N-6-methyladenosine (m6A) Promotes the Nuclear Retention of mRNAs with Intact 5’ Splice Site Motifs

Abstract

AbstractIn eukaryotes, quality control of mRNA represents an important regulatory mechanism for gene expression. Misprocessed mRNAs that contain an intact 5’ Splice Site (5’SS) motif are retained in the nucleus and targeted for decay. Previously, we showed that the nuclear retention of these transcripts requires ZFC3H1, a component of the Poly(A) Exosome Targeting (PAXT) complex, and U1-70K, a component of the U1 snRNP. InS. pombe, the ZFC3H1 homolog, Red1, binds to the YTH-domain containing protein Mmi1 to target certain RNA transcripts for nuclear retention and decay. Here we show that ZFC3H1 and U1-70K interact with YTHDC1 and YTHDC2, two YTH domain-containing proteins that bind to N-6-methyladenosine (m6A) modified RNAs. We then show that YTHDC1 and YTHDC2 are required for the nuclear retention of mRNAs with intact 5’SS motifs. Furthermore, disruption of m6A methyltransferase activity inhibits the nuclear retention of these transcripts. Using m6A-miCLIP analysis, we map m6A methylation marks to intronic polyadenylated (IPA) transcripts, which contain intact 5’SS motifs and are nuclear retained and degraded in a ZFC3H1-dependent manner. We find that m6A is enriched near intact 5’SS motifs and the poly(A)-tail. Overall, this work suggests that the m6A modification acts as part of an evolutionarily conserved quality control mechanism that targets misprocessed mRNAs for nuclear retention and decay.