SAM homeostasis is regulated by CFI_m-mediated splicing of MAT2A

Abstract

SUMMARYS-adenosylmethionine (SAM) is the methyl donor for nearly all cellular methylation events. Cells regulate intracellular SAM levels through intron detention of the MAT2A RNA, which encodes only SAM synthetase expressed in most cells. The N6-adenosine methyltransferase METTL16 promotes splicing of the MAT2A detained intron by an unknown mechanism. Using an unbiased CRISPR knock-out screen, we identified CFIm25 (NUDT21) to be a regulator of MAT2A intron detention and intracellular SAM levels. CFIm25 is a component of the cleavage factor Im (CFIm) complex that regulates poly(A) site selection, but we show it promotes MAT2A splicing, independent of poly(A) site selection. CFIm25-mediated MAT2A splicing induction requires the RS domains of its binding partners, CFIm68 and CFIm59 as well as binding sites in detained intron and 3′ UTR. These studies uncover mechanisms that regulate MAT2A intron detention and reveal previously undescribed roles for CFIm in splicing and SAM metabolism.

Knockdown of METTL16 Disrupts Learning and Memory by Reducing the Stability of MAT2A mRNA

“…4A-B), which is consistent with the study by Pendleton et al [23]. It has been reported that METTL16 had a limited number of validated direct targets, including MAT2A mRNA, U6 snRNA and long non-coding RNA (lncRNA) MALAT [30,31], which distinguishes it from the METTL3/METTL14 complex, who modi es most m 6 A sites on RNA [24,32]. Therefore, the knockdown of METTL16 is unlikely to reduce the overall levels of m 6 A by directly affecting the number of m 6 A modi cations in its target RNAs.…”

“…METTL16 does not form complexes with other m 6 A methyltransferases, unlike METTL3 and METTL14, and has a limited number of m 6 A modi cation targets, including MAT2A mRNA, U6 snRNA, and lncRNA MALAT [30,31]. Interestingly, knockdown of METTL16 was found to reduce the overall levels of m 6 A [23],…”

Integrative Analysis of m6A Regulator-Mediated RNA Methylation Modification Patterns and Immune Characteristics in Lupus Nephritis

“…S-adenosylmethionine (SAM) is a methyl donor for almost all cell methylation events. Scarborough et al (2021) reported that NUDT21 regulates intracellular SAM levels. As shown, m 6 A RNA methylation modification plays a key role in mRNA splicing, suggesting that the m 6 A markers identified in this study are closely related to the m 6 A modification process.…”