Fig. 4

Atypically broad H3K9 acetylation is deposited at photoreceptor identity gene loci and is altered in SCA7 retina. A Genome browser tracks depicting RNAPII, H3K9ac and H3K27ac distributions at a representative housekeeping gene (Rplp0) and two photoreceptor specific genes (Rho and Gnat1) in WT and SCA7 retinas. In WT retina, RNAPII, H3K9ac and H3K27ac show characteristic narrow peaks in the TSS region of Rplp0. In contrast, broad signals of H3K9ac, H3K27ac and RNAPII are found throughout the entire gene bodies of Rho and Gnat1. In SCA7 retina, peak height and peak broadness as illustrated by the called peaks (top straight bar) of RNAPII, H3K9ac and H3K27ac are decreased at Rho and Gnat1 genes. * indicate saturated peak in Rho gene due to repetitive sequences. B ChIP-qPCR analysis shows H3K9ac occupancy on the TSS, gene body (GB) and 3′UTR regions of Rho and Gnat1 genes, as well as occupancy on the TSS, but not on the GB of the housekeeping Hprt gene in WT retina. In SCA7 retina, H3K9ac occupancy is globally decreased on Rho and Gnat1 gene loci and on the TSS of Hprt gene. Data are normalized as a percentage of input DNA, expressed as mean ± SEM (n = 3 mice/genotype) and analyzed using two-tailed Student’s t-test. C Box plots depicting the broadness (in base pairs (bp)) of H3K9ac peaks on photoreceptor specific genes (n = 95) and on housekeeping genes (n = 3485) in WT and SCA7 retina. Data were analyzed using Mann–Whitney test. D ChIP-qPCR analysis shows H3K27ac occupancy along the Rho and Gnat1 gene loci in WT retina and its decrease in SCA7 retina; (upTSS, upstream of TSS). Data are normalized as a percentage of input DNA, expressed as a mean ± SEM (n = 3 mice/genotype) and analyzed using two-tailed Student’s t-test. *p < 0.05; **p < 0.01; ***p < 0.001