Identification of two short peptide motifs from serine/arginine-rich protein ribonucleic acid recognition motif-1 domain acting as splicing regulators

PeerJ. 2023 Sep 18:11:e16103. doi: 10.7717/peerj.16103. eCollection 2023.

Abstract

Background: Serine/arginine-rich (SR) proteins regulate pre-mRNA splicing. However, structurally similar proteins often behave differently in splicing regulation and the underlying mechanisms are largely unknown. Here, using SMN1/2 minigenes we extensively analyzed four SR proteins, SRSF1/5/6/9.

Methods: In this study, the effects of these proteins on SMN1/2 exon 7 splicing when tethered at either intron 6 or 7 were evaluated using an MS2-tethering assay. Deletion analysis in four SR proteins and co-overexpression analysis were performed.

Results: Splicing outcomes varied among all four SR proteins, SRSF1 and SRSF5 function the same at the two sites, acting as repressor and stimulator, respectively; while SRSF6 and SRSF9 promote exon 7 inclusion at only one site. Further, the key domains of each SR proteins were investigated, which identified a potent inhibitory nonapeptide in the C-terminus of SRSF1/9 ribonucleic acid recognition motif-1 (RRM1) and a potent stimulatory heptapeptide at the N-terminus of SRSF5/6 RRM1.

Conclusion: The insight of the four SR proteins and their domains in affecting SMN gene splicing brings a new perspective on the modes of action of SR proteins; and the functional peptides obtained here offers new ideas for developing splice switching-related therapies.

Keywords: Pre-mRNA splicing; RRM; SMN1/2; SR protein; Short peptide motifs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arginine / chemistry
  • Peptides / metabolism
  • Proteins / metabolism
  • RNA Splicing / genetics
  • RNA* / metabolism
  • Serine* / chemistry

Substances

  • RNA
  • Serine
  • Proteins
  • Peptides
  • Arginine

Grants and funding

This work was supported by the National Natural Science Foundation of China (grants 81271423, 81471298 and 81530035) and the, China Postdoctoral Science Foundation (grants 2021M691629). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.