A compendium of RNA-binding motifs for decoding gene regulation

被引：1145

作者：

Ray, Debashish ^{[1
]}

Kazan, Hilal ^{[2
]}

Cook, Kate B. ^{[3
]}

Weirauch, Matthew T. ^{[1
]}

Najafabadi, Hamed S. ^{[1
,4
]}

Li, Xiao ^{[3
]}

Gueroussov, Serge ^{[3
]}

Albu, Mihai ^{[1
]}

Zheng, Hong ^{[1
]}

Yang, Ally ^{[1
]}

Na, Hong ^{[1
]}

Irimia, Manuel ^{[1
]}

Matzat, Leah H. ^{[5
]}

Dale, Ryan K. ^{[5
]}

Smith, Sarah A. ^{[6
]}

Yarosh, Christopher A. ^{[6
]}

Kelly, Seth M. ^{[7
]}

Nabet, Behnam ^{[6
]}

Mecenas, Desirea ^{[8
,9
]}

Li, Weimin ^{[10
]}

Laishram, Rakesh S. ^{[10
]}

Qiao, Mei ^{[11
]}

Lipshitz, Howard D. ^{[3
]}

Piano, Fabio ^{[8
,9
]}

Corbett, Anita H. ^{[7
]}

Carstens, Russ P. ^{[6
]}

Frey, Brendan J. ^{[4
]}

Anderson, Richard A. ^{[10
]}

Lynch, Kristen W. ^{[6
]}

Penalva, Luiz O. F. ^{[11
]}

Lei, Elissa P. ^{[5
]}

Fraser, Andrew G. ^{[1
,3
]}

Blencowe, Benjamin J. ^{[1
,3
]}

Morris, Quaid D. ^{[1
,2
,3
,4
]}

Hughes, Timothy R. ^{[1
,3
]}

机构：

[1] Univ Toronto, Donnelly Ctr, Toronto, ON M5S 3E1, Canada

[2] Univ Toronto, Dept Comp Sci, Toronto, ON M5S 2E4, Canada

[3] Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A8, Canada

[4] Univ Toronto, Dept Elect & Comp Engn, Toronto, ON M5S 3G4, Canada

[5] NIDDK, Lab Cellular & Dev Biol, NIH, Bethesda, MD 20892 USA

[6] Univ Penn, Perelman Sch Med, Dept Med, Philadelphia, PA 19104 USA

[7] Emory Univ, Sch Med, Dept Biochem, Atlanta, GA 30322 USA

[8] NYU, Dept Biol, New York, NY 10003 USA

[9] NYU, Ctr Genom & Syst Biol, New York, NY 10003 USA

[10] Univ Wisconsin, Sch Med & Publ Hlth, Mol & Cellular Pharmacol Program, Madison, WI 53706 USA

[11] UTHSCSA, Childrens Canc Res Inst, San Antonio, TX 78229 USA

来源：

NATURE | 2013年 / 499卷 / 7457期

基金：

加拿大自然科学与工程研究理事会;

关键词：

PRE-MESSENGER-RNA; GENOME-WIDE ANALYSIS; TRANSCRIPTION FACTORS; SPLICING REGULATOR; PROTEINS; SPECIFICITIES; RECOGNITION; REVEALS; FAMILY; CODE;

D O I：

10.1038/nature12311

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

RNA-binding proteins are key regulators of gene expression, yet only a small fraction have been functionally characterized. Here we report a systematic analysis of the RNA motifs recognized by RNA-binding proteins, encompassing 205 distinct genes from 24 diverse eukaryotes. The sequence specificities of RNA-binding proteins display deep evolutionary conservation, and the recognition preferences for a large fraction of metazoan RNA-binding proteins can thus be inferred from their RNA-binding domain sequence. The motifs that we identify in vitro correlate well with in vivo RNA-binding data. Moreover, we can associate them with distinct functional roles in diverse types of post-transcriptional regulation, enabling new insights into the functions of RNA-binding proteins both in normal physiology and in human disease. These data provide an unprecedented overview of RNA-binding proteins and their targets, and constitute an invaluable resource for determining post-transcriptional regulatory mechanisms in eukaryotes.

