Abstract
Gene expression regulation is critical for cells to adapt to external changes and maintain their homeostasis. Transcription is an essential step in gene expression and is controlled by numerous factors and cofactors. One such cofactor is TRRAP, the largest subunit of two distinct chromatin-modifying complexes, SAGA and TIP60. TRRAP interacts with a diverse range of transcription factors including c-MYC and E2Fs, and mediates the recruitment of SAGA and TIP60 to gene promoters. TRRAP is a member of the PIKK family of atypical kinases. Prior studies defined the TTT co-chaperone as an essential regulator of PIKK stability and activity. In contrast to its cognate kinases, TRRAP lacks catalytic residues and is the sole pseudokinase among PIKKs. Although TTT has been shown to stabilize and interact with TRRAP, the role of TTT on TRRAP function remains unknown. Using an inducible degron system that allows the rapid and acute depletion of endogenous proteins, we demonstrated that TTT is required to assemble TRRAP within its functional complexes prior its nuclear import. Additionally, through transcriptomic analyses we determined that TTT regulates a large number of TRRAP-dependent genes in colorectal cancer cells. Profiling of the genome-wide binding of TRRAP via CUT&RUN-seq identified the direct targets of TRRAP, of which only a small fraction overlaps with MYC targets. We also uncovered a direct inhibitory role of TRRAP on a subset of the interferon-stimulated genes, which mediate the interferon response in the innate immune system. Altogether, our data suggest that TRRAP and its chaperone TTT are involved in tumorigenesis through the maintenance of a specific transcriptional program.