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, Gr├╝tzner F, Odom DT, Patient R, Ponting CP, Klose RJ

Elife 2 (-) - [2013-02-26; online 2013-02-26]

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:http://dx.doi.org/10.7554/eLife.00348.001.

Claudia Kutter

SciLifeLab Fellow

PubMed 23467541

DOI 10.7554/elife.00348

Crossref 10.7554/elife.00348

Publications 9.5.0