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Elife February 26, 2013; 2 e00348.
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Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates.

Long HK , Sims D , Heger A , Blackledge NP , Kutter C , Wright ML , Grützner F , Odom DT , Patient R , Ponting CP , Klose RJ .

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 on chromatin. In cold-blooded 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. DOI:

PubMed ID: 23467541
PMC ID: PMC3583005
Article link: Elife
Grant support: [+]

Species referenced: Xenopus
Genes referenced: acta4 aptx dnaja1 ezh2 gnao1 gsx1 nkx2-2 nmi rnf2 smu1 sp9 suz12

GEO Series: GSE43512: NCBI

Article Images: [+] show captions
References [+] :
Aday, Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites. 2011, Pubmed