CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors.

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.

• Publication year

  2010

• Venue

  Genome Research

• Publication date

  2010-11-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1101/gr.109405.110PMID 20693478PMCID PMC2963815
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Global view

  2013cited by this paper
• An atlas of combinatorial transcriptional regulation in mouse and man.

  2010cited by this paper
• Quantitative fine-tuning of photoreceptor cis-regulatory elements through affinity modulation of transcription factor binding sites

  2010influential reference
• Panky, a novel photoreceptor‐specific ankyrin repeat protein, is a transcriptional cofactor that suppresses CRX‐regulated photoreceptor genes

  2010cited by this paper
• Blimp1 controls photoreceptor versus bipolar cell fate choice during retinal development

  2010cited by this paper
• The orphan nuclear hormone receptor ERRβ controls rod photoreceptor survival

  2010cited by this paper
• High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences

  2010cited by this paper
• The UCSC Genome Browser database: update 2011

  2010cited by this paper
• Phenotypic robustness conferred by apparently redundant transcriptional enhancers

  2010cited by this paper
• Retinoic acid receptor‐related orphan receptor α regulates a subset of cone genes during mouse retinal development

  2009cited by this paper
• The DNA-encoded nucleosome organization of a eukaryotic genome

  2009influential reference
• Transcriptional autoregulation in development.

  2009cited by this paper
• Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution.

  2009cited by this paper
• G+C content dominates intrinsic nucleosome occupancy

  2009cited by this paper
• Combinatorial binding predicts spatio-temporal cis-regulatory activity

  2009cited by this paper
• Unraveling a multifactorial late-onset disease: from genetic susceptibility to disease mechanisms for age-related macular degeneration.

  2009cited by this paper
• CRX controls retinal expression of the X-linked juvenile retinoschisis (RS1) gene

  2008cited by this paper
• Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

  2008influential reference
• The UCSC Genome Browser Database: update 2009

  2008cited by this paper
• From the Cover: Gene Networks in Development and Evolution Special Feature Sackler Colloquium: Regulatory logic of neuronal diversity: Terminal selector genes and selector motifs

  2008cited by this paper
• Shadow Enhancers as a Source of Evolutionary Novelty

  2008cited by this paper
• Rod differentiation factor NRL activates the expression of nuclear receptor NR2E3 to suppress the development of cone photoreceptors.

  2008cited by this paper
• Analysis of Combinatorial cis-Regulation in Synthetic and Genomic Promoters

  2008cited by this paper
• A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

  2008cited by this paper
• Genome-Wide Analysis of Transcription Factor Binding Sites Based on ChIP-Seq Data

  2008cited by this paper
• A combinatorial code of maternal GATA, Ets and β-catenin-TCF transcription factors specifies and patterns the early ascidian ectoderm

  2007cited by this paper
• The mouse Crx 5'-upstream transgene sequence directs cell-specific and developmentally regulated expression in retinal photoreceptor cells

  2007cited by this paper
• The Cis-regulatory Logic of the Mammalian Photoreceptor Transcriptional Network

  2007influential reference
• A typology of photoreceptor gene expression patterns in the mouse

  2007influential reference
• Molecular dissection reveals decreased activity and not dominant negative effect in human OTX2 mutants

  2006cited by this paper
• In vivo enhancer analysis of human conserved non-coding sequences

  2006cited by this paper
• Targeting of GFP to newborn rods by Nrl promoter and temporal expression profiling of flow-sorted photoreceptors.

  2006cited by this paper
• In vivo function of the orphan nuclear receptor NR2E3 in establishing photoreceptor identity during mammalian retinal development.

  2006cited by this paper
• The Regulatory Genome: Gene Regulatory Networks In Development And Evolution

  2006cited by this paper
• Enhancer identification through comparative genomics.

  2006cited by this paper
• enoLOGOS: a versatile web tool for energy normalized sequence logos

  2005cited by this paper
• Computational Identification of Regulatory Targets of Tissue–Specific Transcription Factors: Application to Retina–Specific Gene Regulation

  2005cited by this paper
• Retinoid X receptor (gamma) is necessary to establish the S-opsin gradient in cone photoreceptors of the developing mouse retina.

