Enhanced phase separation of BRD4S derived from CDK12 inactivation-induced IPA drives cancer metastasis

CDK12 gene is frequently deleted/mutated in human cancers and CDK12 loss associates with intronic polyadenylation (IPA). Here, we show that CDK12 deficiency induces IPA usage in BRD4 gene locus and expression of the BRD4 short form (BRD4S). Different from the full-length BRD4 (BRD4L) that possesses a C-terminal intrinsically disordered region (IDR), surprisingly, BRD4S has a greater capacity to form phase separation in a manner dependent on oligomerization mediated by a base-interacting structural domain (BID). Through CUT&Tag profiling, we identify BRD4S specifically binds to the promoters of and transcriptionally upregulates TGF-ß signaling genes including TGFB2 and LTBP1. Our study identifies IPA usage at the BRD4 gene locus as a previously unrecognized mechanism responsible for BRD4S genesis. Our findings also reveal an essential role of BRD4S condensation formation and a unique ability of BRD4S to turn on TGF-ß signaling gene expression. Overall design: Genome-wide binding profiling of BRD4L and BRD4S by CUT&Tag in OVCAR8 cells ectopically expressing FLAG-tagged BRD4L or BRD4S individually.