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Hong Hao, Douglas S. Kim, Kory Johnson, Chongzhi Zang, kairong Cui, Janina Gregorski, Fann Yan, Keji Zhao, Anand Swaroop; Chip-seq Aided Elucidation Of Nrl-centered Transcription Regulatory Network And Implications For Retina Degeneration. Invest. Ophthalmol. Vis. Sci. 2011;52(14):38.
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© ARVO (1962-2015); The Authors (2016-present)
Transcription regulatory networks (TRN) consisting of transcription factors, cofactors and target genes, lie at the center of differentiation and disease pathogenesis. The Maf-family bZIP transcription factor NRL plays an important regulatory role in photoreceptor development and homeostasis. Mutations in NRL and its target genes have been associated with inherited retinal degeneration. Our goal is to decipher the NRL-centered TRN, which dictates photoreceptor homeostasis in adult mouse retina.
Genome-wide NRL occupancy was identified by chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-Seq) using both Illumina and ABI-SOLiD sequencing platforms. ChIP-Seq data was then combined with transcription profiling and further in silico analysis to identify candidate target genes for further studies. shRNAs against specific NRL target genes were electroporated in P0 mouse retina to knockdown the corresponding transcripts and determine their relevance in rod photoreceptors.
Our analysis identified 334 direct NRL target genes, 30 secondary regulators and co-regulatory transcription factors including CRX. Knockdown of 15 of the targets by corresponding shRNAs led to photoreceptor cell death or abnormal morphology. Mutations in 20 of the NRL target genes are known to be associated with retinal diseases, whereas 101 human orthologs of the NRL targets mapped within retinal disease loci. In silico analysis indicates feed-forward and feed-back regulatory loops within the NRL-centered TRN.
Genome-wide occupancy analysis of NRL by Illumina and ABI/SOLiD produced remarkably comparable results. Our studies have enabled elucidation of NRL-centered TRN that might control photoreceptor function. Further analysis of NRL targets should assist in discovery of retinal disease genes.
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