Contrasting epigenetic landscapes at transcriptional start sites for protein-coding genes and lncRNAs in mouse intermediate erythroblasts. The heatmap represents the distribution of DNAse I hypersensitive sites (DHS), H3K4me1, H3K4me3, H3K27ac, Gata1 and NanoCAGE signal (red high, green low) in a 4 kbp window centered around the middle of the nanoCAGE-defined TIRs for (A) protein-coding genes and (B) lncRNA loci. Representative novel (C) elncRNA (green, chr12:112754628 to 112804627 (mm9)) and (D) plncRNA (blue, chr9:72229000 to 72364999 (mm9)) were annotated de novo from C57BL/6 erythroid cell poly(A) + RNA (brown). Their transcriptional start sites were defined using strand-specific nanoCAGE (red; plus and minus signs represent density of reads within strand-specific libraries) found within DHS regions (grey). H3K4me1, green; H3K4me3, blue. Arrows on elncRNA and plncRNA and their neighboring transcript indicate the direction of transcription.
Marques et al. Genome Biology 2013 14:R131 doi:10.1186/gb-2013-14-11-r131