ArticlePloS one2007
The cis-regulatory logic of the mammalian photoreceptor transcriptional network.
Article in PloS one, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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Who cites it
101 citing papers in PubMed, 149 citations in OpenAlex.
- Evolution of MAF and OTX families during the emergence and stabilization of rod photoreceptors across Metazoans.Research square · 2026Article
- Human CRX regulates photoreceptor cells development via bidirectional transcriptional control in retinal organoids.Stem cell reports · 2026Article
- Active learning of enhancers and silencers in the developing neural retina.Cell systems · 2025Article
- Enhanced Transcriptional Activation in Developing Mouse Photoreceptors.Investigative ophthalmology & visual science · 2025Article
- AnFrontiers in genetics · 2025Article
- A DNA base-specific sequence interposed between CRX and NRL contributes to RHODOPSIN expression.Scientific reports · 2024Article
- Molecular basis of CRX/DNA recognition and stoichiometry at the Ret4 response element.Structure (London, England : 1993) · 2024Article
- Germline knockout ofProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Transcription factor interactions explain the context-dependent activity of CRX binding sites.PLoS computational biology · 2024Article
- Lamin A upregulation reorganizes the genome during rod photoreceptor degeneration.Cell death & disease · 2023Article
- Active learning of enhancer and silencer regulatory grammar in photoreceptors.bioRxiv : the preprint server for biology · 2023Article
- A single-cell massively parallel reporter assay detects cell-type-specific gene regulation.Nature genetics · 2023Article
- Disease-causing mutations in genes encoding transcription factors critical for photoreceptor development.Frontiers in molecular neuroscience · 2023Review
- Polyglutamine-expanded ATXN7 alters a specific epigenetic signature underlying photoreceptor identity gene expression in SCA7 mouse retinopathy.Journal of biomedical science · 2022Article
- Mutations inScience advances · 2022Article
- MLL5 is involved in retinal photoreceptor maturation through facilitating CRX-mediated photoreceptor gene transactivation.iScience · 2022Article
- Article
- Repeated nuclear translocations underlie photoreceptor positioning and lamination of the outer nuclear layer in the mammalian retina.Cell reports · 2021Article
- A Casz1-NuRD complex regulates temporal identity transitions in neural progenitors.Scientific reports · 2021Article
- Retinoschisin and Cardiac Glycoside Crosstalk at the Retinal Na/K-ATPase.Investigative ophthalmology & visual science · 2020Article
41 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The photoreceptor cells of the retina are subject to a greater number of genetic diseases than any other cell type in the human body. The majority of more than 120 cloned human blindness genes are highly expressed in photoreceptors. In order to establish an integrative framework in which to understand these diseases, we have undertaken an experimental and computational analysis of the network controlled by the mammalian photoreceptor transcription factors, Crx, Nrl, and Nr2e3. Using microarray and in situ hybridization datasets we have produced a model of this network which contains over 600 genes, including numerous retinal disease loci as well as previously uncharacterized photoreceptor transcription factors. To elucidate the connectivity of this network, we devised a computational algorithm to identify the photoreceptor-specific cis-regulatory elements (CREs) mediating the interactions between these transcription factors and their target genes. In vivo validation of our computational predictions resulted in the discovery of 19 novel photoreceptor-specific CREs near retinal disease genes. Examination of these CREs permitted the definition of a simple cis-regulatory grammar rule associated with high-level expression. To test the generality of this rule, we used an expanded form of it as a selection filter to evolve photoreceptor CREs from random DNA sequences in silico. When fused to fluorescent reporters, these evolved CREs drove strong, photoreceptor-specific expression in vivo. This study represents the first systematic identification and in vivo validation of CREs in a mammalian neuronal cell type and lays the groundwork for a systems biology of photoreceptor transcriptional regulation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.