  2005cited by this paper
• A Hybrid Photoreceptor Expressing Both Rod and Cone Genes in a Mouse Model of Enhanced S-Cone Syndrome

  2005cited by this paper
• Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.

  2005cited by this paper
• The Rod Photoreceptor-Specific Nuclear Receptor Nr2e3 Represses Transcription of Multiple Cone-Specific Genes

  2005cited by this paper
• oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes

  2005cited by this paper
• Cone-like morphological, molecular, and electrophysiological features of the photoreceptors of the Nrl knockout mouse.

  2005influential reference
• BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

  2005cited by this paper
• Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information.

  2003influential reference
• Otx2 homeobox gene controls retinal photoreceptor cell fate and pineal gland development

  2003cited by this paper
• BETA2/NeuroD1 Null Mice: A New Model for Transcription Factor-Dependent Photoreceptor Degeneration

  2003influential reference
• Mouse cone arrestin gene characterization: promoter targets expression to cone photoreceptors

  2002cited by this paper
• The Mouse Crx 5′-Upstream Transgene Sequence Directs Cell-Specific and Developmentally Regulated Expression in Retinal Photoreceptor Cells

  2002cited by this paper
• Novel mutations in the NRL gene and associated clinical findings in patients with dominant retinitis pigmentosa.

  2002cited by this paper
• A thyroid hormone receptor that is required for the development of green cone photoreceptors

  2001cited by this paper
• Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes.

  2001cited by this paper
• Nrl is required for rod photoreceptor development

  2001influential reference
• Multiple Phosphorylated Isoforms of NRL Are Expressed in Rod Photoreceptors*

  2001cited by this paper
• A deletion in a photoreceptor-specific nuclear receptor mRNA causes retinal degeneration in the rd7 mouse.

  2000influential reference
• Expression of Chx10 and Chx10-1 in the developing chicken retina.

  2000cited by this paper
• The Leucine Zipper of NRL Interacts with the CRX Homeodomain

  2000cited by this paper
• Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx.

  2000cited by this paper
• Primer3 on the WWW for general users and for biologist programmers.

  2000influential reference
• Molecular genetics of human retinal disease.

  1999cited by this paper
• A mutation in NRL is associated with autosomal dominant retinitis pigmentosa

  1999cited by this paper
• Retinopathy and attenuated circadian entrainment in Crx-deficient mice

  1999influential reference
• De novo mutations in the CRX homeobox gene associated with Leber congenital amaurosis

  1998cited by this paper
• A range of clinical phenotypes associated with mutations in CRX, a photoreceptor transcription-factor gene.

  1998cited by this paper
• The Major Cell Populations of the Mouse Retina

  1998cited by this paper
• Retinal degenerations with truncation mutations in the cone-rod homeobox (CRX) gene.

  1998cited by this paper
• Autoregulation of eukaryotic transcription factors.

  1998cited by this paper
• The First Steps in Seeing

  1998cited by this paper
• Crx, a novel otx-like homeobox gene, shows photoreceptor-specific expression and regulates photoreceptor differentiation.

  1997cited by this paper
• Crx, a novel Otx-like paired-homeodomain protein, binds to and transactivates photoreceptor cell-specific genes.

  1997cited by this paper
• Cone-rod dystrophy due to mutations in a novel photoreceptor-specific homeobox gene (CRX) essential for maintenance of the photoreceptor.

  1997cited by this paper
• Expression of the bZIP transcription factor gene Nrl in the developing nervous system.

  1996cited by this paper
• RER, an Evolutionarily Conserved Sequence Upstream of the Rhodopsin Gene, Has Enhancer Activity (*)

  1996influential reference
• Developmentally important DNA elements within the bovine opsin upstream region.

  1996cited by this paper
• Specific DNA recognition and intersite spacing are critical for action of the bicoid morphogen

  1994cited by this paper
• A global view.

  1994cited by this paper
• The human blue opsin promoter directs transgene expression in short-wave cones and bipolar cells in the mouse retina.

