library_construction_protocol: Lysates were clarified from sonicated cells and RNAP2-DNA or RNA-DNA complexes were isolated with antibody. The crosslinks were reversed for the RNAP2 enriched material, purified, and for the TRIPn-Seq samples - sequencing adapters were ligated before the BrdU immunoprecipitation. Libraries were prepared according to NEBNext Ultra II DNA Library Prep Kit for Illumina.