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Nucleosome organization in the Drosophila genome

Author

Listed:
  • Travis N. Mavrich

    (Center for Gene Regulation, and,
    Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA)

  • Cizhong Jiang

    (Center for Gene Regulation, and,
    Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA)

  • Ilya P. Ioshikhes

    (Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA)

  • Xiaoyong Li

    (Berkeley Drosophila Transcription Network Project, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720, USA)

  • Bryan J. Venters

    (Center for Gene Regulation, and,
    Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA)

  • Sara J. Zanton

    (Center for Gene Regulation, and,
    Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA)

  • Lynn P. Tomsho

    (Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA)

  • Ji Qi

    (Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA)

  • Robert L. Glaser

    (Wadsworth Center, State University of New York, Albany, New York 12201-2002, USA)

  • Stephan C. Schuster

    (Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA)

  • David S. Gilmour

    (Center for Gene Regulation, and,)

  • Istvan Albert

    (Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA)

  • B. Franklin Pugh

    (Center for Gene Regulation, and,
    Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA)

Abstract

Comparative genomics of nucleosome positions provides a powerful means for understanding how the organization of chromatin and the transcription machinery co-evolve. Here we produce a high-resolution reference map of H2A.Z and bulk nucleosome locations across the genome of the fly Drosophila melanogaster and compare it to that from the yeast Saccharomyces cerevisiae. Like Saccharomyces, Drosophila nucleosomes are organized around active transcription start sites in a canonical -1, nucleosome-free region, +1 arrangement. However, Drosophila does not incorporate H2A.Z into the -1 nucleosome and does not bury its transcriptional start site in the +1 nucleosome. At thousands of genes, RNA polymerase II engages the +1 nucleosome and pauses. How the transcription initiation machinery contends with the +1 nucleosome seems to be fundamentally different across major eukaryotic lines.

Suggested Citation

  • Travis N. Mavrich & Cizhong Jiang & Ilya P. Ioshikhes & Xiaoyong Li & Bryan J. Venters & Sara J. Zanton & Lynn P. Tomsho & Ji Qi & Robert L. Glaser & Stephan C. Schuster & David S. Gilmour & Istvan Al, 2008. "Nucleosome organization in the Drosophila genome," Nature, Nature, vol. 453(7193), pages 358-362, May.
    • Handle: RePEc:nat:nature:v:453:y:2008:i:7193:d:10.1038_nature06929
    DOI: 10.1038/nature06929
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    Cited by:

    1. Sarvesh Nikumbh & Boris Lenhard, 2023. "Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation," PLOS Computational Biology, Public Library of Science, vol. 19(11), pages 1-32, November.

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