ArticleEpigenetics & chromatin2015
DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements.
Article in Epigenetics & chromatin, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 66 citations in OpenAlex.
- A robust cis-regulatory network ensures Otx2 expression during retinal development.Development (Cambridge, England) · 2026Article
- Epigenomic signatures of cis-regulatory elements in the developing mouse and pig forelimb.Scientific data · 2025Article
- Cardiac GR Mediates the Diurnal Rhythm in Ventricular Arrhythmia Susceptibility.Circulation research · 2024Article
- Pathogenic variants inGenome research · 2024Article
- Pathogenic variants in Crx have distinct cis-regulatory effects on enhancers and silencers in photoreceptors.bioRxiv : the preprint server for biology · 2023Article
- Rho enhancers play unexpectedly minor roles in Rhodopsin transcription and rod cell integrity.Scientific reports · 2023Article
- Multiomics Analysis Reveals Novel Genetic Determinants for Lens Differentiation, Structure, and Transparency.Biomolecules · 2023Review
- Key transcription factors influence the epigenetic landscape to regulate retinal cell differentiation.Nucleic acids research · 2023Article
- Disease-causing mutations in genes encoding transcription factors critical for photoreceptor development.Frontiers in molecular neuroscience · 2023Review
- Cell fate decisions, transcription factors and signaling during early retinal development.Progress in retinal and eye research · 2022Review
- An enhancer located in a Pde6c intron drives transient expression in the cone photoreceptors of developing mouse and human retinas.Developmental biology · 2022Article
- Construction and characterization of EGFP reporter plasmid harboring putative human RAX promoter for in vitro monitoring of retinal progenitor cells identity.BMC molecular and cell biology · 2021Article
- Initiation of Otx2 expression in the developing mouse retina requires a unique enhancer and either Ascl1 or Neurog2 activity.Development (Cambridge, England) · 2021Article
- Building a Mammalian Retina: An Eye on Chromatin Structure.Frontiers in genetics · 2021Review
- TheProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Prdm1 overexpression causes a photoreceptor fate-shift in nascent, but not mature, bipolar cells.Developmental biology · 2020Article
- Cell type- and stage-specific expression of Otx2 is regulated by multiple transcription factors andDevelopment (Cambridge, England) · 2020Article
- Mapping theProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Enhancer transcription identifiesDevelopment (Cambridge, England) · 2020Article
- Epigenetics in neuronal regeneration.Seminars in cell & developmental biology · 2020Review
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Authors and funding
13 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundThe brain, spinal cord, and neural retina comprise the central nervous system (CNS) of vertebrates. Understanding the regulatory mechanisms that underlie the enormous cell-type diversity of the CNS is a significant challenge. Whole-genome mapping of DNase I-hypersensitive sites (DHSs) has been used to identify cis-regulatory elements in many tissues. We have applied this approach to the mouse CNS, including developing and mature neural retina, whole brain, and two well-characterized brain regions, the cerebellum and the cerebral cortex.
resultsFor the various regions and developmental stages of the CNS that we analyzed, there were approximately the same number of DHSs; however, there were many DHSs unique to each CNS region and developmental stage. Many of the DHSs are likely to mark enhancers that are specific to the specific CNS region and developmental stage. We validated the DNase I mapping approach for identification of CNS enhancers using the existing VISTA Browser database and with in vivo and in vitro electroporation of the retina. Analysis of transcription factor consensus sites within the DHSs shows distinct region-specific profiles of transcriptional regulators particular to each region. Clustering developmentally dynamic DHSs in the retina revealed enrichment of developmental stage-specific transcriptional regulators. Additionally, we found reporter gene activity in the retina driven from several previously uncharacterized regulatory elements surrounding the neurodevelopmental gene Otx2. Identification of DHSs shared between mouse and human showed region-specific differences in the evolution of cis-regulatory elements.
conclusionsOverall, our results demonstrate the potential of genome-wide DNase I mapping to cis-regulatory questions regarding the regional diversity within the CNS. These data represent an extensive catalogue of potential cis-regulatory elements within the CNS that display region and temporal specificity, as well as a set of DHSs common to CNS tissues. Further examination of evolutionary conservation of DHSs between CNS regions and different species may reveal important cis-regulatory elements in the evolution of the mammalian CNS.
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