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Exploring long-range genome interactions using the WashU Epigenome Browser

Nature Methods volume 10, pages 375–376 (2013)Cite this article

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To the Editor:

Eukaryotic chromosomes are a highly organized three-dimensional entity folded through a tightly regulated process1,2 with important functions that include bringing distal regulatory elements into the vicinity of their target gene promoters and arranging the chromosomes into distinct compartments3,4,5,6. Recent technological innovations, including chromosome conformation capture carbon copy (5C), Hi-C and chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), have facilitated the discovery of chromosomal organization principles and folding architectures at unprecedented scales and resolution. Each technology also comes with corresponding computational tools7,8 to process and visualize its specific data type (Supplementary Note 1). However, visualizing and navigating long-range interaction data, as well as integrating these interactions with other epigenomics data, remains a much-desired capability and a daunting challenge9.

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Figure 1: Two genomic regions as viewed in the WashU Epigenome Browser.

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Acknowledgements

We thank the laboratories of B. Ren, C.-L. Wei, Y. Ruan, J. Dekker; the UCSC Genome Browser team; and the ENCODE Consortium for providing long-range interaction data sets; and the Roadmap Epigenomics Consortium for providing epigenomics data sets. We thank many collaborators in the Roadmap Epigenomics Consortium who participated in software testing and provided helpful comments. We acknowledge support from the US National Institutes of Health (NIH) Roadmap Epigenomics Program, sponsored by the National Institute on Drug Abuse (NIDA) and the National Institute of Environmental Health Sciences (NIEHS). J.F.C. and T.W. are supported by NIH grant 5U01ES017154. X.Z. is supported by NIDA's R25 program DA027995. T.W. is supported in part by the March of Dimes Foundation, the Edward Jr. Mallinckrodt Foundation, NIH P50CA134254 and a grant from the Foundation for Barnes-Jewish Hospital.

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Authors and Affiliations

  1. Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA

    Xin Zhou, Rebecca F Lowdon, Daofeng Li, Heather A Lawson & Ting Wang

  2. Department of Psychiatry, Washington University in St. Louis, St. Louis, Missouri, USA

    Pamela A F Madden

  3. Department of Neurological Surgery, Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA

    Joseph F Costello

  4. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA

    Joseph F Costello

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  1. Xin Zhou
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  2. Rebecca F Lowdon
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Corresponding authors

Correspondence to Joseph F Costello or Ting Wang.

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The authors declare no competing financial interests.

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Supplementary Text and Figures

Supplementary Figures 1–5, Supplementary Methods and Supplementary Notes 1 and 2 (PDF 4734 kb)

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Zhou, X., Lowdon, R., Li, D. et al. Exploring long-range genome interactions using the WashU Epigenome Browser. Nat Methods 10, 375–376 (2013). https://doi.org/10.1038/nmeth.2440

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