Expression of photoreceptor genes is decreased in R-DCKO retinas.

A. Summarized microarray findings for R-DCKO vs. Cre neg retinas. Each gene was categorized by the cell process in which it functioned, and results for each category are represented as a percentage of all the down- or up-regulated genes (see Supplemental Tables 2 & 3 for details). B. Schematic distribution of the 62 down-regulated photoreceptor or phototransduction-related genes in R-DCKO microarrays (red), compared with the 247 retinal disease loci listed in RetNet (https://sph.uth.edu/RetNet/home.htm; green) and a list of 230 genes down-regulated in Crx−/− retinas compiled from published sources [51]–[53]. Numbers in overlapping areas indicate the numbers of genes affected in both/all three conditions. All overlapping genes are listed in Supplementary Tables S4 and S5. C–F. Expression of the indicated rod gene (C. Nrl; D. Crx; E. Rhodopsin (Rho); F. Rod Transducin (Gnat1)) was assessed by quantitative RT-PCR (qRT-PCR) at P14, and is expressed as percent of the level of Cre-negative littermate controls (% Cre neg). Protein localization was verified by immunohistochemistry (IHC) at P30. Scale bar = 20 µm for all images. Levels of acetylated histone H3 (AcH3) or H4 (AcH4) on the respective promoter was determined by quantitative chromatin immunoprecipitation (qChIP) at P14, and is expressed as the value from the immunoprecipitated sample divided by the value from the untreated “input” sample, multiplied by 100 (“IP/input”).