  1994cited by this paper
• A sequence upstream of the mouse blue visual pigment gene directs blue cone-specific transgene expression in mouse retinas

  1994cited by this paper
• Shared nuclear protein binding sites in the upstream region of the rat opsin gene.

  1993cited by this paper
• Spacing ensures autonomous expression of different stripe enhancers in the even-skipped promoter.

  1993cited by this paper
• A conserved retina-specific gene encodes a basic motif/leucine zipper domain.

  1992cited by this paper
• Characterization of developmentally regulated and retina-specific nuclear protein binding to a site in the upstream region of the rat opsin gene.

  1991cited by this paper
• Unusual topography of bovine rhodopsin promoter-lacZ fusion gene expression in transgenic mouse retinas.

  1991cited by this paper
• A genetic model for interaction of the homeodomain recognition helix with DNA.

  1991cited by this paper
• Br. J. Cancer

  1991cited by this paper

• Massively parallel reporter assay for mapping gene-specific regulatory regions at single-nucleotide resolution.

  2026influential citation
• Decoding Pediatric Inherited Retinal Dystrophies: Bridging Genetic Complexity and Clinical Heterogeneity.

  2025cites this paper
• Massively parallel reporter assay for mapping gene-specific regulatory regions at single nucleotide resolution

  2025cites this paper
• Active DNA demethylation is upstream of rod-photoreceptor fate determination and required for retinal development

  2025cites this paper
• Active DNA demethylation upstream of rod-photoreceptor fate determination is required for retinal development

  2025cites this paper
• Genetic and epigenetic control of photoreceptor development.

  2025cites this paper
• Conservation of cis-regulatory codes over half a billion years of evolution

  2025cites this paper
• Integration of multiomic data identifies core-module of inherited-retinal diseases.

  2025cites this paper
• Human CRX regulates photoreceptor cells development via bidirectional transcriptional control in retinal organoids.

  2025cites this paper
• Maf-family bZIP transcription factor NRL interacts with RNA-binding proteins and R-loops in retinal photoreceptors

  2025cites this paper
• CRX/NRL/NR2E3-regulated tbx2b integrates BMP2 signaling to control opsin expression and larval feeding in fish

  2025cites this paper
• Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain

  2024cites this paper
• Active learning of enhancers and silencers in the developing neural retina.

  2024cites this paper
• Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models

  2024cites this paper
• Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain

  2024cites this paper
• Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors

  2024influential citation
• Ccrk-Mak/Ick signaling is a ciliary transport regulator essential for retinal photoreceptor survival

  2024cites this paper
• Transcriptional precision in photoreceptor development and diseases – Lessons from 25 years of CRX research

  2024cites this paper
• Maf-family bZIP transcription factor NRL interacts with RNA-binding proteins and R-loops in retinal photoreceptors

  2024cites this paper
• Homeobox gene‐encoded transcription factors in development and mature circadian function of the rodent pineal gland

  2024cites this paper
• Molecular basis of CRX/DNA recognition and stoichiometry at the Ret4 response element.

  2024cites this paper
• Genotypic Profile and Clinical Characteristics of CRX-Associated Retinopathy in Koreans

  2023cites this paper
• Active learning of enhancer and silencer regulatory grammar in photoreceptors

  2023cites this paper
• Disease-causing mutations in genes encoding transcription factors critical for photoreceptor development

  2023cites this paper
• Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms

  2023cites this paper
• Pathogenic variants in Crx have distinct cis-regulatory effects on enhancers and silencers in photoreceptors

  2023cites this paper
• Unleashing the potential of CRISPR multiplexing: Harnessing Cas12 and Cas13 for precise gene modulation in eye diseases.

