N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions

Nature. 2015 Feb 26;518(7540):560-4. doi: 10.1038/nature14234.

Abstract

RNA-binding proteins control many aspects of cellular biology through binding single-stranded RNA binding motifs (RBMs). However, RBMs can be buried within their local RNA structures, thus inhibiting RNA-protein interactions. N(6)-methyladenosine (m(6)A), the most abundant and dynamic internal modification in eukaryotic messenger RNA, can be selectively recognized by the YTHDF2 protein to affect the stability of cytoplasmic mRNAs, but how m(6)A achieves its wide-ranging physiological role needs further exploration. Here we show in human cells that m(6)A controls the RNA-structure-dependent accessibility of RBMs to affect RNA-protein interactions for biological regulation; we term this mechanism 'the m(6)A-switch'. We found that m(6)A alters the local structure in mRNA and long non-coding RNA (lncRNA) to facilitate binding of heterogeneous nuclear ribonucleoprotein C (HNRNPC), an abundant nuclear RNA-binding protein responsible for pre-mRNA processing. Combining photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) and anti-m(6)A immunoprecipitation (MeRIP) approaches enabled us to identify 39,060 m(6)A-switches among HNRNPC-binding sites; and global m(6)A reduction decreased HNRNPC binding at 2,798 high-confidence m(6)A-switches. We determined that these m(6)A-switch-regulated HNRNPC-binding activities affect the abundance as well as alternative splicing of target mRNAs, demonstrating the regulatory role of m(6)A-switches on gene expression and RNA maturation. Our results illustrate how RNA-binding proteins gain regulated access to their RBMs through m(6)A-dependent RNA structural remodelling, and provide a new direction for investigating RNA-modification-coded cellular biology.

Publication types

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

MeSH terms

  • Adenosine / analogs & derivatives*
  • Adenosine / metabolism
  • Alternative Splicing / genetics
  • Base Sequence
  • Cross-Linking Reagents
  • HEK293 Cells
  • HeLa Cells
  • Heterogeneous-Nuclear Ribonucleoprotein Group C / metabolism*
  • Humans
  • Immunoprecipitation
  • Nucleic Acid Conformation*
  • Nucleotide Motifs
  • Protein Binding
  • RNA, Messenger / analysis
  • RNA, Messenger / chemistry*
  • RNA, Messenger / metabolism*
  • Transcriptome

Substances

  • Cross-Linking Reagents
  • Heterogeneous-Nuclear Ribonucleoprotein Group C
  • RNA, Messenger
  • N6-methyladenosine (m6A)
  • Adenosine

Associated data

  • GEO/GSE56010