Genomewide CRISPR/Cas9 Screen Identifies Network of Repressor Complexes That Regulate TRIM24

TRIM24 is an oncogenic chromatin reader that is frequently overexpressed in human tumors and associated with poor prognosis. However, TRIM24 is rarely mutated, duplicated, or rearranged in cancer. This raises questions about how TRIM24 is regulated and whether changes in its regulation are responsible for its activity in cancer. Here, we perform a genomewide CRISPR/Cas9 screen by fluorescence activated cell sorting (FACS) that nominated 220 negative regulators and elucidated a regulatory network that includes the KAP1 corepressor, CNOT deadenylase, and GID/CTLH E3 ligase. Knocking out required components of these three complexes caused TRIM24 overexpression, confirming their negative regulation of TRIM24. Our findings identify regulators of TRIM24 that nominate previously unexplored contexts for this oncoprotein in biology and disease. These findings were enabled by a new scoring system designed and vetted in our study as a broadly applicable tool for analysis of CRISPR screens performed by FACS.Funding Information: This study was supported by National Institutes of Health grant RO1 CA214871 and a research award from the Emerson Collective to MCB. LRP was funded by the John J Kopchick fellowship and by the National Center for Advancing Translational Sciences of the National Institutes of Health under Award Numbers TL1TR003169 and UL1TR003167. Sequencing was performed at MD Anderson Cancer Center Science Park Next-Generation Sequencing Facility supported by CPRIT Core Facility Support Grants (RP120348 and RP170002). The Flow Cytometry and Cell Imaging Core shared resource is partially funded by NCI Cancer Center Support Grant P30CA16672.Conflict of Interests: None to declare.