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.

ChIPs and regulatory bits

Nature Biotechnology volume 28, pages 142–143 (2010)Cite this article

Subjects

Machine learning reveals combinatorial patterns of transcription factor binding that drive gene expression.

Gene expression patterns are orchestrated largely by promoters and enhancers, which integrate a multitude of signaling and transcriptional inputs1. But exactly how these cis-regulatory modules control transcription on a global scale has been devilishly hard to decipher. A recent study by Zinzen et al.2 in Nature marks exciting progress on this problem. The authors' key innovation is a technique to predict the expression activity driven by any genomic segment using transcription factor occupancy data generated from high-throughput chromatin immunoprecipitation (ChIP) assays. The approach led to the discovery of dozens of novel cis-regulatory modules involved in mesoderm and muscle development in the Drosophila melanogaster embryo, while providing new insights into the underlying regulatory code.

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

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Learn more

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

Figure 1: Pipeline for discovery of cis-regulatory modules involved in mesoderm specification.

References

  1. Davidson, E.H. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution (Academic Press, 2006).

    Google Scholar 

  2. Zinzen, R.P., Girardot, C., Gagneur, J., Braun, M. & Furlong, E.E. Nature 462, 65–70 (2009).

    Article  CAS  Google Scholar 

  3. Janssens, H. et al. Nat. Genet. 38, 1159–1165 (2006).

    Article  CAS  Google Scholar 

  4. Segal, E. & Widom, J. Nat. Rev. Genet. 10, 443–456 (2009).

    Article  CAS  PubMed Central  Google Scholar 

  5. Beer, M.A. & Tavazoie, S. Cell 117, 185–198 (2004).

    Article  CAS  Google Scholar 

  6. Arnosti, D.N. & Kulkarni, M.M. J. Cell. Biochem. 94, 890–898 (2005).

    Article  CAS  Google Scholar 

  7. Warner, J.B. et al. Nat. Methods 5, 347–353 (2008).

    Article  CAS  PubMed Central  Google Scholar 

  8. Tomancak, P. et al. Genome Biol. 8, R145 (2007).

    Article  PubMed Central  Google Scholar 

  9. Venter, M. Trends Plant Sci. 12, 118–124 (2007).

    Article  CAS  Google Scholar 

  10. Haseltine, E.L. & Arnold, F.H. Annu. Rev. Biophys. Biomol. Struct. 36, 1–19 (2007).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Xin He and Saurabh Sinha are at the University of Illinois at Urbana-Champaign, Urbana, Illinois.,

    Xin He & Saurabh Sinha

Authors
  1. Xin He
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Saurabh Sinha
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Xin He or Saurabh Sinha.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

He, X., Sinha, S. ChIPs and regulatory bits. Nat Biotechnol 28, 142–143 (2010). https://doi.org/10.1038/nbt0210-142

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt0210-142

This article is cited by

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