NUDT21 regulates intron detention of the SAM synthetase MAT2A RNA

NUDT21 encodes the CFIm25 protein, a component of the CFIm complex that regulates alternative polyadenylation (APA). Our data suggest that the CFIm complex also induces splicing of a detained intron in the the S-adenosylmethionine (SAM) synthetase MAT2A to control intracellular levels of SAM. To genetically separate these functions, we used poly(A) Click-seq (PAC-seq) to determine the changes in poly(A) site selection in two cell lines. The parental cell line is the colorectal cell line HCT116 and a derivative line that has the detained intron of MAT2A deleted in both alleles of MAT2A (116-DDI). We found few differences in alternative polyadenylation after CFIm25 depletion were similar supporting teh conclusion that CFIm's role in APA is mechanistically distinct from its role in regulation of MATA splicing. Overall design: We used siRNAs to knockdown NUDT21/CFIm25 expression for four days in either the parental HCT116 cell line or in 116-?DI cells. A nontargeting (NT) siRNA was used as a control. We then performed PAC-seq with ClickSeq Technologies (Galveston, TX) to analyze changes in APA. Three independent biological replicates were performed.