A compendium of RNA-binding motifs for decoding gene regulation

Nature. 2013 Jul 11;499(7457):172-7. doi: 10.1038/nature12311.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Autistic Disorder / genetics
  • Base Sequence
  • Binding Sites / genetics
  • Conserved Sequence / genetics
  • Eukaryotic Cells / metabolism
  • Gene Expression Regulation / genetics*
  • Humans
  • Molecular Sequence Data
  • Nucleotide Motifs / genetics*
  • Protein Structure, Tertiary / genetics
  • RNA Splicing Factors
  • RNA Stability / genetics
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*

Substances

  • RBFOX1 protein, human
  • RNA Splicing Factors
  • RNA-Binding Proteins

Associated data

  • GEO/GSE41235