Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets

RNA. 2014 Jul;20(7):1090-102. doi: 10.1261/rna.045005.114. Epub 2014 May 23.


Recent studies implicated the RNA-binding protein with multiple splicing (RBPMS) family of proteins in oocyte, retinal ganglion cell, heart, and gastrointestinal smooth muscle development. These RNA-binding proteins contain a single RNA recognition motif (RRM), and their targets and molecular function have not yet been identified. We defined transcriptome-wide RNA targets using photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) in HEK293 cells, revealing exonic mature and intronic pre-mRNA binding sites, in agreement with the nuclear and cytoplasmic localization of the proteins. Computational and biochemical approaches defined the RNA recognition element (RRE) as a tandem CAC trinucleotide motif separated by a variable spacer region. Similar to other mRNA-binding proteins, RBPMS family of proteins relocalized to cytoplasmic stress granules under oxidative stress conditions suggestive of a support function for mRNA localization in large and/or multinucleated cells where it is preferentially expressed.

Keywords: PAR-CLIP; RBPMS; RNA recognition element; RNA-binding protein.

Publication types

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

MeSH terms

  • Adult
  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Cells, Cultured
  • Female
  • Gene Expression Profiling*
  • HEK293 Cells
  • Humans
  • Male
  • Mice
  • Molecular Sequence Data
  • Multigene Family
  • Protein Binding
  • Protein Interaction Domains and Motifs* / genetics
  • RNA / genetics
  • RNA / metabolism*
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / metabolism*
  • Sequence Homology, Amino Acid
  • Transcriptome


  • RBPMS protein, human
  • RNA-Binding Proteins
  • RNA

Associated data

  • SRA/PRJNA241095
  • SRA/SRX484627
  • SRA/SRX484628