Figure 2

Brain region-specific regulatory elements identified by DHSs. (A) Heatmap of cluster analysis of the DHSs present in CNS samples clustered according to the percent of overlapping DHS peaks in each tissue, indicated by color intensity. (B-D) Examples of region-specific DNase I hypersensitivity landscapes with matching, previously generated RNA-seq data [24]. (B) DHS in the cerebellum associated with the Neurod1 locus that is not present in the cerebral cortex (tan shading). (C) DHS associated with the Gabra1 gene with examples of region-specific DHSs (tan shading). (D) Extensive differences in DNase I landscape (and DHS peaks, indicated as blocks over signal tracks) at the Rorb locus. (D’, D”) Rorb is expressed in the cerebral cortex (Ctx; arrows point to the layer of Rorb mRNA signal; higher magnification in D”) but not in the cerebellum (Cbm), shown by in situ hybridization (Allen Brain Atlas); there are specific DHSs associated with this gene in the cerebral cortex (tan shaded regions). E14.5, embryonic day 14.5 whole brain; E18.5, embryonic day 18.5 whole brain; Cbm, 8-week adult cerebellum; Ctx, 8-week adult cerebral cortex.