Fig. 2

Mapping of RNA:DNA hybrids within the ribosomal DNA repeat unit. The upper panel shows the results of RDIP-seq (gray) and RNA-seq (red), with genomic annotations and results of ChIP-seq analysis in K562 cells [55] plotted below. RDIP-seq and RNA-seq data are both represented using a smoothed plot showing the number of reads aligned to each basepair of the repeating unit, while the ChIP-seq data signal intensity represents the mean value of non-overlapping 50 bp windows. RDIP-seq values were normalized by subtracting the frequencies of aligned reads of the input sample in each window. We find that RNA:DNA hybrids co-localize with the rRNA transcripts, but that there are also RDIP-seq peaks of comparable magnitude in the intergenic spacer (IGS) where no transcriptional activity is apparent from RNA-seq. The RNA:DNA hybrids in the IGS are upstream of the promoter region and flank the upstream candidate cis-regulatory sequence where there is H3K4 methylation and acetylation of H3K9 and H3K27