Fig. 1

Overview of paused genes across multiple human and mouse cell types. a Estimation of a gene’s “pausing index” (PI) from RNAP2 ChIP-seq data. b Occurrence of paused genes across cell types. The frequency of paused genes (PI ≥2) was similar in diverse human and mouse cell types. c Functional annotations enriched among the most or least paused genes in human cell lines. The top quartile of genes by PI rank had similar GO biological process term enrichment across both normal and cancer cell types, as did the bottom quartile. Similar enrichments were observed when considering genes with pausing greater than (“high average PI”) or less than (“low average PI”) the median PI across all cell types. d Sequence composition analysis of gene promoters. All DNA 6-mers were tested for enrichment in human paused promoters versus non-paused promoters. Each 6-mer was ranked by its enrichment score (see “Methods”). Human paused promoters were over-represented for 6-mers with high GC and CpG content and depleted for the TATA motif