TFIIIC and MYCN link the three-dimensional chromatin structure of promoters to transcription termination of stalled RNA polymerase (ChIPseq CnR)

MYC proteins bind to virtually all active promoters transcribed by RNA polymerase II (RNAPII), but whether they interact with the three-dimensional chromatin architecture is unknown. Here we used HiChIP sequencing of the MYCN oncoprotein and found that MYCN localizes to three-dimensional hubs formed by active promoters and enhancers. In these hubs, MYCN interacts with TFIIIC, an architectural protein complex. MYCN recruits TFIIIC to promoters when transcription elongation is inhibited, and the complex of both proteins induces premature transcription termination. Termination correlates closely with the TFIIIC-dependent removal of MYCN from promoter hubs and with corresponding alterations in the three-dimensional interactions of cohesin complexes. This limits DNA damage by removing RNAPII that stalls proximal to double-strand breaks. Binding of TFIIIC to MYCN is limited by competition with Aurora-A and this protects genes involved in mRNA processing from termination, arguing that MYCN contributes to the unusual proliferative capacity of neuroblastoma cells via removing stalled RNAPII from promoter hubs and via increasing the capacity for RNA processing. Overall design: CUT&RUN, ChIP and ChIP-Rx DNA-sequencing was done with SH-EP NMYC-ER cells where the NMYC expression can be induced with 4-OHT. For all CUT&Run sequencing and some ChIP-seq and ChIP-Rx sequencing experiments, SH-EP NMYC-ER cells were used that carry a doxycycline inducible shRNA against TF3C5. For CUT&Run sequencing samples, the immunoprecipitation of digested DNA was done for EXOSC5 with or without NMYC expression and with or without expression of shTF3C5. As control, DNA was sequenced following immunoprecipitation with an unspecific IgG antibody. For ChIP-seq and ChIP-Rx sequencing experiments, the immunopresipitated antibodies are listed below. All experiments were done with or without NMYC expression and where indicated, a shRNA targeting TF3C5 was induced via doxycycline or one of the below listed inhibitors was applied.