m⁶A‐mediated alternative splicing coupled with nonsense‐mediated mRNA decay regulates SAM synthetase homeostasis

Abstract

Alternative splicing of pre-mRNAs can regulate gene expression levels by coupling with nonsense-mediated mRNA decay (NMD). In order to elucidate a repertoire of mRNAs regulated by alternative splicing coupled with NMD (AS-NMD) in an organism, we performed long-read RNA sequencing of poly(A) + RNAs from an NMD-deficient mutant strain of Caenorhabditis elegans, and obtained full-length sequences for mRNA isoforms from 259 highconfidence AS-NMD genes. Among them are the S-adenosyl-L-methionine (SAM) synthetase (sams) genes sams-3 and sams-4. SAM synthetase activity autoregulates sams gene expression through AS-NMD in a negative feedback loop. We furthermore find that METT-10, the orthologue of human U6 snRNA methyltransferase METTL16, is required for the splicing regulation in vivo, and specifically methylates the invariant AG dinucleotide at the distal 3 0 splice site (3 0 SS) in vitro. Direct RNA sequencing coupled with machine learning confirms m 6 A modification of endogenous sams mRNAs. Overall, these results indicate that homeostasis of SAM synthetase in C. elegans is maintained by alternative splicing regulation through m 6 A modification at the 3 0 SS of the sams genes.

The Prognostic Role of m6A-Related Genes in Paediatric Neuroblastoma Patients

“…In the studies of four endocrine tumors, the expression level of METTL16 was positively correlated with overall survival. It was observed that METTL16 plays an important role in the development of endocrine system tumors, and METTL16 is a protective gene [ 20 ]. Nevertheless, several limitations should be noted.…”

Functional interplay within the epitranscriptome: Reality or fiction?

“…Methylation at this site prevents the binding of the splicing factor U2AF65 and thereby alters the proper splicing of SAM synthetase. [113,114] While the sam pre-mRNA is not regulated in this fashion in mammals, the mechanism of splicing inhibition by 3′ss-m 6 A appears conserved. More studies are needed to decipher to which extent this mechanism participates in splicing regulation in higher eukaryotes and if an interplay with RNA editing occurs.…”

The XRN1-regulated RNA helicase activity of YTHDC2 ensures mouse fertility independently of m6A recognition

“…Presence of the m 6 A methylation can have two major consequences: they can either repel proteins that would otherwise normally bind the unmethylated sequence or enable specific binding by ''reader'' proteins that can recognize the mark (Edupuganti et al, 2017). As an example of the former situation, 3 0 splice site m 6 A is shown to repel binding of the splicing factor U2AF35, inhibiting RNA splicing (Mendel et al, 2021;Watabe et al, 2021;Yoshida et al, 2020). However, much of the biology of m 6 A is believed to be mediated by ''reader'' proteins, with the conserved YTH family of proteins being the best studied (Patil et al, 2018;Stoilov et al, 2002;Zhang et al, 2010).…”