Association of rod photoreceptor transcription factors CRX and NRL with rod TSS.

Abstract

<p><b>A, C.</b> Number of TSS with different CRX (<b>A</b>) and NRL (<b>C</b>) binding 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 TF-binding; red–TF-binding. <b>B, D.</b> CRX (<b>B</b>) and NRL (<b>D</b>) accumulation at TSS (normalized number of reads 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>E, G.</b> Combined genome-wide tracks of chromatin features, as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0179230#pone.0179230.g001" target="_blank">Fig <b>1B</b></a> for <i>Wdr17</i> (<b>E</b>) and <i>Tnfaip3</i> (<b>G</b>) genes. 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 maps. <b>F, H.</b> Relative gene expressions from rod and common TSS by RT-PCR with primer pairs depicted at <b>E and G</b> for <i>Wdr17</i> (<b>F</b>) and <i>Tnfaip3</i> (<b>H</b>) for mouse retina samples at PN1, PN15, adult and RD1 mutant, compare with mouse liver. For comparison, normalized to <i>Gapdh</i> delta Ct values for each sample are in table below. Experiments done in duplicates with three technical replicas; ***—p < 0.0001.</p