title: CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors.
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.
authors.affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110-1024, USA. jcorbo@pathology.wustl.edu
authors.forename: Joseph C
authors.initials: JC
authors.lastname: Corbo
authors.forename: Karen A
authors.initials: KA
authors.lastname: Lawrence
authors.forename: Marcus
authors.initials: M
authors.lastname: Karlstetter
authors.forename: Connie A
authors.initials: CA
authors.lastname: Myers
authors.forename: Musa
authors.initials: M
authors.lastname: Abdelaziz
authors.forename: William
authors.initials: W
authors.lastname: Dirkes
authors.forename: Karin
authors.initials: K
authors.lastname: Weigelt
authors.forename: Martin
authors.initials: M
authors.lastname: Seifert
authors.forename: Vladimir
authors.initials: V
authors.lastname: Benes
authors.forename: Lars G
authors.initials: LG
authors.lastname: Fritsche
authors.forename: Bernhard H F
authors.initials: BH
authors.lastname: Weber
authors.forename: Thomas
authors.initials: T
authors.lastname: Langmann
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002874:Chromosome Mapping / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism*; D051379:Mice; D008810:Mice, Inbred C57BL; D018345:Mice, Knockout; D008969:Molecular Sequence Data; D010802:Phylogeny; D011485:Protein Binding; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D017949:Retinal Cone Photoreceptor Cells / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods; D012689:Sequence Homology, Nucleic Acid; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism*
chemical_list: D018398:Homeodomain Proteins; D015534:Trans-Activators; C109288:cone rod homeobox protein