udRNAs overlap with divergent lncRNAs and are associated with transcriptionally active genes. (A) Venn diagram showing that 70.5% of genes with an associated divergent lncRNA in the upstream region  overlap with udRNAs. (B) Box plot of RNA-seq expression values, averaged over the control ASO samples, of genes associated with udRNAs, stratified by change in expression after 7SK knockdown (see also Figure 3A). (C) Venn diagram showing the proportion of expressed genes (RPKM > 5 in control ASO samples) found to be associated with udRNAs. (D) Overlap between genes and udRNAs with genomic regions enriched for histone modifications H3K4me3, H3K27me3 or both (bivalent) in mouse ESCs  (see also Figure 3C). Similar results were obtained when comparing with Young et al. . *P < 0.05, **P < 0.01; Kolmogorov-Smirnov test.
Castelo-Branco et al. Genome Biology 2013 14:R98 doi:10.1186/gb-2013-14-9-r98