Cell type-specific epigenetic signatures accompany late stages of mouse retina development

We have used ChIP-seq to map the distribution of two important histone H3 modifications, H3K4me2 and H3K27me3, over the whole genome at multiple time points during late mouse retina development. We merged these data with our previous retina developmental expression profiles and show that there are several epigenetic signatures specific for different functional groups of genes. The main conclusion from our study is that epigenetic signatures defined by H3K4me2 and H3K27me3 can distinguish cell-type specific genes from widespread transcripts and may be reflective of cell specificity during retina maturation. Rod photoreceptor-specific genes have a striking signature, a de novo accumulation of H3K4me2 and a complete absence of H3K27me3. We were able to use this signature in an unbiased search of the whole genome and identified essentially all the known rod photoreceptor genes as well as a group of novel genes that have a high probability of being rod photoreceptor specific. Comparison of our genome-wide chromatin signature maps with available data sets for Polymerase-II (Pol-II) and CRX binding sites and DNase1 Hypersensitive Sites (DHS) for retina shows great agreement. Because our approach is not dependent on high levels of gene expression, it provides a new way of identifying cell type-specific genes, particularly genes that may be involved in retinal diseases.