GSE201033
Genomic Profiling of MYC in 797 cells containing BRD4-NUT with JQ1 treatment
The oncogene cMYC (HGNC ID: HGNC:7553) is a critical genomic target of the BRD4-NUT (B4N) protein that defines many of the NUTM1-rearrangement cancer subtypes.  B4N interacts with the EP300 lysine acetyltransferase (KAT) to create hyperacetylated “megadomains” that activate downstream genes such as MYC. However, it is less well understood how mis-regulation of MYC in turn affects its protein interactions and target genes.  The goals of this study are to define the protein and genomic interactions of MYC in NUT carcinoma, and to test whether those change in response to B4N inactivation.  We used CRISPR-Cas9 mediated knock-in of a BioTAP affinity tag to analyze MYC protein expressed from its normal chromosomal context.  This allowed us to adapt a crosslinking purification method termed BioTAP-XL to preserve MYC integrity and chromatin association for genomic and mass spectrometry-based proteomic analyses.  We found that MYC interacts primarily with NuA4 KAT subunits and that the interactions were maintained despite a decrease in MYC levels after JQ1 treatment. We propose that future analysis of MYC transcriptional regulation in NUT carcinoma, and likely other cancers, should prioritize how MYC recruits KAT complexes to modify the chromatin of its many gene targets. Overall design: Chromatin immunoprecipitation of MYC-BioTAP in 797 cells containing the BRD4-NUT fusion protein treated with DMSO or JQ1