chimeras, pairing to the miRNA seed emerged as the predominant motif associated with functional interactions. Unexpectedly, we discovered that additional pairing to 3' sequences is prevalent in the majority of target sites and leads to specific targeting by members of miRNA families. By editing an endogenous target site, we demonstrate that 3' pairing determines targeting by specific miRNA family members and that seed pairing is not always sufficient for functional target interactions. Finally, we present a simplified method, chimera PCR (ChimP), for the detection of specific miRNA-target interactions. Overall, our analysis revealed that sequences in the 5' as well as the 3' regions of a miRNA provide the information necessary for stable and specific miRNA-target interactions in vivo.

引用

页码：320 / 333

页数：14

共 51 条

[1] The let-7 microRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans [J].

Abbott, AL ;

Alvarez-Saavedra, E ;

Miska, EA ;

Lau, NC ;

Bartel, DP ;

Horvitz, HR ;

Ambros, V .

DEVELOPMENTAL CELL, 2005, 9 (03) :403-414

[2] Predicting effective microRNA target sites in mammalian mRNAs [J].

Agarwal, Vikram ;

Bell, George W. ;

Nam, Jin-Wu ;

Bartel, David P. .

ELIFE, 2015, 4

[3] Many Families of C. elegans MicroRNAs Are Not Essential for Development or Viability [J].

Alvarez-Saavedra, Ezequiel ;

Horvitz, H. Robert .

CURRENT BIOLOGY, 2010, 20 (04) :367-373

[4]

Bailey T L, 1994, Proc Int Conf Intell Syst Mol Biol, V2, P28

[5] MicroRNAs: Target Recognition and Regulatory Functions [J].

Bartel, David P. .

CELL, 2009, 136 (02) :215-233

[6] The role of let-7 in cell differentiation and cancer [J].

Boyerinas, Benjamin ;

Park, Sun-Mi ;

Hau, Annika ;

Murmann, Andrea E. ;

Peter, Marcus E. .

[7] Principles of MicroRNA-target recognition [J].

Brennecke, J ;

Stark, A ;

Russell, RB ;

Cohen, SM .

PLOS BIOLOGY, 2005, 3 (03) :404-418

[8] Identifying Argonaute binding sites in Caenorhabditis elegans using iCLIP [J].

Broughton, James P. ;

Pasquinelli, Amy E. .

METHODS, 2013, 63 (02) :119-125

[9] A Dynamic Search Process Underlies MicroRNA Targeting [J].

Chandradoss, Stanley D. ;

Schirle, Nicole T. ;

Szczepaniak, Malwina ;

MacRae, Ian J. ;

Joo, Chirlmin .

CELL, 2015, 162 (01) :96-107

[10] Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps [J].

Chi, Sung Wook ;

Zang, Julie B. ;

Mele, Aldo ;

Darnell, Robert B. .

NATURE, 2009, 460 (7254) :479-486

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