MYC assembles and stimulates topoisomerases 1 & 2 in a “topisome” [CAD-seq]

High-intensity transcription and replication supercoil DNA to levels that can impede or halt these processes. As a potent transcription amplifier and replication accelerator, the proto-oncogene MYC must somehow manage these high levels of torsional stress. By comparing gene expression with the recruitment of topoisomerases and MYC to promoters, we surmised a direct association of MYC with Topoisomerases 1 (TOP1) and 2A (TOP2A) that was confirmed in vitro and in vivo. Beyond recruiting topoisomerases, MYC directly stimulates their activities in vitro and in vivo. We identify a MYC-nucleated “topoisome” complex that unites and increases the levels of both both TOP1 and TOP2, as well as their activities at promoters and enhancers. Whether TOP2A or TOP2B is included in the topoisome, is dictated by the presence of c-MYC or MYCN, respectively. Thus, in vivo and in vitro, MYC assembles tools that simplify DNA topology and promote genome function under high output conditions. To probe binding profiles of TOP2A, MYC and RNAPII chromatin immunoprecipitation sequencing (ChIP-seq) experiments were perfromed. ChIP-seq of TOP2A in TOP2A-FLAG HCT116 and MYC in asynchronous wild type HCT116 cells and ChIP-seq of MYC and RNAPII in asynchronous TOP1/TOP2A auxin inducible degron HCT116 cells (-mAID). For mapping of topoisomerase activity we designed CAD-seq method which enables mapping of topoisomerase cleavage complexes. TOP1cc CAD-seq was performed in K562 MYC-mAID cells. To pull down the "topisome" complex we designed cross CAD-seq method which involves trapping of TOP2A by etoposide treatment and then proceeding with a pull down against TOP1. TOP1cc cross-CAD-seq was performed in U2OS cell with and without MYC induction to look at the formation of the topisome. Please note that the processed data generated from both replicates is linked to the corresponding rep1 sample records.