  2023cites this paper
• Cat LCA-CRX Model, Homozygous for an Antimorphic Mutation Has a Unique Phenotype

  2023cites this paper
• CRX haploinsufficiency compromises photoreceptor precursor translocation and differentiation in human retinal organoids

  2023cites this paper
• Transcription factor interactions explain the context-dependent activity of CRX binding sites

  2023influential citation
• Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms

  2023cites this paper
• The LHX2-OTX2 transcriptional regulatory module controls retinal pigmented epithelium differentiation and underlies genetic risk for age-related macular degeneration

  2023cites this paper
• Structural and functional analysis of the human cone‐rod homeobox transcription factor

  2022cites this paper
• Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives

  2022cites this paper
• Relationship between miR-203a inhibition and oil-induced toxicity in early life stage zebrafish (Danio rerio)

  2022cites this paper
• Temporal and Isoform-Specific Expression of CTBP2 Is Evolutionarily Conserved Between the Developing Chick and Human Retina

  2022cites this paper
• Interaction of human CRX and NRL in live HEK293T cells measured using fluorescence resonance energy transfer (FRET)

  2022cites this paper
• Mutations in BCOR, a co-repressor of CRX/OTX2, are associated with early-onset retinal degeneration

  2022cites this paper
• Protein kinase CK2 modulates the activity of Maf-family bZIP transcription factor NRL in rod photoreceptors of mammalian retina.

  2022cites this paper
• Rho enhancers play unexpectedly minor roles in Rhodopsin transcription and rod cell integrity

  2022cites this paper
• Cell fate decisions, transcription factors and signaling during early retinal development

  2022cites this paper
• MLL5 is involved in retinal photoreceptor maturation through facilitating CRX-mediated photoreceptor gene transactivation

  2022influential citation
• Developmental genome-wide occupancy analysis of bZIP transcription factor NRL uncovers the role of c-Jun in early differentiation of rod photoreceptors in the mammalian retina.

  2022cites this paper
• Polyglutamine-expanded ATXN7 alters a specific epigenetic signature underlying photoreceptor identity gene expression in SCA7 mouse retinopathy

  2022cites this paper
• Caenorhabditis elegans sine oculis/SIX-type homeobox genes act as homeotic switches to define neuronal subtype identities

  2022cites this paper
• Building a Mammalian Retina: An Eye on Chromatin Structure

  2021cites this paper
• Allele-specific gene editing to rescue dominant CRX-associated LCA7 phenotypes in a retinal organoid model

  2021cites this paper
• The initiation and maintenance of a differentiated state in development.

  2021cites this paper
• Foxq2 determines blue cone identity in zebrafish

  2021cites this paper
• A combinatorial cis-regulatory logic restricts color-sensing Rhodopsins to specific photoreceptor subsets in Drosophila

  2021cites this paper
• In silico analysis of the transcriptional regulatory logic of neuronal identity specification throughout the C. elegans nervous system

  2021cites this paper
• Ubiquitous Chromatin Modifiers in Congenital Retinal Diseases: Implications for Disease Modeling and Regenerative Medicine.

  2021cites this paper
• The role of homeobox gene‐encoded transcription factors in regulation of phototransduction: Implementing the primary pinealocyte culture as a photoreceptor model

  2021cites this paper
• Multi-omics analysis of intertumoral heterogeneity within medulloblastoma uncharted-pathway subtypes

  2021cites this paper
• Information content differentiates enhancers from silencers in mouse photoreceptors

  2021influential citation
• Information content differentiates enhancers from silencers in mouse photoreceptors.

  2021cites this paper
• Human MiniPromoters for ocular-rAAV expression in ON bipolar, cone, corneal, endothelial, Müller glial, and PAX6 cells

  2021cites this paper
• The initiation of Otx2 expression in the developing mouse retina requires a unique enhancer and either Ascl1 or Neurog2 activity.

  2021cites this paper
• Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types

  2020influential citation
• Recapitulating Evolutionary Divergence in a Single Cis-Regulatory Element Is Sufficient to Cause Expression Changes of the Lens Gene Tdrd7

  2020cites this paper
• Functional and Evolutionary Diversification of Otx2 and Crx in Vertebrate Retinal Photoreceptor and Bipolar Cell Development.

  2020cites this paper
• Retina Development in Vertebrates: Systems Biology Approaches to Understanding Genetic Programs

  2020cites this paper
• Mapping the cis-regulatory architecture of the human retina reveals noncoding genetic variation in disease

  2020cites this paper
• COCO enhances the efficiency of photoreceptor precursor differentiation in early human embryonic stem cell-derived retinal organoids

  2020cites this paper
• Core-clock genes Period 1 and 2 regulate visual cascade and cell cycle components during mouse eye development.

