ArticleGenome research2010
CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 141 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
141 citing papers in PubMed, 1 synthesis or guideline pooled it, 235 citations in OpenAlex.
- Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration.Human molecular genetics · 2011Pooled it
- Common variant in VEGFA and response to anti-VEGF therapy for neovascular age-related macular degeneration.Current molecular medicine · 2013Trial
- The long noncoding RNA Peanut (Gm11454) biases progenitors towards neurogenesis and rod photoreceptor differentiation during postnatal retinal development.Developmental biology · 2026Article
- The human THRB thyroid hormone receptor gene and the puzzle of retinal disease phenotypes.Developmental biology · 2026Review
- A robust cis-regulatory network ensures Otx2 expression during retinal development.Development (Cambridge, England) · 2026Article
- Article
- Human CRX regulates photoreceptor cells development via bidirectional transcriptional control in retinal organoids.Stem cell reports · 2026Article
- Conservation of cis-regulatory codes over half a billion years of evolution.Science advances · 2025Article
- Active DNA demethylation upstream of rod-photoreceptor fate determination is required for retinal development.PLoS biology · 2025Article
- Article
- Active learning of enhancers and silencers in the developing neural retina.Cell systems · 2025Article
- Ccrk-Mak/Ick signaling is a ciliary transport regulator essential for retinal photoreceptor survival.Life science alliance · 2024Article
- Mutational scanning ofGenome research · 2024Article
- Molecular basis of CRX/DNA recognition and stoichiometry at the Ret4 response element.Structure (London, England : 1993) · 2024Article
- Mutational scanning ofbioRxiv : the preprint server for biology · 2024Article
- Pathogenic variants inGenome research · 2024Article
- Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominantbioRxiv : the preprint server for biology · 2024Article
- Transcriptional precision in photoreceptor development and diseases - Lessons from 25 years of CRX research.Frontiers in cellular neuroscience · 2024Review
- Transcription factor interactions explain the context-dependent activity of CRX binding sites.PLoS computational biology · 2024Article
- CRX haploinsufficiency compromises photoreceptor precursor translocation and differentiation in human retinal organoids.Stem cell research & therapy · 2023Article
81 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
12 authors at 3 institutions in 3 countries.
Funding
Abstract
Approximately 98% of mammalian DNA is noncoding, yet we understand relatively little about the function of this enigmatic portion of the genome. The cis-regulatory elements that control gene expression reside in noncoding regions and can be identified by mapping the binding sites of tissue-specific transcription factors. Cone-rod homeobox (CRX) is a key transcription factor in photoreceptor differentiation and survival, but its in vivo targets are largely unknown. Here, we used chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) on CRX to identify thousands of cis-regulatory regions around photoreceptor genes in adult mouse retina. CRX directly regulates downstream photoreceptor transcription factors and their target genes via a network of spatially distributed regulatory elements around each locus. CRX-bound regions act in a synergistic fashion to activate transcription and contain multiple CRX binding sites which interact in a spacing- and orientation-dependent manner to fine-tune transcript levels. CRX ChIP-seq was also performed on Nrl(-/-) retinas, which represent an enriched source of cone photoreceptors. Comparison with the wild-type ChIP-seq data set identified numerous rod- and cone-specific CRX-bound regions as well as many shared elements. Thus, CRX combinatorially orchestrates the transcriptional networks of both rods and cones by coordinating the expression of photoreceptor genes including most retinal disease genes. In addition, this study pinpoints thousands of noncoding regions of relevance to both Mendelian and complex retinal disease.
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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.