SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing [RNA-seq I]

In this study, we identified SFSWAP as a negative regulator of O-GlcNAc transferase (OGT) intron 4 detention and global pre-mRNA splicing using a CRISPR knockout screen in an O-GlcNAc responsive GFP reporter cell line. In order to characterize the functions of the protein, we performed siRNA mediated knockdown of SFSWAP followed by RNA-seq analysis under untreated conditions. Alternate splicing analysis using rMATS (and other tools) revealed enhanced splicing of retained introns and increased inclusion of cassette exons upon knockdown of SFSWAP, supporting an inhibitory role for SFSWAP in splicing. Overall design: RNA-seq was performed in biological triplicates in either siNT (non-target) or siSFSWAP (SFSWAP knockdown) cells. Knockdowns were done for 5 days and cells were left untreated.