Genome-wide Co-regulation Of Photoreceptor Genes By Nrl And Crx

Abstract

Purpose: : NRL determines rod versus cone photoreceptor cell fate and regulates the expression of many rod-specific genes. CRX does not appear to be required for photoreceptor cell fate determination, but is essential for their maturation and for appropriate expression of phototransduction genes. Mutations in NRL, CRX and their target genes cause inherited retinal degeneration. The goal of this project is to map the NRL-centered gene regulatory network, which modulates rod photoreceptor homeostasis in adult mouse retina, and to address the extent of co-regulation of photoreceptors genes by NRL and CRX at the global level.

Methods: : Genomewide NRL binding events were identified by chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-Seq) using both Illumina and ABI-SOLiD sequencing platforms. NRL ChIP-Seq data was combined with global expression profiles of photoreceptors to identify direct NRL target genes. Co-regulation by NRL and CRX was indicated by analysis of NRL ChIP-Seq data by overlapping with published CRX ChIP-Seq data. Function of specific NRL target genes was tested by shRNA in vivo electroporation, immunohistochemistry and gene expression profile analysis.

Results: : Our analyses identified genomewide NRL target genes, which can serve as excellent candidate disease genes. Genes that are involved in photoreceptor functions are largely positive for both NRL and CRX ChIP-Seq peaks. Knockdown of 16 targets by shRNAs led to photoreceptor cell death or abnormal morphology. Furthermore, we identified novel secondary nodes downstream of NRL in the regulatory network.

Conclusions: : Global targetome analysis has enabled elucidation of transcriptional networks that control photoreceptor function and provided targets for therapeutic interventions in diseases involving photoreceptor dysfunction.

Keywords: photoreceptors • genetics • transcription factors