Fig. 5

Transcriptional relationships of RNA:DNA hybrids. In a the proportion of RNA:DNA hybrid peaks in transcribed genes is shown to be higher than in non-transcribed genes, but that the majority of genes do not contain RNA:DNA hybrids. In b a metaplot of RNA:DNA hybrid peaks is shown, illustrating the number of peaks intersecting with 100 bp windows, with the RNA of the hybrid on the transcribed strand of the gene (red) or the opposite strand (blue). This revealed an enrichment of the RNA-derived sequence on the transcribed strand in the first ~1.5 kb downstream from the transcription start site (TSS). A depletion of RNA:DNA hybrids is found at the transcription end site (TES). In c we show that the region immediately downstream from the TSS is purine-skewed, represented by skewing values of 100 bp windows averaged for all genes, but that this is to the same degree in genes that form RNA:DNA hybrids (blue) as those genes that do not form these structures (red). In d a metaplot of RefSeq genes (left) shows that the transcription level of genes (as measured by RNA-seq) is positively associated with the number of RN:DNA hybrids intersecting with 100 bp windows immediately downstream of the TSS. This reflects only modest increases in the small proportions of genes forming peaks (right), though found to be a significant relationship using a proportions test