For ChIP-seq, HeLa cells were crosslinked with 1% paraformaldehyde for 10 minutes and were quenched by glycine for 5 minutes at room temperature. Fixed chromatin was sonicated with a Misionix sonicator 3000 and immunoprecipitated with a specific antibody. ChIP-sequencing libraries were prepared with Illumina’s Tru-seq DNA sample prep kit using standard protocols. Nascent RNA-seq libraries were prepared with Illumina’s Ribo-Zero Gold and TruSeq RNA sample Prep Kit using standard protocols.