引用

页码：172 / 177

页数：6

共 47 条

[1]

The RNA-binding protein SUP-12 controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans [J].

Anyanful, A ;

Ono, K ;

Johnsen, RC ;

Ly, H ;

Jensen, V ;

Baillie, DL ;

Ono, S .

JOURNAL OF CELL BIOLOGY, 2004, 167 (04) :639-647

[2]

Sequence-specific binding of single-stranded RNA: is there a code for recognition? [J].

Auweter, Sigrid D. ;

Oberstrass, Florian C. ;

Allain, Frederic H. -T. .

NUCLEIC ACIDS RESEARCH, 2006, 34 (17) :4943-4959

[3]

Deciphering the splicing code [J].

Barash, Yoseph ;

Calarco, John A. ;

Gao, Weijun ;

Pan, Qun ;

Wang, Xinchen ;

Shai, Ofer ;

Blencowe, Benjamin J. ;

Frey, Brendan J. .

NATURE, 2010, 465 (7294) :53-59

[4]

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences [J].

Berger, Michael F. ;

Badis, Gwenael ;

Gehrke, Andrew R. ;

Talukder, Shaheynoor ;

Philippakis, Anthony A. ;

Pena-Castillo, Lourdes ;

Alleyne, Trevis M. ;

Mnaimneh, Sanie ;

Botvinnik, Olga B. ;

Chan, Esther T. ;

Khalid, Faiqua ;

Zhang, Wen ;

Newburger, Daniel ;

Jaeger, Savina A. ;

Morris, Quaid D. ;

Bulyk, Martha L. ;

Hughes, Timothy R. .

CELL, 2008, 133 (07) :1266-1276

[5]

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors [J].

Berger, Michael F. ;

Bulyk, Martha L. .

NATURE PROTOCOLS, 2009, 4 (03) :393-411

[6]

The quaking family of RNA-binding proteins Coordinators of the cell cycle and differentiation [J].

Biedermann, Bjoern ;

Hotz, Hans-Rudolf ;

Ciosk, Rafal .

CELL CYCLE, 2010, 9 (10) :1929-1933

[7]

Genome-wide Analysis of Alternative Pre-mRNA Splicing and RNA-Binding Specificities of the Drosophila hnRNP A/B Family Members [J].

Blanchette, Marco ;

Green, Richard E. ;

MacArthur, Stewart ;

Brooks, Angela N. ;

Brenner, Steven E. ;

Eisen, Michael B. ;

Rio, Donald C. .

MOLECULAR CELL, 2009, 33 (04) :438-449

[8]

Conservation of an RNA regulatory map between Drosophila and mammals [J].

Brooks, Angela N. ;

Yang, Li ;

Duff, Michael O. ;

Hansen, Kasper D. ;

Park, Jung W. ;

Dudoit, Sandrine ;

Brenner, Steven E. ;

Graveley, Brenton R. .

GENOME RESEARCH, 2011, 21 (02) :193-202

[9]

RNA-BINDING SPECIFICITY OF HNRNP A1 - SIGNIFICANCE OF HNRNP A1 HIGH-AFFINITY BINDING-SITES IN PRE-MESSENGER-RNA SPLICING [J].

BURD, CG ;

DREYFUSS, G .

EMBO JOURNAL, 1994, 13 (05) :1197-1204

[10]

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins [J].

Castello, Alfredo ;

Fischer, Bernd ;

Eichelbaum, Katrin ;

Horos, Rastislav ;

Beckmann, Benedikt M. ;

Strein, Claudia ;

Davey, Norman E. ;

Humphreys, David T. ;

Preiss, Thomas ;

Steinmetz, Lars M. ;

Krijgsveld, Jeroen ;

Hentze, Matthias W. .

CELL, 2012, 149 (06) :1393-1406

← 1 2 3 4 5 →