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Chromatin

Methods and Protocols

  • Book
  • © 2022

Overview

Editors:
  1. Julia Horsfield

    1. Department of Pathology Dunedin School of Medicine, University of Otago, Dunedin, New Zealand

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  2. Judith Marsman

    1. Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht, The Netherlands

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 2458)

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About this book

This volume provides cutting-edge techniques to further the study chromatin biology. Chapters include both novel and well-established methods for the analysis of DNA-associated proteins, DNA methylation, three-dimensional chromatin interactions, deep sequencing-based tools, and data analysis pipelines. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, provides details of the necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and describes step-by-step, readily reproducible protocols.

 Authoritative and cutting-edge, Chromatin: Methods and Protocols aims to further the understanding of how modified DNA and associated proteins affect the transcriptional output of the genome.

Chapter Genome-wide map** and microscopy visualization of protein-DNA interactions by pA-DamID [Chapter 12] is available open access undera Creative Commons Attribution 4.0 International License via springer.longhoe.net.

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Table of contents (20 protocols)

  1. Front Matter

    Pages i-xi
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  2. DNA Methylation

    1. Front Matter

      Pages 1-1
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    2. Generating Sequencing-Based DNA Methylation Maps from Low DNA Input Samples

      • Suzan Al Momani, Euan J. Rodger, Peter A. Stockwell, Michael R. Eccles, Aniruddha Chatterjee
      Pages 3-21

    3. Data Analysis of DNA Methylation Epigenome-Wide Association Studies (EWAS) : A Guide to the Principles of Best Practice

      • Basharat Bhat, Gregory T. Jones
      Pages 23-45

    4. Next-Generation Bisulfite Sequencing for Targeted DNA Methylation Analysis

      • Jim Smith, Robert C. Day, Robert J. Weeks
      Pages 47-62

    5. Editing of DNA Methylation Patterns Using CRISPR-Based Tools

      • Jim Smith, Rakesh Banerjee, Robert J. Weeks, Aniruddha Chatterjee
      Pages 63-74

    6. Nanopore Sequencing and Data Analysis for Base-Resolution Genome-Wide 5-Methylcytosine Profiling

      • Allegra Angeloni, James Ferguson, Ozren Bogdanovic
      Pages 75-94

  3. Protein-DNA Interactions

    1. Front Matter

      Pages 95-95
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    2. Chromatin Immunoprecipitation Sequencing (ChIP-seq) Protocol for Small Amounts of Frozen Biobanked Cardiac Tissue

      • Jiayi Pei, Noortje A. M. van den Dungen, Folkert W. Asselbergs, Michal Mokry, Magdalena Harakalova
      Pages 97-111

    3. A Robust Protocol for Investigating the Cohesin Complex by ChIP-Sequencing

      • Macarena Moronta Gines, Kerstin S. Wendt
      Pages 113-122

    4. Epi-Decoder: Decoding the Local Proteome of a Genomic Locus by Massive Parallel Chromatin Immunoprecipitation Combined with DNA-Barcode Sequencing

      • Maria Elize van Breugel, Fred van Leeuwen
      Pages 123-150

    5. A Protocol for Studying Transcription Factor Dynamics Using Fast Single-Particle Tracking and Spot-On Model-Based Analysis

      • Asmita Jha, Anders S. Hansen
      Pages 151-174

    6. Characterization of Mammalian Regulatory Complexes at Single-Locus Resolution Using TINC

      • Anja S. Knaupp, Ralf B. Schittenhelm, Jose M. Polo
      Pages 175-193

    7. Profiling Protein–DNA Interactions Cell-Type-Specifically with Targeted DamID

      • Owen J. Marshall, Caroline Delandre
      Pages 195-213

    8. Genome-Wide Map** and Microscopy Visualization of Protein–DNA Interactions by pA-DamID

      • Tom van Schaik, Stefano G. Manzo, Bas van Steensel
      Pages 215-229Open Access

    9. The dCypher Approach to Interrogate Chromatin Reader Activity Against Posttranslational Modification-Defined Histone Peptides and Nucleosomes

      • Matthew R. Marunde, Irina K. Popova, Ellen N. Weinzapfel, Michael-C. Keogh
      Pages 231-255

  4. Chromatin Accessibility

    1. Front Matter

      Pages 257-257
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    2. High-Resolution ATAC-Seq Analysis of Frozen Clinical Tissues

      • Paloma Cejas, Henry W. Long
      Pages 259-267

    3. Single-Molecule Multikilobase-Scale Profiling of Chromatin Accessibility Using m6A-SMAC-Seq and m6A-CpG-GpC-SMAC-Seq

      • Georgi K. Marinov, Zohar Shipony, Anshul Kundaje, William J. Greenleaf
      Pages 269-298

  5. Genome Structure and Organization

    1. Front Matter

      Pages 299-299
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Editors and Affiliations

  • Department of Pathology Dunedin School of Medicine, University of Otago, Dunedin, New Zealand

    Julia Horsfield

  • Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht, The Netherlands

    Judith Marsman

Bibliographic Information

  • Book Title: Chromatin

  • Book Subtitle: Methods and Protocols

  • Editors: Julia Horsfield, Judith Marsman

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2140-0

  • 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 2022

  • Hardcover ISBN: 978-1-0716-2139-4Published: 02 February 2022

  • Softcover ISBN: 978-1-0716-2142-4Published: 03 February 2023

  • eBook ISBN: 978-1-0716-2140-0Published: 01 February 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 379

  • Number of Illustrations: 11 b/w illustrations, 64 illustrations in colour

  • Topics: Genetics and Genomics, Chemistry/Food Science, general

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