Alternative splicing of precursor messenger RNAs (pre-mRNAs) contributes not only to proteome diversity but also to regulation of gene expression levels by generating mRNA isoforms with a premature termination codon (PTC). Such unproductively spliced mRNAs are unstable and almost undetectable due to an mRNA surveillance system termed nonsense-mediated mRNA decay (NMD). In order to elucidate a repertoire of mRNAs regulated by alternative splicing coupled with NMD (AS-NMD), we performed long-read RNA sequencing of poly(A)+ RNAs from an NMD-deficient mutant,
smg-2, and obtained full-length sequences for mRNA isoforms from 259 high-confidence AS-NMD genes. Gene ontology (GO) analysis revealed enrichment of genes related to metabolism in addition to those related to RNA translation and processing. Among them are S-adenosyl-L-methionine (SAM) synthetase (sams) genes. SAM synthetase activity negatively autoregulates sams gene expression through AS-NMD. METT-10, the orthologue of human U6 snRNA methyltransferase METTL16, is required for the splicing regulation of the sams genes in vivo and specifically methylates in vitro the invariant AG dinucleotide at the distal 3' splice site (3'SS) used for the productive mRNAs. RNA immunoprecipitation with anti-
m6A antibody and direct RNA sequencing with Nanopore technologies coupled with machine learning confirmed
m6A modification of endogenous sams mRNAs. These results indicate that homeostasis of SAM synthetase in C. elegans is maintained by alternative splicing regulation through
m6A modification at the 3'SS of the sams genes.