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TET Proteins and DNA Demethylation

Methods and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Ozren Bogdanovic

    1. Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Australia

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Michiel Vermeulen

    1. Radboud University, Nijmegen, 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 2272)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Detection and Quantification of DNA Methylation Turnover

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Reduced Bisulfite Sequencing: Quantitative Base-Resolution Sequencing of 5-Formylcytosine

      • Michael J. Booth, Shankar Balasubramanian
      Pages 3-12

    3. Aba-Seq : High-Resolution Enzymatic Mapping of Genomic 5-Hydroxymethylcytosine

      • Zhiyi Sun, Jolyon Terragni, Zhenyu Zhu, Yu Zheng, Sriharsa Pradhan
      Pages 13-27

    4. Estimating Global Methylation and Erasure Using Low-Coverage Whole-Genome Bisulfite Sequencing (WGBS )

      • Oscar Ortega-Recalde, Julian R. Peat, Donna M. Bond, Timothy A. Hore
      Pages 29-44Open Access

    5. ELISA-Based Quantitation of Global 5hmC Levels

      • Nelly N. Olova
      Pages 45-63

    6. Avidin-Biotin ELISA-Based Detection of 5hmC

      • Nelly N. Olova
      Pages 65-76

    7. Quantification of DNA Methylation and Its Oxidized Derivatives Using LC-MS

      • Franziska R. Traube, Sarah Schiffers, Thomas Carell
      Pages 77-94

  3. Bioinformatic Analysis of DNA Methylation and Hydroxymethylation

    1. Front Matter

      Pages 95-95
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    2. Distinguishing Active Versus Passive DNA Demethylation Using Illumina MethylationEPIC BeadChip Microarrays

      • Rochelle L. Tiedemann, Hope E. Eden, Zhijun Huang, Keith D. Robertson, Scott B. Rothbart
      Pages 97-140Open Access

    3. Bioinformatic Estimation of DNA Methylation and Hydroxymethylation Proportions

      • Samara Flamini Kiihl
      Pages 141-162

    4. TAB-seq and ACE-seq Data Processing for Genome-Wide DNA hydroxymethylation Profiling

      • Ksenia Skvortsova, Ozren Bogdanovic
      Pages 163-178

  4. Precise Epigenome Manipulation Using TET Enzymes

    1. Front Matter

      Pages 179-179
      Download chapter PDF

    2. Genomic Targeting of TET Activity for Targeted Demethylation Using CRISPR/Cas9

      • Trung Viet Nguyen, Ryan Lister
      Pages 181-194

    3. High-Fidelity CRISPR/Cas9-Based Gene-Specific Hydroxymethylation

      • Xingbo Xu, Elisabeth M. Zeisberg
      Pages 195-206

  5. TET and DNA Hydroxymethylation Biochemistry

    1. Front Matter

      Pages 207-207
      Download chapter PDF

    2. Identifying Protein–(Hydroxy)Methylated DNA Interactions Using Quantitative Interaction Proteomics

      • Velin Marita Sequeira, Michiel Vermeulen
      Pages 209-224

    3. Purification of TET Proteins

      • Zhijun Huang, Jiyoung Yu, Jennifer Johnson, Seung-Gi Jin, Gerd P. Pfeifer
      Pages 225-237

    4. Uncovering Sequence-Specific Transcription Factors Interacting with TET2

      • Tian V. Tian, José Luis Sardina
      Pages 239-250

    5. ChIP-Sequencing of TET Proteins

      • Kasper D. Rasmussen, Kristian Helin
      Pages 251-262
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Keywords

About this book

This volume explores the latest methods used to study various aspects of TET proteins and their biology. Chapters in this book are divided into five parts. Part One describes technologies aimed at detecting and quantifying DNA methylation turnover using massively parallel sequencing, ELISA, and mass spectrometry approaches. Part Two looks at data analyses protocols for distinguishing acting versus passive DNA demethylation and estimation of 5mC and 5hmC levels. Part Three deals with a new topic that takes advantage of modified CRISPR/Cas9 genome editing systems to target DNA demethylation activity to genomic loci of interest. Part Four discusses protocols that detail how to purify TET proteins and unravel their protein interactions, and Part Five looks at the assessment of TET protein function and activity in vivo and in vitro. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Cutting-edge and thorough, TET Proteins and DNA Demethylation: Methods and Protocols is a valuable resource that aims to help research scientists at all levels working in the fields of DNA demethylation dynamics.

Chapters 3, 7 and 17 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.




Editors and Affiliations

  • Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Australia

    Ozren Bogdanovic

  • Radboud University, Nijmegen, The Netherlands

    Michiel Vermeulen

Bibliographic Information

  • Book Title: TET Proteins and DNA Demethylation

  • Book Subtitle: Methods and Protocols

  • Editors: Ozren Bogdanovic, Michiel Vermeulen

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1294-1

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-1293-4Published: 20 May 2021

  • Softcover ISBN: 978-1-0716-1296-5Published: 20 May 2021

  • eBook ISBN: 978-1-0716-1294-1Published: 19 May 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 320

  • Number of Illustrations: 10 b/w illustrations, 46 illustrations in colour

  • Topics: Protein Science, Human Genetics

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