  2020cites this paper
• Cell type- and stage-specific expression of Otx2 is regulated by multiple transcription factors and cis-regulatory modules in the retina

  2020cites this paper
• Nrl Is Dispensable for Specification of Rod Photoreceptors in Adult Zebrafish Despite Its Deeply Conserved Requirement Earlier in Ontogeny

  2020cites this paper
• The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development

  2020cites this paper
• Establishment and maintenance of motor neuron identity via temporal modularity in terminal selector function

  2020cites this paper
• Genome-wide Profiling Identifies DNA Methylation Signatures of Aging in Rod Photoreceptors Associated with Alterations in Energy Metabolism.

  2020influential citation
• RNA sequencing analysis of the human retina and associated ocular tissues

  2020cites this paper
• Nrl is dispensable for specification of rod photoreceptors in adult zebrafish contrasting a deeply conserved requirement earlier in ontogeny

  2020cites this paper
• Cell type- and stage-specific expression of Otx2 is coordinated by a cohort of transcription factors and multiple cis-regulatory modules in the retina

  2019cites this paper
• Ciliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation

  2019cites this paper
• NRL- and CRX-guided gene network modulates photoreceptor presynapse size and positioning during retinal development

  2019cites this paper
• Incomplete penetrance of CRX gene for autosomal dominant form of cone-rod dystrophy

  2019cites this paper
• Expression of deubiquitinating enzyme genes in the developing mammal retina

  2019cites this paper
• Cis-regulatory basis of sister cell type divergence in the vertebrate retina

  2019cites this paper
• Six6 and Six7 coordinately regulate expression of middle-wavelength opsins in zebrafish

  2019influential citation
• Insights Into the Epigenetics of Retinal Development and Diseases

  2019cites this paper
• High-Throughput Analysis of Retinal Cis-Regulatory Networks by Massively Parallel Reporter Assays.

  2019cites this paper
• Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types

  2019cites this paper
• TFforge utilizes large-scale binding site divergence to identify transcriptional regulators involved in phenotypic differences

  2018cites this paper
• Characterizing epigenetic regulation in the developing chicken retina

  2018cites this paper
• Targeted deletion of an NRL‐ and CRX‐regulated alternative promoter specifically silences FERM and PDZ domain containing 1 (Frmpd1) in rod photoreceptors

  2018cites this paper
• REforge Associates Transcription Factor Binding Site Divergence in Regulatory Elements with Phenotypic Differences between Species

  2018cites this paper
• A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivo

  2018influential citation
• Cone‐rod homeobox CRX controls presynaptic active zone formation in photoreceptors of mammalian retina

  2018cites this paper
• CRX-linked macular dystrophy with intrafamilial variable expressivity

  2018cites this paper
• CRX directs photoreceptor differentiation by accelerating chromatin remodeling at specific target sites

  2018cites this paper
• Novel Approaches to Studying the Effects of Cis-Regulatory Variants in the Central Nervous System

  2018influential citation
• ZAG-1/ZEB and EGL-44/TEAD form a negative feedback loop to safeguard the choice of cell fate

  2018cites this paper
• Role of the Glycogen Synthase Kinase 3 for the Retinal Development and Homeostasis

  2018cites this paper
• Inhibition of cell fate repressors secures the differentiation of the touch receptor neurons of Caenorhabditis elegans

  2018cites this paper
• Immunophenotyping of cone photoreceptors during postnatal retinal development

  2018cites this paper
• Epigenomic Profiling and Single-Nucleus-RNA-Seq Reveal Cis-Regulatory Elements in Human Retina, Macula and RPE and Non-Coding Genetic Variation

  2018influential citation
• In silico modeling of epigenetic-induced changes in photoreceptor cis-regulatory elements

  2018influential citation
• Can We Predict Gene Expression by Understanding Proximal Promoter Architecture?

  2017cites this paper
• Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution

  2017cites this paper
• Cell Type-Specific Epigenomic Analysis Reveals a Uniquely Closed Chromatin Architecture in Mouse Rod Photoreceptors

  2017cites this paper