Figure 4

Examination of the developmentally dynamic DNase I landscape reveals stage specific cis-regulatory elements and transcription factors. DNase I landscape at representative gene loci near genes expressed in (A) developing (Neurog2, Olig2) or (B) mature (Rho, Guca1b) retina at P0 (red), P7 (blue), and adult (Ad; green) stages, along with mammalian sequence conservation (Con; black). ChIP-seq peak locations for CRX and NRL are indicated by black boxes [42, 43]. (C) Heatmap profile of accessibility at each DHS (columns) across developmental stages (rows), grouped by k-means clustering. Color intensity indicates the normalized DNase I accessibility according to the included scale. (D) Condensed heatmap of k-means-clustered DHSs (rows) in the retina between P0, P7, and adult stages (columns). Color intensity indicates median DNase I accessibility of DHSs in each cluster. Also shown are the number of DHSs contained in each cluster, the percentage of DHSs within each cluster that overlap a gene promoter (1 kb upstream of the transcription start site) and the percentage of total CRX or NRL ChIP-seq binding sites that overlap a DHS contained within each cluster. E, early; M, mid; L, late; O, other; C, constitutive. (E) Transcription factor binding motif enrichment analysis of all cluster groups shown for a selected group of transcription factors. Motif enrichment (-log10(P value)) indicated as color intensity for each transcription factor (rows) within each temporal cluster group (columns).