A compendium of RNA-binding motifs for decoding gene regulation

Debashish Ray, Hilal Kazan, Kate B. Cook, Matthew T. Weirauch, Hamed S. Najafabadi, Xiao Li, Serge Gueroussov, Mihai Albu, Hong Zheng, Ally Yang, Hong Na, Manuel Irimia, Leah H. Matzat, Ryan K. Dale, Sarah A. Smith, Christopher A. Yarosh, Seth M. Kelly, Behnam Nabet, Desirea Mecenas, Weimin LiRakesh S. Laishram, Mei Qiao, Howard D. Lipshitz, Fabio Piano, Anita H. Corbett, Russ P. Carstens, Brendan J. Frey, Richard A. Anderson, Kristen W. Lynch, Luiz O F Penalva, Elissa P. Lei, Andrew G. Fraser, Benjamin J. Blencowe, Quaid D. Morris, Timothy R. Hughes

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)172-177
Number of pages6
JournalNature
Volume499
Issue number7457
DOIs
StatePublished - 2013

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RNA-Binding Proteins
Genes
Eukaryota
Nucleotide Motifs
Regulator Genes
RNA-Binding Motifs
RNA
Gene Expression

ASJC Scopus subject areas

  • General

Cite this

Ray, D., Kazan, H., Cook, K. B., Weirauch, M. T., Najafabadi, H. S., Li, X., ... Hughes, T. R. (2013). A compendium of RNA-binding motifs for decoding gene regulation. Nature, 499(7457), 172-177. https://doi.org/10.1038/nature12311

A compendium of RNA-binding motifs for decoding gene regulation. / Ray, Debashish; Kazan, Hilal; Cook, Kate B.; Weirauch, Matthew T.; Najafabadi, Hamed S.; Li, Xiao; Gueroussov, Serge; Albu, Mihai; Zheng, Hong; Yang, Ally; Na, Hong; Irimia, Manuel; Matzat, Leah H.; Dale, Ryan K.; Smith, Sarah A.; Yarosh, Christopher A.; Kelly, Seth M.; Nabet, Behnam; Mecenas, Desirea; Li, Weimin; Laishram, Rakesh S.; Qiao, Mei; Lipshitz, Howard D.; Piano, Fabio; Corbett, Anita H.; Carstens, Russ P.; Frey, Brendan J.; Anderson, Richard A.; Lynch, Kristen W.; Penalva, Luiz O F; Lei, Elissa P.; Fraser, Andrew G.; Blencowe, Benjamin J.; Morris, Quaid D.; Hughes, Timothy R.

In: Nature, Vol. 499, No. 7457, 2013, p. 172-177.

Research output: Contribution to journalArticle

Ray, D, Kazan, H, Cook, KB, Weirauch, MT, Najafabadi, HS, Li, X, Gueroussov, S, Albu, M, Zheng, H, Yang, A, Na, H, Irimia, M, Matzat, LH, Dale, RK, Smith, SA, Yarosh, CA, Kelly, SM, Nabet, B, Mecenas, D, Li, W, Laishram, RS, Qiao, M, Lipshitz, HD, Piano, F, Corbett, AH, Carstens, RP, Frey, BJ, Anderson, RA, Lynch, KW, Penalva, LOF, Lei, EP, Fraser, AG, Blencowe, BJ, Morris, QD & Hughes, TR 2013, 'A compendium of RNA-binding motifs for decoding gene regulation', Nature, vol. 499, no. 7457, pp. 172-177. https://doi.org/10.1038/nature12311
Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 2013;499(7457):172-177. https://doi.org/10.1038/nature12311
Ray, Debashish ; Kazan, Hilal ; Cook, Kate B. ; Weirauch, Matthew T. ; Najafabadi, Hamed S. ; Li, Xiao ; Gueroussov, Serge ; Albu, Mihai ; Zheng, Hong ; Yang, Ally ; Na, Hong ; Irimia, Manuel ; Matzat, Leah H. ; Dale, Ryan K. ; Smith, Sarah A. ; Yarosh, Christopher A. ; Kelly, Seth M. ; Nabet, Behnam ; Mecenas, Desirea ; Li, Weimin ; Laishram, Rakesh S. ; Qiao, Mei ; Lipshitz, Howard D. ; Piano, Fabio ; Corbett, Anita H. ; Carstens, Russ P. ; Frey, Brendan J. ; Anderson, Richard A. ; Lynch, Kristen W. ; Penalva, Luiz O F ; Lei, Elissa P. ; Fraser, Andrew G. ; Blencowe, Benjamin J. ; Morris, Quaid D. ; Hughes, Timothy R. / A compendium of RNA-binding motifs for decoding gene regulation. In: Nature. 2013 ; Vol. 499, No. 7457. pp. 172-177.
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