IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v446y2007i7135d10.1038_nature05632.html
   My bibliography  Save this article

Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome

Author

Listed:
  • Istvan Albert

    (Center for Comparative Genomics and Bioinformatics,)

  • Travis N. Mavrich

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

  • Lynn P. Tomsho

    (Center for Comparative Genomics and Bioinformatics,)

  • Ji Qi

    (Center for Comparative Genomics and Bioinformatics,)

  • Sara J. Zanton

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

  • Stephan C. Schuster

    (Center for Comparative Genomics and Bioinformatics,)

  • B. Franklin Pugh

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

Abstract

The nucleosome is the fundamental building block of eukaryotic chromosomes. Access to genetic information encoded in chromosomes is dependent on the position of nucleosomes along the DNA. Alternative locations just a few nucleotides apart can have profound effects on gene expression1. Yet the nucleosomal context in which chromosomal and gene regulatory elements reside remains ill-defined on a genomic scale. Here we sequence the DNA of 322,000 individual Saccharomyces cerevisiae nucleosomes, containing the histone variant H2A.Z, to provide a comprehensive map of H2A.Z nucleosomes in functionally important regions. With a median 4-base-pair resolution, we identify new and established signatures of nucleosome positioning. A single predominant rotational setting and multiple translational settings are evident. Chromosomal elements, ranging from telomeres to centromeres and transcriptional units, are found to possess characteristic nucleosomal architecture that may be important for their function. Promoter regulatory elements, including transcription factor binding sites and transcriptional start sites, show topological relationships with nucleosomes, such that transcription factor binding sites tend to be rotationally exposed on the nucleosome surface near its border. Transcriptional start sites tended to reside about one helical turn inside the nucleosome border. These findings reveal an intimate relationship between chromatin architecture and the underlying DNA sequence it regulates.

Suggested Citation

  • Istvan Albert & Travis N. Mavrich & Lynn P. Tomsho & Ji Qi & Sara J. Zanton & Stephan C. Schuster & B. Franklin Pugh, 2007. "Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome," Nature, Nature, vol. 446(7135), pages 572-576, March.
    • Handle: RePEc:nat:nature:v:446:y:2007:i:7135:d:10.1038_nature05632
    DOI: 10.1038/nature05632
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/nature05632
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1038/nature05632?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Ji-Ping Wang & Yvonne Fondufe-Mittendorf & Liqun Xi & Guei-Feng Tsai & Eran Segal & Jonathan Widom, 2008. "Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae," PLOS Computational Biology, Public Library of Science, vol. 4(9), pages 1-10, September.
    2. Wolfram Möbius & Ulrich Gerland, 2010. "Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites," PLOS Computational Biology, Public Library of Science, vol. 6(8), pages 1-11, August.
    3. Guo-Cheng Yuan & Jun S Liu, 2008. "Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion," PLOS Computational Biology, Public Library of Science, vol. 4(1), pages 1-11, January.
    4. Kuan Pei Fen & Huebert Dana & Gasch Audrey & Keles Sunduz, 2009. "A Non-Homogeneous Hidden-State Model on First Order Differences for Automatic Detection of Nucleosome Positions," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-47, June.
    5. Sai Li & Michael R. Wasserman & Olga Yurieva & Lu Bai & Michael E. O’Donnell & Shixin Liu, 2022. "Nucleosome-directed replication origin licensing independent of a consensus DNA sequence," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    6. Alexander W. Blocker & Edoardo M. Airoldi, 2016. "Template-Based Models for Genome-Wide Analysis of Next-Generation Sequencing Data at Base-Pair Resolution," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 111(515), pages 967-987, July.
    7. Jiayi Fan & Andrew T. Moreno & Alexander S. Baier & Joseph J. Loparo & Craig L. Peterson, 2022. "H2A.Z deposition by SWR1C involves multiple ATP-dependent steps," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    8. Zing Tsung-Yeh Tsai & Shin-Han Shiu & Huai-Kuang Tsai, 2015. "Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast," PLOS Computational Biology, Public Library of Science, vol. 11(8), pages 1-22, August.
    9. Shuxiang Li & Tiejun Wei & Anna R. Panchenko, 2023. "Histone variant H2A.Z modulates nucleosome dynamics to promote DNA accessibility," Nature Communications, Nature, vol. 14(1), pages 1-10, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:nature:v:446:y:2007:i:7135:d:10.1038_nature05632. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.