N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions

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. N6-methyladenosine (m6A), 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 m6A achieves its wide-ranging physiological role needs further exploration. Here we show in human cells that m6A controls the RNA-structure-dependent accessibility of RBMs to affect RNA–protein interactions for biological regulation; we term this mechanism ‘the m6A-switch’. We found that m6A 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-m6A immunoprecipitation (MeRIP) approaches enabled us to identify 39,060 m6A-switches among HNRNPC-binding sites; and global m6A reduction decreased HNRNPC binding at 2,798 high-confidence m6A-switches. We determined that these m6A-switch-regulated HNRNPC-binding activities affect the abundance as well as alternative splicing of target mRNAs, demonstrating the regulatory role of m6A-switches on gene expression and RNA maturation. Our results illustrate how RNA-binding proteins gain regulated access to their RBMs through m6A-dependent RNA structural remodelling, and provide a new direction for investigating RNA-modification-coded cellular biology.

• Publication year

  2015

• Venue

  Nature

• Publication date

  2015-02-19

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1038/nature14234PMID 25719671PMCID 4355918
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• m6A-switch-regulated HNRNPC binding affects both target mRNA abundance and alternative splicing.

  Confidence 0.93

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review
• Global m6A reduction decreased HNRNPC binding at 2,798 high-confidence m6A-switches.

  Confidence 0.94

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review
• Combining PAR-CLIP and MeRIP enabled identification of 39,060 m6A-switches among HNRNPC-binding sites.

  Confidence 0.95

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review
• m6A alters local RNA structure in mRNA and long non-coding RNA to facilitate HNRNPC binding.

  Confidence 0.96

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review
• m6A controls RNA-structure-dependent accessibility of RNA-binding motifs to modulate RNA-protein interactions.

  Confidence 0.97

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review

• alternative splicing

  process

  A post-transcriptional process that produces different mRNA isoforms from the same pre-mRNA.

  Aliases: splicing

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review
• global m6a reduction

  experimental perturbation

  An experimental perturbation that lowers the overall cellular level of m6A modification.

  Aliases: reduced m6A, m6A depletion

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review
• high-confidence m6a-switches

  site set

  A subset of m6A-switch sites supported strongly by the combined binding and modification data.

  Aliases: high-confidence switches

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review
• hnrnpc

  protein

  An abundant nuclear RNA-binding protein involved in pre-mRNA processing.

  Aliases: heterogeneous nuclear ribonucleoprotein C

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review
• m6a-switch

  mechanism

  A regulatory RNA element in which N6-methyladenosine changes local RNA structure to alter access of RNA-binding motifs to proteins.

  Aliases: m6A switch

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review
• merip

  method

  An anti-m6A immunoprecipitation method used to enrich and map m6A-modified RNAs.

  Aliases: anti-m6A immunoprecipitation, m6A immunoprecipitation

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review
• mrna abundance

  outcome

  The cellular level of messenger RNA measured as transcript abundance.

  Aliases: transcript abundance, mRNA levels

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review
• n6-methyladenosine (m6a)

  RNA modification

  An internal methylated adenosine modification present in eukaryotic RNA.

  Aliases: m6A, N6-methyladenosine

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review
• par-clip

  method

  A photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation method used to map RNA-protein interactions.

  Aliases: photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review
• rna-binding motifs

  molecular feature

  Short RNA sequence or structural motifs recognized by RNA-binding proteins.

  Aliases: RBMs, RNA binding motifs

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review
• rna structural remodeling

  process

  A change in local RNA folding or accessibility that can alter molecular recognition.

  Aliases: RNA structure change

  박진우 (dztg5apj7m) extractionKiller Whale (322360f1c1) reviewB (s683577b42) reviewq (76h6bfydm6) reviewjaeyoung (rb9u4m834j) review

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