Genes with the same expression patterns show different histone signatures in retina.

Abstract

<p>(<b>A</b>) H3K4me2 and H3K27 accumulation in examples of genes up-regulated during retina maturation. (<b>B</b>) H3K4me2 and H3K27 accumulation in examples of genes down-regulated during retina maturation. Closed arrowheads show TSS of each gene (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046867#pone.0046867.s018" target="_blank">Text S1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046867#pone.0046867.s006" target="_blank">Tables S4</a> &S5). (<b>C</b>) Cluster analysis of H3K4me2 and H3K27me3 occupancy around TSS (+/−2.5 Kb) at all developmental stages for the genes upregulated in mature retina. Tree-view shows 4 clusters (C1–C4) with distinct epigenetic patterns for H3K4me2 (upper panel) and H3K27me3 (middle panel) but with same expression patterns (lower panel). (<b>D</b>) Same analysis as in (<b>C</b>) for the genes downregulated in mature retina. Cluster analysis of H3K4me2 and Tree-view shows 3 clusters (C1′–C3′) with distinct epigenetic patterns for H3K4me2 (upper panel) and H3K27me3 (middle panel) but with same expression patterns (lower panel). For <b>A</b> and <b>B</b> y-axis is the number of reads in a 100 bp interval. For <b>C</b> and <b>D</b>, (upper panels) y-axis is the normalized occupancy, or the number of reads for a given histone modification in an interval +/−2.5 kb around the TSS of given gene, normalized for the total number of mapped reads in given experiment.</p