Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing

Mol Cell. 2016 Feb 18;61(4):507-519. doi: 10.1016/j.molcel.2016.01.012. Epub 2016 Feb 11.

Abstract

The regulatory role of N(6)-methyladenosine (m(6)A) and its nuclear binding protein YTHDC1 in pre-mRNA splicing remains an enigma. Here we show that YTHDC1 promotes exon inclusion in targeted mRNAs through recruiting pre-mRNA splicing factor SRSF3 (SRp20) while blocking SRSF10 (SRp38) mRNA binding. Transcriptome assay with PAR-CLIP-seq analysis revealed that YTHDC1-regulated exon-inclusion patterns were similar to those of SRSF3 but opposite of SRSF10. In vitro pull-down assay illustrated a competitive binding of SRSF3 and SRSF10 to YTHDC1. Moreover, YTHDC1 facilitates SRSF3 but represses SRSF10 in their nuclear speckle localization, RNA-binding affinity, and associated splicing events, dysregulation of which, as the result of YTHDC1 depletion, can be restored by reconstitution with wild-type, but not m(6)A-binding-defective, YTHDC1. Our findings provide the direct evidence that m(6)A reader YTHDC1 regulates mRNA splicing through recruiting and modulating pre-mRNA splicing factors for their access to the binding regions of targeted mRNAs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine / analogs & derivatives
  • Adenosine / metabolism
  • Binding Sites
  • Cell Cycle Proteins / metabolism*
  • Exons
  • HeLa Cells
  • Humans
  • Nerve Tissue Proteins / metabolism*
  • RNA Splicing Factors
  • RNA Splicing*
  • RNA, Messenger / metabolism
  • RNA-Binding Proteins / metabolism*
  • Repressor Proteins / metabolism*
  • Serine-Arginine Splicing Factors

Substances

  • Cell Cycle Proteins
  • Nerve Tissue Proteins
  • RNA Splicing Factors
  • RNA, Messenger
  • RNA-Binding Proteins
  • Repressor Proteins
  • SRSF10 protein, human
  • SRSF3 protein, human
  • YTHDC1 protein, human
  • Serine-Arginine Splicing Factors
  • N(6)-methyladenosine
  • Adenosine