PUBLICATION

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

Authors
Long, H.K., Sims, D., Heger, A., Blackledge, N.P., Kutter, C., Wright, M.L., Grützner, F., Odom, D.T., Patient, R., Ponting, C.P., and Klose, R.J.
ID
ZDB-PUB-130329-9
Date
2013
Source
eLIFE   2: e00348 (Journal)
Registered Authors
Patient, Roger K.
Keywords
none
Datasets
GEO:GSE43512
MeSH Terms
  • Animals
  • Base Sequence
  • Biological Evolution
  • Chickens/genetics
  • Chromatin Assembly and Disassembly
  • Conserved Sequence
  • CpG Islands*
  • DNA Methylation*
  • Databases, Genetic
  • Epigenesis, Genetic*
  • Gene Expression Profiling*/methods
  • Humans
  • Lizards/genetics
  • Mice
  • Platypus/genetics
  • Promoter Regions, Genetic*
  • Species Specificity
  • Xenopus/genetics
  • Zebrafish/genetics
PubMed
23467541 Full text @ Elife
Abstract

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.

Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping