Stage and gene specific signatures defined by histones H3K4me2 and H3K27me3 accompany mammalian retina maturation in vivo

• Published in: PloS one 2012-10, Vol.7 (10), p.e46867-e46867
• Main Authors: Popova, Evgenya Y, Xu, Xuming, DeWan, Andrew T, Salzberg, Anna C, Berg, Arthur, Hoh, Josephine, Zhang, Samuel S, Barnstable, Colin J
• Format: Article
• Language: English
• Subjects: Accumulation; Analysis; Animals; Behavioral sciences; Bioinformatics; Biology; Cell Lineage - genetics; Chromatin Immunoprecipitation; DNA binding proteins; Epidemiology; Epigenesis, Genetic; Epigenetic inheritance; Epigenetics; Gene expression; Gene regulation; Genes; Genomes; Genomics; Group dynamics; Histone H3; Histones; Histones - chemistry; Histones - metabolism; Labeling; Lysine - metabolism; Maturation; Medicine; Methylation; Mice; Mutation; Neurogenesis; Neurosciences; Organogenesis - genetics; Photoreception; Photoreceptors; Public health; Retina; Retina - cytology; Retina - growth & development; Retina - metabolism; Retinal Rod Photoreceptor Cells - cytology; Retinal Rod Photoreceptor Cells - metabolism; Signatures; Transcription; Transcription (Genetics); Transcriptome
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0046867

The epigenetic contribution to neurogenesis is largely unknown. There is, however, growing evidence that posttranslational modification of histones is a dynamic process that shows many correlations with gene expression. Here we have followed the genome-wide distribution of two important histone H3 modifications, H3K4me2 and H3K27me3 during late mouse retina development. The retina provides an ideal model for these studies because of its well-characterized structure and development and also the extensive studies of the retinal transcriptome and its development. We found that a group of genes expressed only in mature rod photoreceptors have a unique signature consisting of de-novo accumulation of H3K4me2, both at the transcription start site (TSS) and over the whole gene, that correlates with the increase in transcription, but no accumulation of H3K27me3 at any stage. By in silico analysis of this unique signature we have identified a larger group of genes that may be selectively expressed in mature rod photoreceptors. We also found that the distribution of H3K4me2 and H3K27me3 on the genes widely expressed is not always associated with their transcriptional levels. Different histone signatures for retinal genes with the same gene expression pattern suggest the diversities of epigenetic regulation. Genes without H3K4me2 and H3K27me3 accumulation at any stage represent a large group of transcripts never expressed in retina. The 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. In addition to the developmental patterns seen in wild type retina, the dramatic changes of histone modification in the retinas of mutant animals lacking rod photoreceptors provide a tool to study the epigenetic changes in other cell types and thus describe a broad range of epigenetic events in a solid tissue in vivo.