Extended Data Fig. 8. Histone genes have a promoter with TATA-box and CCAAT-box motifs and do not require BRD4 for productive transcription.

a, Gene ontology term enrichment for genes with promoters containing both TATA-box and CCAAT-box motifs. Top 5 terms for cellular compartment (top), molecular function (middle) and biological process (bottom) categories are shown. Bars show fold-enrichment and are colored according to the P-value of the one-sided hypergeometric test. b, Occurrence of TATA- and CCAAT-boxes in histone genes promoters relative to TSSs. c, Loci of the histone genes HIST1H2BJ and HIST1H2AG (left) and ribosomal protein gene RPS9 (right) with nascent transcription (normalized PRO-seq signal for merged replicates) in BRD4- and MED14-AID cells with and without auxin treatment. While RPS9 shows typical pause release defect with loss of RNA polymerase II signal throughout the gene body and increase at the promoter, the two histone genes do not lose signal in the gene body and still have high levels of actively elongating RNA polymerase II. d, Log2 fold-change of endogenous nascent transcription for histone genes from previously published datasets. Left: SLAM-seq in different cell lines upon rapid BRD4 degradation via AID system or BRD4 inhibition by JQ1 (from ref. ³³); Right: NET-seq in MOLT4 cell line upon BRD4 inhibition by JQ1 or dBET6 (from ref. ³²). e, STARR-seq signal enrichment over input in BRD4-AID cell line separated by strand for enhancers overlapping TATA-box promoters (N=190), distal enhancers not overlapping promoters (N=4917) and random inactive regions (negative control; N=5151). Sense strand corresponds to orientation of the gene for enhancers overlapping promoters and is randomly assigned for distal enhancers and random regions. In d and e, boxes: median and interquartile range; whiskers: 5th and 95th percentiles. f, Examples of STARR-seq enhancers overlapping TATA-box promoters with evidence of endogenous initiation (CAGE): promoter of the MMP13 gene (left) and an instance of LTR12 repeat element (right). STARR-seq signal in BRD4-AID cell line and input library coverage is shown for + and − strands separately. Fragments from both strands are enriched over input, i.e. these promoter-overlapping fragments work as enhancers in both orientations.