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Kenneth P. Mitton, Jason Sotzen, Alvaro E. Guzman, Wojciech Gryc, Padmaja Tummala; Identifying Photoreceptor-Specific Genes Within Unidentified Disease Loci Using Genome-wide ChIP. Invest. Ophthalmol. Vis. Sci. 2011;52(14):2561.
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To identify genes located in mapped intervals of unidentified human retinal diseases that have photoreceptor specific or photoreceptor rich expression.
We recently mapped RNA-Polymerase-II binding throughout gene promoters in the P2 and P25 mouse neural retina by Chromatin Immuno-Precipitation with promoter tiling arrays (ChIP-on-Chip). Novel gene activation events were predicted from increased binding of Pol-II during photoreceptor maturation. Cross-indexing, with NEIBank and RetNet, identified genes with a human homolog located in mapped intervals of unidentified retinal diseases. Relative expression in rod, cone, and non-photoreceptor neurons, was determined by transcript-specific RT-qPCR of normal, rod-less (Rd1 P33) and photoreceptor-less (Rd1 >P99) retinas. Expression patterns were compared to cell-specific markers of rods (Nrl) and cones (Opn1mw).
Pol-II ChIP-on-Chip identified numerous novel gene activation events during photoreceptor maturation in the mouse neural retina. Over 130 genes were identified that have a human homolog located in mapped intervals of unidentified retinal diseases. Genes with photoreceptor rich or photoreceptor specific expression were systematically confirmed by a loss of expression in rod-less or photoreceptor-less retinas. Some examples included Lpcat1 (Lysophosphatidylcholine acyltransferase) and Psma5 (proteasome alpha 5 subunit). Lpcat1 had photoreceptor-rich expression. Psma5 had a rod-specific expression pattern.
We developed an objective strategy to combine data from genome-wide Pol-II ChIP, mapped retinal disease loci, and gene expression analysis of photoreceptorless retinas, to highlight candidate disease genes based on cell-specific expression. Lpcat1 was captured by this strategy (Padmaja et al., 2010, Mol Vis), and its more recent identification as the mouse Rd11 gene, validates this approach. Psma5, a gene in the human RP32 locus, appears to have a photoreceptor-specific expression pattern in the mouse neural retina.
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