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Chromatin Accessibility

Methods and Protocols

  • Book
  • © 2023

Overview

Editors:
  1. Georgi K. Marinov

    1. Stanford University, Stanford, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. William J. Greenleaf

    1. Stanford University, Stanford, USA

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2611)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Bulk Cleavage-Based Methods

    1. Front Matter

      Pages 1-1
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    2. Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq

      • Georgi K. Marinov, Zohar Shipony, Anshul Kundaje, William J. Greenleaf
      Pages 3-19

    3. Mapping Nucleosome Location Using FS-Seq

      • Barry Milavetz, Brenna Hanson, Kincaid Rowbotham, Jacob Haugen
      Pages 21-38

    4. Universal NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells

      • Hang Gyeong Chin, Udayakumar S. Vishnu, Zhiyi Sun, V. K. Chaithanya Ponnaluri, Guoqiang Zhang, Shuang-yong Xu et al.
      Pages 39-52

    5. Measuring Inaccessible Chromatin Genome-Wide Using Protect-seq

      • George Spracklin, Liyan Yang, Sriharsa Pradhan, Job Dekker
      Pages 53-61

    6. Determination of the Chromatin Openness in Bacterial Genomes

      • Mahmoud M. Al-Bassam, Karsten Zengler
      Pages 63-69

    7. Profiling Chromatin Accessibility on Replicated DNA with repli-ATAC-Seq

      • Kathleen R. Stewart-Morgan, Anja Groth
      Pages 71-84Open Access

    8. Analysis of Chromatin Interaction and Accessibility by Trac-Looping

      • Shuai Liu, Qingsong Tang, Keji Zhao
      Pages 85-97

  3. Methods for Measuring the Absolute Levels of Occupancy/Accessibility

    1. Front Matter

      Pages 99-99
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    2. Single-Molecule Mapping of Chromatin Accessibility Using NOMe-seq/dSMF

      • Michaela Hinks, Georgi K. Marinov, Anshul Kundaje, Lacramioara Bintu, William J. Greenleaf
      Pages 101-119

    3. ORE-Seq: Genome-Wide Absolute Occupancy Measurement by Restriction Enzyme Accessibilities

      • Elisa Oberbeckmann, Michael Roland Wolff, Nils Krietenstein, Mark Heron, Andrea Schmid, Tobias Straub et al.
      Pages 121-152

  4. Methods for Profiling Chromatin Accessibility at the Single-Cell Level

    1. Front Matter

      Pages 153-153
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    2. Single-Cell Joint Profiling of Open Chromatin and Transcriptome by Paired-Seq

      • Chenxu Zhu, Zhaoning Wang, Bing Ren
      Pages 155-185

    3. Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-seq

      • Samuel H. Kim, Georgi K. Marinov, S. Tansu Bagdatli, Soon Il Higashino, Zohar Shipony, Anshul Kundaje et al.
      Pages 187-230

    4. Simultaneous Measurement of DNA Methylation and Nucleosome Occupancy in Single Cells Using scNOMe-Seq

      • Michael Wasney, Sebastian Pott
      Pages 231-247

    5. Massively Parallel Profiling of Accessible Chromatin and Proteins with ASAP-Seq

      • Eleni P. Mimitou, Peter Smibert, Caleb A. Lareau
      Pages 249-267

    6. Concomitant Sequencing of Accessible Chromatin and Mitochondrial Genomes in Single Cells Using mtscATAC-Seq

      • Leif S. Ludwig, Caleb A. Lareau
      Pages 269-282

  5. Imaging Methods for Visualization of Accessible DNA

    1. Front Matter

      Pages 283-283
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    2. ATAC-See: A Tn5 Transposase-Mediated Assay for Detection of Chromatin Accessibility with Imaging

      • Yonglong Dang, Ram Prakash Yadav, Xingqi Chen
      Pages 285-291
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Keywords

About this book

This detailed volume provides a comprehensive resource covering the existing and state-of-the-art tools in the field of profiling chromatin accessibility and its dynamics. Beginning with a section on bulk-cell methods for profiling chromatin accessibility and nucleosome positioning that rely on enzymatic cleavage of accessible DNA and produce information about relative accessibility, the book continues with methods that use single-molecule and enzymatic approaches to solving the problem of mapping absolute occupancy/accessibility, emerging tools for mapping DNA accessibility and nucleosome positioning in single cells, imaging-based methods for visualizing accessible chromatin in its nuclear context, as well as computational methods for the processing and analysis of chromatin accessibility datasets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and up-to-date, Chromatin Accessibility: Methods and Protocols serves as an extensive and useful reference for researchers studying different facets of chromatin accessibility in a wide variety of biological contexts. 


Chapter 6 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Editors and Affiliations

  • Stanford University, Stanford, USA

    Georgi K. Marinov, William J. Greenleaf

Bibliographic Information

  • Book Title: Chromatin Accessibility

  • Book Subtitle: Methods and Protocols

  • Editors: Georgi K. Marinov, William J. Greenleaf

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2899-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-2898-0Published: 21 February 2023

  • Softcover ISBN: 978-1-0716-2901-7Published: 21 February 2024

  • eBook ISBN: 978-1-0716-2899-7Published: 20 February 2023

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 341

  • Number of Illustrations: 7 b/w illustrations, 50 illustrations in colour

  • Topics: Cell Biology, Biological Techniques, Genetics and Genomics

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