IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v523y2015i7561d10.1038_nature14590.html
   My bibliography  Save this article

Single-cell chromatin accessibility reveals principles of regulatory variation

Author

Listed:
  • Jason D. Buenrostro

    (Stanford University School of Medicine
    Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford University School of Medicine)

  • Beijing Wu

    (Stanford University School of Medicine)

  • Ulrike M. Litzenburger

    (Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford University School of Medicine)

  • Dave Ruff

    (Fluidigm Corporation)

  • Michael L. Gonzales

    (Fluidigm Corporation)

  • Michael P. Snyder

    (Stanford University School of Medicine)

  • Howard Y. Chang

    (Program in Epithelial Biology and the Howard Hughes Medical Institute, Stanford University School of Medicine)

  • William J. Greenleaf

    (Stanford University School of Medicine
    Stanford University)

Abstract

A single-cell method for probing genome-wide chromatin accessibility has been developed; the results provide insight into the relationship between cell-to-cell variation associated with specific trans-factors and cis-elements, as well insights into the relationship between chromatin accessibility and three-dimensional genome organization.

Suggested Citation

  • Jason D. Buenrostro & Beijing Wu & Ulrike M. Litzenburger & Dave Ruff & Michael L. Gonzales & Michael P. Snyder & Howard Y. Chang & William J. Greenleaf, 2015. "Single-cell chromatin accessibility reveals principles of regulatory variation," Nature, Nature, vol. 523(7561), pages 486-490, July.
    • Handle: RePEc:nat:nature:v:523:y:2015:i:7561:d:10.1038_nature14590
    DOI: 10.1038/nature14590
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/nature14590
    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/nature14590?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. Songming Tang & Xuejian Cui & Rongxiang Wang & Sijie Li & Siyu Li & Xin Huang & Shengquan Chen, 2024. "scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    2. Shengen Shawn Hu & Lin Liu & Qi Li & Wenjing Ma & Michael J. Guertin & Clifford A. Meyer & Ke Deng & Tingting Zhang & Chongzhi Zang, 2022. "Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    3. Youtao Lu & Jaehee Lee & Jifen Li & Srinivasa Rao Allu & Jinhui Wang & HyunBum Kim & Kevin L. Bullaughey & Stephen A. Fisher & C. Erik Nordgren & Jean G. Rosario & Stewart A. Anderson & Alexandra V. U, 2023. "CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    4. Aaron T L Lun & Hervé Pagès & Mike L Smith, 2018. "beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types," PLOS Computational Biology, Public Library of Science, vol. 14(5), pages 1-15, May.
    5. Jingyang Qian & Jie Liao & Ziqi Liu & Ying Chi & Yin Fang & Yanrong Zheng & Xin Shao & Bingqi Liu & Yongjin Cui & Wenbo Guo & Yining Hu & Hudong Bao & Penghui Yang & Qian Chen & Mingxiao Li & Bing Zha, 2023. "Reconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    6. Haowen Zhang & Li Song & Xiaotao Wang & Haoyu Cheng & Chenfei Wang & Clifford A. Meyer & Tao Liu & Ming Tang & Srinivas Aluru & Feng Yue & X. Shirley Liu & Heng Li, 2021. "Fast alignment and preprocessing of chromatin profiles with Chromap," Nature Communications, Nature, vol. 12(1), pages 1-6, December.
