Rod TSSs are associated with DNase1 hypersensitive sites in retina.

Abstract

<p><b>A.</b> Number of TSS with different ratio of DHS changes during retina development (comparison of DHS occupancy at PN56 and PN1; PN56/PN1) for rod genes with single TSS (upper panel) and for rod (middle panel) or common (bottom panel) TSS of retina genes with multiple TSS. Blue–no changes; red–low PN56/PN1; green- high PN56/PN1. <b>B.</b> Developmental changes in accessibility of different TSS by DHS (PN56/PN1 DHS at TSS+/-1000bp) for rod and common TSS of retina genes with multiple TSS, compared with control groups of genes (non-rod, cell-cycle and synapse). ***—p < 0.0001. <b>C.</b> Combine genome-wide tracks of chromatin features, as in <b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0179230#pone.0179230.g001" target="_blank">Fig 1B</a></b> for <i>Tmem229b</i> gene. Common TSS is depicted as C/ red box, rod TSS–as R/ blue box. Position of the specific primer sets and PCR product that were used to assess and distinguish TSS-specific gene expression by RT-PCR depicted as double arrow below gene map. <b>D.</b> Relative gene expressions from rod and common TSS by RT-PCR with primer pairs depicted at <b>C</b> for <i>Tmem229b</i> for mouse retina samples at PN1, PN15, adult and RD1 mutant, compare with mouse liver. For comparison, normalized to <i>Gapdh</i> ΔCt values for each sample are in table below. Experiments done in duplicates with three technical replicas; **—p < 0.001. <b>E, F.</b> Accessibility of different TSS by DHS (number of DHS at TSS+/-1000bp) during mouse retina (PN1, PN7, PN56) and brain (E14.5, E18.5, PN56) developments for rod (<b>F</b>) and common TSS (<b>E</b>) of retina genes with multiple TSS.*—p = 0.026 (<b>E</b>); ***—p = 0.0003 (<b>F</b>); *—p = 0.037/ 0.01.</p