SAM homeostasis is regulated by CFI-mediated splicing of MAT2A.

S-adenosylmethionine (SAM) is the methyl donor for nearly all cellular methylation events. Cells regulate intracellular SAM levels through intron detention of MAT2A, the only SAM synthetase expressed in most cells. The N-adenosine methyltransferase METTL16 promotes splicing of the MAT2A detained intron by an unknown mechanism. Using an unbiased CRISPR knock-out screen, we identified CFI25 (NUDT21) as a regulator of MAT2A intron detention and intracellular SAM levels. CFI25 is a component of the cleavage factor Im (CFI) complex that regulates poly(A) site selection, but we show it promotes MAT2A splicing independent of poly(A) site selection. CFI25-mediated MAT2A splicing induction requires the RS domains of its binding partners, CFI68 and CFI59 as well as binding sites in the detained intron and 3´ UTR. These studies uncover mechanisms that regulate MAT2A intron detention and reveal a previously undescribed role for CFI in splicing and SAM metabolism.