CRISPR screen identifies NUDT21 as a regulator of intron detention of the SAM synthetase MAT2A RNA

The only S-adenosymethionine (SAM) synthetase expressed in most human cells, MAT2A, is regulated by intron detention. Using a GFP fusion reporter, we conducted a CRISPR screen to identify regulators of this alternative splicing event. The screen identified METTL16, a known regulator of this process, and NUDT21. NUDT21 encodes the CFIm25 protein a member of the CFIm complex involved in alternative polyadenylation. Validation and follow-up studies support the idea that CFIm25 and the larger CFIm complex plays an unanticipated role in splicing of the MAT2A detained intron. Overall design: We generated a GFP reporter containng the MAT2A detained intron that responds to SAM depletion by increasing splicing, and therefore GFP signal. Using the Brunello knockout CRISPR lentivirus library (Doench et al. 2016; Addgene #73179), we looked for genes that were necessary for GFP induction upon SAM depletion. We performed three replicates of the screen and compared the sgRNAs found in sorted cells (those with low GFP signal) to sgRNAs found in the unselected pool of cells. In the data below, the samples called "sort2-4" are the selected cells and the unselected control are referred to as the "input2-4". The sequencing data were then analyzed by MAGeCK (Li et al. 2014).