The TRRAP transcription cofactor represses interferon-stimulated genes in colorectal cancer cells

Transcription is essential for cells to respond to signaling cues and involves factors with multiple distinct activities. One such factor, TRRAP, functions as part of two large complexes, SAGA and TIP60, which have essential roles during transcription activation. Structurally, TRRAP belongs to the family PIKKs but is the only member classified as a pseudokinase. Recent studies established that a dedicated HSP90 co-chaperone, the TTT complex, is essential for PIKK maturation and activity. Here we used endogenous auxin-inducible degron alleles to show that the TTT subunit TELO2 promotes TRRAP assembly into SAGA and TIP60 in human colorectal cancer cells (CRC). Transcriptomic analysis revealed that TELO2 contribute to TRRAP regulatory roles in CRC cells, most notably of MYC target genes. Surprisingly, TELO2 and TRRAP depletion also induced the expression of type I interferon genes. Using a combination of nascent RNA, antibody-targeted chromatin profiling (CUT&RUN) and kinetic analyses, we show that TRRAP directly represses the expression of IRF9, which is a master regulator of interferon stimulated genes. We have therefore uncovered a new, unexpected transcriptional repressor role for TRRAP, suggesting a previously unidentified mechanism by which TRRAP may contribute to tumorigenesis. mRNA profiles from HCT116 cells edited using CRISPR-Cas9 and treated with either NaOH or auxin were generated by deep sequencing, in triplicate, in one lane of either an Illumina HiSeq 2500 (TELO2-AID) or 4000 (AID-TRRAP), with 1x 50bp single reads.