title: Epigenomic landscapes of retinal rods and cones.
abstract: Rod and cone photoreceptors are highly similar in many respects but they have important functional and molecular differences. Here, we investigate genome-wide patterns of DNA methylation and chromatin accessibility in mouse rods and cones and correlate differences in these features with gene expression, histone marks, transcription factor binding, and DNA sequence motifs. Loss of NR2E3 in rods shifts their epigenomes to a more cone-like state. The data further reveal wide differences in DNA methylation between retinal photoreceptors and brain neurons. Surprisingly, we also find a substantial fraction of DNA hypo-methylated regions in adult rods that are not in active chromatin. Many of these regions exhibit hallmarks of regulatory regions that were active earlier in neuronal development, suggesting that these regions could remain undermethylated due to the highly compact chromatin in mature rods. This work defines the epigenomic landscapes of rods and cones, revealing features relevant to photoreceptor development and function.
authors.affiliation: Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States.|Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States.
authors.forename: Alisa
authors.initials: A
authors.lastname: Mo
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.|Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, United States.
authors.forename: Chongyuan
authors.initials: C
authors.lastname: Luo
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Fred P
authors.initials: FP
authors.lastname: Davis
authors.affiliation: Department of Cognitive Science, University of California San Diego, La Jolla, United States.
authors.forename: Eran A
authors.initials: EA
authors.lastname: Mukamel
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Gilbert L
authors.initials: GL
authors.lastname: Henry
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Nery
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Urich
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Serge
authors.initials: S
authors.lastname: Picard
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.|The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Australia.
authors.forename: Ryan
authors.identifier: http://orcid.org/0000-0001-6637-7239
authors.initials: R
authors.lastname: Lister
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.
authors.forename: Sean R
authors.identifier: http://orcid.org/0000-0001-6676-4706
authors.initials: SR
authors.lastname: Eddy
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.|Department of Biomedical Engineering, Johns Hopkins University, Baltimore, United States.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Beer
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States.|Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, United States.
authors.forename: Joseph R
authors.identifier: http://orcid.org/0000-0001-5799-5895
authors.initials: JR
authors.lastname: Ecker
authors.affiliation: Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States.|Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States.|Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, United States.|Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States.
authors.forename: Jeremy
authors.identifier: http://orcid.org/0000-0001-8106-5460
authors.initials: J
authors.lastname: Nathans
mesh_terms: D000818:Animals; D004247:DNA / Q000378:metabolism; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D006657:Histones / Q000378:metabolism; D008745:Methylation; D051379:Mice; D017949:Retinal Cone Photoreceptor Cells / Q000502:physiology*; D017948:Retinal Rod Photoreceptor Cells / Q000502:physiology*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D006657:Histones; D014157:Transcription Factors; D004247:DNA
keywords: DNA methylation; chromatin; evolutionary biology; genomics; mouse; neuroscience; retinal development; retinal photoreceptors; transcription factors