Epigenomic landscapes of retinal rods and cones

被引：97

作者：

Mo, Alisa ^{[1
,2
]}

Luo, Chongyuan ^{[3
,4
]}

Davis, Fred P. ^{[5
,12
]}

Mukamel, Eran A. ^{[6
]}

Henry, Gilbert L. ^{[5
]}

Nery, Joseph R. ^{[3
]}

Urich, Mark A. ^{[3
]}

Picard, Serge ^{[5
]}

Lister, Ryan ^{[3
,7
]}

Eddy, Sean R. ^{[5
,13
,14
,15
]}

Beer, Michael A. ^{[8
,9
]}

Ecker, Joseph R. ^{[3
,4
]}

Nathans, Jeremy ^{[1
,2
,10
,11
]}

机构：

[1] Johns Hopkins Univ, Sch Med, Dept Mol Biol & Genet, Baltimore, MD 21205 USA

[2] Johns Hopkins Univ, Sch Med, Dept Neurosci, Baltimore, MD 21205 USA

[3] Salk Inst Biol Studies, Genom Anal Lab, 10010 N Torrey Pines Rd, La Jolla, CA 92037 USA

[4] Salk Inst Biol Studies, Howard Hughes Med Inst, La Jolla, CA 92037 USA

[5] Howard Hughes Med Inst, Janelia Res Campus, Ashburn, VA USA

[6] Univ Calif San Diego, Dept Cognit Sci, La Jolla, CA 92093 USA

[7] Univ Western Australia, ARC Ctr Excellence Plant Energy Biol, Crawley, WA, Australia

[8] Johns Hopkins Univ, Sch Med, McKusick Nathans Inst Genet Med, Baltimore, MD USA

[9] Johns Hopkins Univ, Dept Biomed Engn, Baltimore, MD USA

[10] Johns Hopkins Univ, Sch Med, Dept Ophthalmol, Baltimore, MD 21205 USA

[11] Johns Hopkins Univ, Sch Med, Howard Hughes Med Inst, Baltimore, MD 21205 USA

[12] NIAMSD, Mol Immunol & Inflammat Branch, NIH, Bethesda, MD 20892 USA

[13] Harvard Univ, Howard Hughes Med Inst, Cambridge, MA 02138 USA

[14] Harvard Univ, Dept Mol & Cellular Biol, Cambridge, MA 02138 USA

[15] Harvard Univ, John A Paulson Sch Engn & Appl Sci, Cambridge, MA 02138 USA

来源：

ELIFE | 2016年 / 5卷

基金：

美国国家卫生研究院;

关键词：

DNA METHYLATION; CHIP-SEQ; HIERARCHICAL MODEL; CRE RECOMBINASE; HOMEOBOX GENE; TRANSCRIPTION; EXPRESSION; PHOTORECEPTORS; CHROMATIN; SEQUENCE;

D O I：

10.7554/eLife.11613

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：29

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