title: A compendium of RNA-binding motifs for decoding gene regulation.
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.
authors.affiliation: Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.
authors.forename: Debashish
authors.initials: D
authors.lastname: Ray
authors.forename: Hilal
authors.initials: H
authors.lastname: Kazan
authors.forename: Kate B
authors.initials: KB
authors.lastname: Cook
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Weirauch
authors.forename: Hamed S
authors.initials: HS
authors.lastname: Najafabadi
authors.forename: Xiao
authors.initials: X
authors.lastname: Li
authors.forename: Serge
authors.initials: S
authors.lastname: Gueroussov
authors.forename: Mihai
authors.initials: M
authors.lastname: Albu
authors.forename: Hong
authors.initials: H
authors.lastname: Zheng
authors.forename: Ally
authors.initials: A
authors.lastname: Yang
authors.forename: Hong
authors.initials: H
authors.lastname: Na
authors.forename: Manuel
authors.initials: M
authors.lastname: Irimia
authors.forename: Leah H
authors.initials: LH
authors.lastname: Matzat
authors.forename: Ryan K
authors.initials: RK
authors.lastname: Dale
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Smith
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Yarosh
authors.forename: Seth M
authors.initials: SM
authors.lastname: Kelly
authors.forename: Behnam
authors.initials: B
authors.lastname: Nabet
authors.forename: Desirea
authors.initials: D
authors.lastname: Mecenas
authors.forename: Weimin
authors.initials: W
authors.lastname: Li
authors.forename: Rakesh S
authors.initials: RS
authors.lastname: Laishram
authors.forename: Mei
authors.initials: M
authors.lastname: Qiao
authors.forename: Howard D
authors.initials: HD
authors.lastname: Lipshitz
authors.forename: Fabio
authors.initials: F
authors.lastname: Piano
authors.forename: Anita H
authors.initials: AH
authors.lastname: Corbett
authors.forename: Russ P
authors.initials: RP
authors.lastname: Carstens
authors.forename: Brendan J
authors.initials: BJ
authors.lastname: Frey
authors.forename: Richard A
authors.initials: RA
authors.lastname: Anderson
authors.forename: Kristen W
authors.initials: KW
authors.lastname: Lynch
authors.forename: Luiz O F
authors.initials: LO
authors.lastname: Penalva
authors.forename: Elissa P
authors.initials: EP
authors.lastname: Lei
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Fraser
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Blencowe
authors.forename: Quaid D
authors.initials: QD
authors.lastname: Morris
authors.forename: Timothy R
authors.initials: TR
authors.lastname: Hughes
mesh_terms: D001321:Autistic Disorder / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D005057:Eukaryotic Cells / Q000378:metabolism; D005786:Gene Expression Regulation / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs / Q000235:genetics*; D017434:Protein Structure, Tertiary / Q000235:genetics; D000072260:RNA Splicing Factors; D020871:RNA Stability / Q000235:genetics; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: C455479:RBFOX1 protein, human; D000072260:RNA Splicing Factors; D016601:RNA-Binding Proteins