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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
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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.
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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.
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Contributor(s) |
Long HK, Sims D, Ponting CP, Klose RJ |
Citation(s) |
23467541, 27084945 |
Submission date |
Jan 15, 2013 |
Last update date |
May 15, 2019 |
Contact name |
David Sims |
E-mail(s) |
david.sims@dpag.ox.ac.uk
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Phone |
+44 1865 82362
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URL |
http://www.cgat.org
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Organization name |
University of Oxford
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Department |
MRC Functional Genomics Unit
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Lab |
CGAT
|
Street address |
Parks Road
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City |
Oxford |
ZIP/Postal code |
OX1 3PT |
Country |
United Kingdom |
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Platforms (10)
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GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
GPL13741 |
Illumina Genome Analyzer IIx (Xenopus (Silurana) tropicalis) |
GPL15103 |
Illumina HiSeq 1000 (Mus musculus) |
GPL15433 |
Illumina HiSeq 1000 (Homo sapiens) |
GPL15583 |
Illumina Genome Analyzer IIx (Danio rerio) |
GPL16505 |
Illumina HiSeq 1000 (Ornithorhynchus anatinus) |
GPL16506 |
Illumina HiSeq 1000 (Gallus gallus) |
GPL16507 |
Illumina Genome Analyzer IIx (Anolis carolinensis) |
GPL16508 |
Illumina HiSeq 1000 (Xenopus (Silurana) tropicalis) |
GPL16509 |
Illumina HiSeq 1000 (Danio rerio) |
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Samples (24)
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Relations |
SRA |
SRP017952 |
BioProject |
PRJNA186672 |