Genome-Wide Analysis of Target Genes for Nrl in Developing and Mature Retina

Abstract

Purpose: : To fully understand the mechanism of Nrl function in regulating rod photoreceptor development and maintenance of mature rods, we sought to identify direct Nrl target genes in mouse retina at different developmental stages.

Methods: : Nrl target genes were identified by ChIP-chip. Candidate targets were evaluated by real-time RT-PCR and sub-retinal injection of siRNA and electroporation.

Results: : Here, through genome-wide analysis combining chromatin immunoprecipitation (ChIP) with profiling with mouse genome tiling arrays, we identify 40,582 putative Nrl binding regions in adult mouse retina. ChIP-chip targets were enriched in sequences similar to known Nrl binding motifs. ChIP-qPCRs were performed to confirm Nrl binding to the regions identified by ChIP-chip. We are evaluating Nrl targets in vivo at different developmental stages by ChIP-sequencing (ChIP-seq), that combines ChIP with massively parallel sequencing. The function of some of the candidate genes is being examined by sub-retinal injection of siRNA and electroporation.

Conclusions: : A comprehensive in vivo analysis of NRL targets in the mouse retina will contribute to establishing transcriptional regulatory networks that dictate photoreceptor development and function.

Keywords: gene/expression • retinal development • photoreceptors