Figure 2. Validation of RNA-Polymerase-II (Pol-II) ChIP-on-chip predictions: changes in activated Pol-II association within genes during terminal maturation of photoreceptors. Q-ChIP assays were performed using an antibody specific for active RNA polymerase-II, which is phosphorylated at serine-2 of the C-terminal repeat domain (Pol-II-S2). Genes assayed represent a full range of ChIP-on-chip Pol-II peak signal ratios (P25/P2) from 14 to 0.5 (Table 1). Pol-II binding is proportional to the amount of target DNA captured by ChIP, graphed as copies of target DNA detected per 1,000 genome equivalents of input genomic DNA. Most assays target in the gene, downstream of the TSS. Results were normalized for chromatin input and PCR efficiency. Error bars indicate standard deviation (n=3). An untranslated region (Untr6) on chromosome 6 provided a negative control. The relative position of each PCR target is indicated with the gene symbol. For example, Slc24a1+1798 indicates the 5′-end of the PCR target was 1,798 bases downstream of the Slc24a1 TSS. Rho, Rcvn, Pde6b, and Sag1 are key markers of photoreceptor-specific gene expression. Grik2 and Casc5 were included as genes with ChIP-on-chip Pol-II peak signal ratios <1. Genes: Solute carrier family 24, Na/K/Ca exchanger, member 1 (Slc24a1), Actin binding LIM protein1 (Ablim1), Recoverin (Rcvrn), Rhodopsin (Rho), Family with sequence similarity 53, member B (A930008G19Rik, Fam53b), Retinoschisis 1 homolog (Rs1h), G protein-coupled receptor kinase 1 (Grk1), D4, zinc and double PHD fingers, family 3 (Dpf3), Retinol dehydrogenase-12 (Rdh12), Myeloid/lymphoid or mixed-lineage leukemia 6 (Mllt6), Jumonji domain containing 2C (Jmjd2c), S-antigen (Sag), Phosphodiesterase 6b (Pde6b), Spectrin repeat containing, nuclear envelope 1 (Syne1), Cyclin-dependent kinase 5, regulatory subunit 2 (Cdk5r2), Vitronectin (Vtn), Cholecystokinin-2 receptor (Cckbr), Peripherin 2 (Rds), Uridine-cytidine kinase 1-like 1 (Uckl1), Bardet-Biedl syndrome 9 (E130103I17Rik, Bbs9), Solute carrier family 38, Na/H -coupled glutamine transporter, member 3 (Slc38a3), Transducin alpha (Gnat1), Coiled coil domain containing 126 (6330407D12Rik, Ccdc126), Tetratricopeptide repeat domain 8 (Ttc8), Retinitis pigmentosa 1 (Rp1h), Retinol binding protein 3, interstitial (Rbp3), Coronin, actin binding protein, 2B (Coro2b), Nuclear receptor subfamily 1, group D, member 1 (Nr1d1), G430022H21Rik, RAB14, member RAS oncogene family (Rab14), Elongation of very long chain fatty acids-like 4 (Elovl4), Ras homolog enriched in brain (Rheb), Histone deacetylase 10 (Hdac10), Histone deacetylase 9 (Hdac9), Ring finger protein 11 (Rnf11), Glutamate receptor, ionotropic, kainate 2 (beta 2) (Grik2), Cancer susceptibility candidate 5 (Casc5).