Rod TSSs are associated with PolII-binding sites in retina.

Abstract

<p><b>A.</b> Number of TSS with different ratio of PolII-binding during development (comparison of PolII occupancy at PN25 and PN2; PN25-PN2) for rod-specific 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 PN25-PN2; green- high PN25-PN2. <b>B.</b> Developmental changes in PolII-binding (PN25-PN2 at TSS+/-1000bp) for rod and common TSS of retina genes with multiple TSS, compared with PolII-binding at TSS for control groups of genes (non-rod, cell-cycle and synapse). ***—p < 0.0001. <b>C.</b> Combined 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>Kdm4c</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>Kdm4c</i> for mouse retina samples at PN1, PN15, adult and RD1 mutant. 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 < 0.0001.</p