BRD4 ChIP

Single end 50-bp reads were filtered using TagDust (Lassmann et al., 2009) as above and aligned to hg19 using Bowtie (Langmead et al., 2009) as described for H4a ChIP. Peaks were called with MACS2 callpeak (Zhang et al., 2008) using default parameters. BED-Tools (Quinlan and Hall, 2010) was used to merge overlapping peaks between replicates and across treatments to identify shared and unique peaks. Enrichment for genomic features was analyzed using CEAS (Shin et al., 2009). Each peak was matched with its closest genes within 1000 kb using the Genomic Regions Enrichment of Annotations Tool (GREAT) (McLean et al., 2010). Genes were matched to differentially expressed genes from RNA-seq. Genes with BRD4 signal within gene bodies were identified as previously described for H4ac.