Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

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.

Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

“…This likely coincides with differential transcriptional activities in rapidly dividing and differentiated cells, similar to observations from animal systems (Tillemans et al ., 2006; Spector & Lamond, 2011; Reddy et al ., 2012). Because m 6 A affects splicing in mammals and D. melanogaster (Liu et al ., 2014; Ping et al ., 2014; Alarcón et al ., 2015a; Haussmann et al ., 2016; Lence et al ., 2016) possibly by recruiting splicing factors (Xiao et al ., 2016), it is interesting to speculate whether m 6 A could also regulate splicing in plants. The rather normal splicing patterns observed in vir‐1 root tip suggests that m 6 A is not involved in large‐scale regulation of splicing in plants or that splicing regulation only occurs at the transcript or tissue‐specific level, which is below the detection limit of the root‐tip RNA‐Seq.…”

ALKBH1-Mediated tRNA Demethylation Regulates Translation

“…Defects of the m 6 A methyltransferase complex result in a battery of development problems in various eukaryotic species (Yue et al, 2015). The YTH domain proteins, the m 6 A readers, influence the stability, translation, and splicing of the m 6 A-containing mRNAs Wang et al, 2015;Xiao et al, 2016;Xu et al, 2014;Zhou et al, 2015).…”

Publisher's Note

“…While modifications have long been studied in the context of tRNA and rRNA, over the last 5-6 y there has been a renewed focus on mRNA modifications. The most well characterized, m 6 A, has now been shown to play a role in mRNA decay, 9 translation, 11,13 splicing, 5,15 and alternative polyadenylation, 80 the circadian clock, 81 stem cell differentiation, 82 and heat shock response, 12 among others. The transcriptome-wide distributions of other mRNA modifications such as C, m 1 A, and m 5 C have recently been mapped, and we will likely see more in the near future.…”

“…It will also be interesting to see whether other YTH domain-containing proteins show the same versatility: YTHDF1 binds m 6 A in mRNA and promotes translation initiation, 13 and recently YTHDC1 was shown to affect splicing as a nuclear m 6 A reader protein. 14,15 It remains to be seen what other functions these proteins may have in cells.…”

“…In the context of mRNA, the m 6 A-binding protein YTHDC1 has been implicated in splicing, 15 so it could represent another case in which an m 6 A-binding protein coordinates different cellular processes in different contexts.…”