Extended Data Figure 8. Epigenetic changes in MG-derived neurons.

a, Violin plots of ATAC–seq tag density in the region 1 kb upstream of the promoters of genes that either decrease by twofold or increase by twofold between the wild-type and ANT-reprogrammed MG to show that the changes in gene expression are accompanied by changes in DNA accessibility during reprogramming with Ascl1, NMDA and TSA. The changes in gene expression were taken from the average of all Ascl1⁺ cells in the single-cell RNA-seq data from the Fluidigm data and compared with the wild-type MG from the same dataset. Notably, many progenitor genes, like Hes6 and Ascl1, show chromatin accessibility at putative cis-regulatory regions in all treatment conditions (including wild type) even though these genes are not normally expressed in the mature retina. b, H3K27ac ChIP was carried out on FACS-purified ANT-reprogrammed MG and wild-type MG. The data are shown as a per cent of control for three neural genes that show increases in expression and a control gene (Hoxb2) that does not change with ANT treatment. There was a substantial increase in H3K27ac for each of the genes tested. ChIP-PCR data are from ANT-treated retinas that were collected 19 days post-TSA.