library_construction_protocol: Nuclear input RNA and BrU IP RNA after nuclear run-on assay was extracted using TRIzol reagent (Ambion). The RNA samples were then treated with Turbo DNase using Turbo DNA-free kit (Invitrogen). Ribosomal RNA depletion and library preparation were done using KAPA Hyper RNA with Riboerase HMR kit following manufacturer's protocols.