    7. B. Edginton-White & A. Maytum & S. G. Kellaway & D. K. Goode & P. Keane & I. Pagnuco & S. A. Assi & L. Ames & M. Clarke & P. N. Cockerill & B. Göttgens & J. B. Cazier & C. Bonifer, 2023. "A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    8. Parashar Dhapola & Johan Rodhe & Rasmus Olofzon & Thomas Bonald & Eva Erlandsson & Shamit Soneji & Göran Karlsson, 2022. "Scarf enables a highly memory-efficient analysis of large-scale single-cell genomics data," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    9. Vianne R. Gao & Rui Yang & Arnav Das & Renhe Luo & Hanzhi Luo & Dylan R. McNally & Ioannis Karagiannidis & Martin A. Rivas & Zhong-Min Wang & Darko Barisic & Alireza Karbalayghareh & Wilfred Wong & Yi, 2024. "ChromaFold predicts the 3D contact map from single-cell chromatin accessibility," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    10. Suhas V. Vasaikar & Adam K. Savage & Qiuyu Gong & Elliott Swanson & Aarthi Talla & Cara Lord & Alexander T. Heubeck & Julian Reading & Lucas T. Graybuck & Paul Meijer & Troy R. Torgerson & Peter J. Sk, 2023. "A comprehensive platform for analyzing longitudinal multi-omics data," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    11. Wenjing Ma & Jiaying Lu & Hao Wu, 2023. "Cellcano: supervised cell type identification for single cell ATAC-seq data," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    12. Zhijian Li & Christoph Kuppe & Susanne Ziegler & Mingbo Cheng & Nazanin Kabgani & Sylvia Menzel & Martin Zenke & Rafael Kramann & Ivan G. Costa, 2021. "Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    13. Anna Laddach & Song Hui Chng & Reena Lasrado & Fränze Progatzky & Michael Shapiro & Alek Erickson & Marisol Sampedro Castaneda & Artem V. Artemov & Ana Carina Bon-Frauches & Eleni-Maria Amaniti & Jens, 2023. "A branching model of lineage differentiation underpinning the neurogenic potential of enteric glia," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    14. Xiang Lin & Tian Tian & Zhi Wei & Hakon Hakonarson, 2022. "Clustering of single-cell multi-omics data with a multimodal deep learning method," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    15. Samir Rachid Zaim & Mark-Phillip Pebworth & Imran McGrath & Lauren Okada & Morgan Weiss & Julian Reading & Julie L. Czartoski & Troy R. Torgerson & M. Juliana McElrath & Thomas F. Bumol & Peter J. Ske, 2024. "MOCHA’s advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
    16. Yoshiharu Muto & Eryn E. Dixon & Yasuhiro Yoshimura & Haojia Wu & Kohei Omachi & Nicolas Ledru & Parker C. Wilson & Andrew J. King & N. Eric Olson & Marvin G. Gunawan & Jay J. Kuo & Jennifer H. Cox & , 2022. "Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    17. Alan Yue Yang Teo & Jordan W. Squair & Gregoire Courtine & Michael A. Skinnider, 2024. "Best practices for differential accessibility analysis in single-cell epigenomics," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    18. Ruohan Wang & Yumin Zheng & Zijian Zhang & Kailu Song & Erxi Wu & Xiaopeng Zhu & Tao P. Wu & Jun Ding, 2024. "MATES: a deep learning-based model for locus-specific quantification of transposable elements in single cell," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    19. Alan Selewa & Kaixuan Luo & Michael Wasney & Linsin Smith & Xiaotong Sun & Chenwei Tang & Heather Eckart & Ivan P. Moskowitz & Anindita Basu & Xin He & Sebastian Pott, 2023. "Single-cell genomics improves the discovery of risk variants and genes of atrial fibrillation," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    20. Fangfang Yan & Akiko Suzuki & Chihiro Iwaya & Guangsheng Pei & Xian Chen & Hiroki Yoshioka & Meifang Yu & Lukas M. Simon & Junichi Iwata & Zhongming Zhao, 2024. "Single-cell multiomics decodes regulatory programs for mouse secondary palate development," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    21. Kristina Handler & Karsten Bach & Costanza Borrelli & Salvatore Piscuoglio & Xenia Ficht & Ilhan E. Acar & Andreas E. Moor, 2023. "Fragment-sequencing unveils local tissue microenvironments at single-cell resolution," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    22. Lei Xiong & Kang Tian & Yuzhe Li & Weixi Ning & Xin Gao & Qiangfeng Cliff Zhang, 2022. "Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space," Nature Communications, Nature, vol. 13(1), pages 1-17, 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:523:y:2015:i:7561:d:10.1038_nature14590. 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.