Figure 3

DNase I hypersensitivity identifies (rare) cell type-specific regulatory elements. (A) DNase I (P0, P7, and 8-week adult retina) and RNA-seq (P2 and P21 retina) [45] landscape near genes expressed exclusively in minority cell populations in the retina: ganglion cells (Pou4f2) and cone photoreceptors (Opn1sw). Black bars below DNase I signal tracks indicate DNase I peaks. Yellow boxes indicate DHS within promoter regions. (B) The number of DHSs near genes expressed specifically in indicated retinal cell types, sorted by column. Color intensity increases with DHS number. (C) Gene Ontology - Mouse Phenotype enriched terms for retinal, but not brain, DHSs as determined by GREAT analysis. Numbers indicate the number of genes associated with each term. (D) Overlap between ChIP-seq peaks for two key photoreceptor-specific transcription factors, CRX and NRL. Although nearly all of the ChIP-seq peaks for these TFs overlap a DHS in the retina, there are still many retinal DHSs that are associated with genes expressed in other retinal cell types. (E) Overlap between CRX and NRL ChIP-seq peaks (including co-binding regions) with retina-specific DHSs (rsDHSs).