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Series GSE43512 Query DataSets for GSE43512
Status Public on Jan 22, 2013
Title Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates
Organisms Danio rerio; Xenopus tropicalis; Gallus gallus; Ornithorhynchus anatinus; Homo sapiens; Mus musculus; Anolis carolinensis
Experiment type Methylation profiling by high throughput sequencing
Summary Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive effects of DNA methylation. In lower vertebrates, computational CGI predictions often reside away from gene promoters, suggesting a major divergence in gene promoter architecture across vertebrates. By experimentally identifying non-methylated DNA in the genomes of seven diverse vertebrates, we instead reveal that non-methylated islands (NMIs) of DNA are a central feature of vertebrate gene promoters. Furthermore, NMIs are present at orthologous genes across vast evolutionary distances, revealing a surprising level of conservation in this epigenetic feature. By profiling NMIs in different tissues and developmental stages we uncover a unifying set of features that are central to the function of NMIs in vertebrates. Together these findings demonstrate an ancient logic for NMI usage at gene promoters and reveal an unprecedented level of epigenetic conservation across vertebrate evolution.
 
Overall design Bio-CAP was used to identify non-methylated regions of the genome in seven diverse vertebrates (human, mouse, platypus, chicken, lizard, frog and zebrafish) across a number of tissues.
 
Contributor(s) Long HK, Sims D, Ponting CP, Klose RJ
Citation(s) 23467541, 27084945
Submission date Jan 15, 2013
Last update date Feb 25, 2019
Contact name David Sims
E-mail david.sims@dpag.ox.ac.uk
Phone +44 1865 82362
URL http://www.cgat.org
Organization name University of Oxford
Department MRC Functional Genomics Unit
Lab CGAT
Street address Parks Road
City Oxford
ZIP/Postal code OX1 3PT
Country United Kingdom
 
Platforms (10)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13741 Illumina Genome Analyzer IIx (Xenopus (Silurana) tropicalis)
GPL15103 Illumina HiSeq 1000 (Mus musculus)
Samples (24)
GSM1064674 Human testes INPUT
GSM1064675 Human testes Bio-CAP
GSM1064676 Human liver Bio-CAP
Relations
SRA SRP017952
BioProject PRJNA186672

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE43512_RAW.tar 4.9 Mb (http)(custom) TAR (of BED)
Raw data are available in SRA
Processed data provided as supplementary file

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