Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Research Highlight
  • Published:

DNA methylation

Looking beyond promoters

Nature Reviews Genetics volume 11, page 596 (2010)Cite this article

Subjects

Maunakea and colleagues surveyed DNA methylation patterns across the genome in human brain tissue. They found that 34% of CpG islands (CGIs) in gene bodies are methylated compared with 16% of all CGIs and just 2% of CGIs at 5′ promoters. Using published data from mouse tissues, the authors found that this general pattern and the methylation status of individual CGIs that are orthologous in mice and humans are highly conserved between the two species. Importantly, this tissue-specific DNA methylation is much more common at CGIs in gene bodies than those in 5′ promoters.

Do these patterns of intragenic DNA methylation relate to effects on gene expression? Transcriptomic studies have shown that many genes have alternative promoters within gene bodies. Maunakea and colleagues showed an inverse relationship between intragenic CGI methylation status and transcriptional initiation in mouse and human tissues. They also showed that histone H3 lysine 4 trimethylation (H3K4me3), a chromatin modification that is associated with promoters, is inversely correlated with DNA methylation at intragenic CGIs. These results provide strong correlative support for a role of intragenic DNA methylation in regulating transcription from alternative promoters.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to the full article PDF.

USD 39.95

Prices may be subject to local taxes which are calculated during checkout

References

ORIGINAL RESEARCH PAPER

  1. Maunakea, A. K. et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466, 253–257 (2010)

    Article  CAS  Google Scholar 

FURTHER READING

  1. Hawkins, R. D., Hon, G. C. & Ren, B. Next-generation genomics: an integrative approach. Nature Rev. Genet. 11, 476–486 (2010)

    Article  CAS  Google Scholar 

  2. Suzuki, M. M. & Bird, A. DNA methylation landscapes: provocative insights from epigenomics. Nature Rev. Genet. 9, 465–476 (2008)

    Article  CAS  Google Scholar 

Download references

Authors
  1. Louisa Flintoft
    View author publications

    Search author on:PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Flintoft, L. Looking beyond promoters. Nat Rev Genet 11, 596 (2010). https://doi.org/10.1038/nrg2851

Download citation

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/nrg2851

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing