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Regulation of cell type-specific gene expression is critical for generating neuronal diversity. Transcriptome analyses have unraveled extensive heterogeneity of transcribed sequences in retinal photoreceptors because of alternate splicing and/or promoter usage. Here we show that Frmpd1 (FERM and PDZ domain containing 1) is transcribed from an alternative promoter specifically in the retina. Electroporation of Frmpd1 promoter region, -505 to +382 bp, activated reporter gene expression in mouse retina in vivo. A proximal promoter sequence (-8 to +33 bp) of Frmpd1 binds to NRL and CRX, two rod-specific differentiation factors, and is necessary for activating reporter gene expression in vitro and in vivo. CRISPR/Cas9-mediated deletion of the genomic region including NRL and CRX binding sites in vivo completely eliminated Frmpd1 expression in rods and dramatically reduced expression in rod bipolar cells, thereby overcoming embryonic lethality caused by germline Frmpd1 deletion. Our studies demonstrate that a cell-type-specific regulatory control region is a credible target for creating loss-of-function alleles of widely-expressed genes.

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Journal article


Hum Mol Genet

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