N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

Abstract

RNA modifications are integral to the regulation of RNA metabolism. One abundant mRNA modification is N6-methyladenosine (m6A), which affects various aspects of RNA metabolism, including splicing, translation and degradation. Current knowledge about the proteins recruited to m6A to carry out these molecular processes is still limited. Here we describe comprehensive and systematic mass-spectrometry-based screening of m6A interactors in various cell types and sequence contexts. Among the main findings, we identified G3BP1 as a protein that is repelled by m6A and positively regulates mRNA stability in an m6A-regulated manner. Furthermore, we identified FMR1 as a sequence-context-dependent m6A reader, thus revealing a connection between an mRNA modification and an autism spectrum disorder. Collectively, our data represent a rich resource and shed further light on the complex interplay among m6A, m6A interactors and mRNA homeostasis.

The m6A‐epitranscriptomic signature in neurobiology: from neurodevelopment to brain plasticity

“…; Edupuganti et al . ). Thus, RNA processing can be modulated by m6A through either recruitment or repulsion of specific RBPs.…”

“…, ; Edupuganti et al . ). Co‐regulation of m6A and hnRNPs in vivo has also been validated by their overlapping binding sites in the transcriptome (Alarcón et al .…”

“…; Edupuganti et al . ). An in vivo association is supported by co‐immunoprecipitation of m6A‐containing mRNAs in the FMRP pull‐down sample.…”

Nuclear TARBP2 drives oncogenic dysregulation of RNA splicing and decay

“…We note that this analysis was limited to proteins with available CLIP-seq data, and therefore does not include all known m 6 A binding proteins. This analysis identified SRSF1 (Serine and arginine rich splicing factor 1), a major modulator of both premRNA splicing and alternative splicing (Das and Krainer, 2014), and a factor that exhibits decreased binding to methylated RNA (Edupuganti et al, 2017), as a top candidate. As shown in Figure 3G, our analysis of SRSF1 CLIP-seq data (Van Nostrand et al, 2016) revealed a highly significant overlap between SRSF1-bound and TARBP2-bound targets.…”

“…Based on this model, it is plausible that pre-mRNA m 6 A marks may modulate local binding of regulators of the splicing machinery. To address this possibility, we compiled a list of RNA-binding proteins that differentially bind methylated RNA (Alarcón et al, 2015b;Edupuganti et al, 2017;Liu et al, 2015). We then systematically analyzed the distribution of binding sites of each RBP (derived from CLIP-seq data and known RBP binding motifs, 33 RBPs were included in this analysis) to determine if each candidate RBP binds to introns (and their flanking exons) that are also bound by TARBP2 and/or contain m6A marks.…”