Constitutive patterns of gene expression regulated by RNA-binding proteins

Genome Biol. 2014 Jan 2;15(1):R13. doi: 10.1186/gb-2014-15-1-r13.

Abstract

Background: RNA-binding proteins regulate a number of cellular processes, including synthesis, folding, translocation, assembly and clearance of RNAs. Recent studies have reported that an unexpectedly large number of proteins are able to interact with RNA, but the partners of many RNA-binding proteins are still uncharacterized.

Results: We combined prediction of ribonucleoprotein interactions, based on catRAPID calculations, with analysis of protein and RNA expression profiles from human tissues. We found strong interaction propensities for both positively and negatively correlated expression patterns. Our integration of in silico and ex vivo data unraveled two major types of protein-RNA interactions, with positively correlated patterns related to cell cycle control and negatively correlated patterns related to survival, growth and differentiation. To facilitate the investigation of protein-RNA interactions and expression networks, we developed the catRAPID express web server.

Conclusions: Our analysis sheds light on the role of RNA-binding proteins in regulating proliferation and differentiation processes, and we provide a data exploration tool to aid future experimental studies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • ELAV-Like Protein 1 / genetics
  • ELAV-Like Protein 1 / metabolism
  • Gene Expression Regulation*
  • Humans
  • Immunoprecipitation
  • Protein Interaction Domains and Motifs
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*
  • Sequence Analysis, RNA
  • Transcriptome

Substances

  • ELAV-Like Protein 1
  • ELAVL1 protein, human
  • LIN28B protein, human
  • RNA, Messenger
  • RNA-Binding Proteins