TET Proteins and DNA Demethylation : Methods and Protocols / edited by Ozren Bogdanovic, Michiel Vermeulen.

Format:

Book

Contributor:

Bogdanovic, Ozren, Editor.

Vermeulen, Michiel, Editor.

SpringerLink (Online service)

Series:

Springer Protocols (Springer-12345)

Methods in molecular biology 1940-6029 ; 2272

Methods in Molecular Biology, 1940-6029 ; 2272

Language:

English

Subjects (All):

Proteins.

Medical genetics.

Protein Biochemistry.

Medical Genetics.

Local Subjects:

Protein Biochemistry.

Medical Genetics.

Physical Description:

1 online resource (X, 320 pages) : 56 illustrations, 46 illustrations in color.

Edition:

1st ed. 2021.

Contained In:

Springer Nature eBook

Place of Publication:

New York, NY : Springer US : Imprint: Humana, 2021.

System Details:

text file PDF

Summary:

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.

Contents:

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

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

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

ELISA-Based Quantitation of Global 5hmC Levels

Avidin-Biotin ELISA-Based Detection of 5hmC

Quantification of DNA Methylation and Its Oxidized Derivatives using LC-MS

Distinguishing Active Versus Passive DNA Demethylation using Illumina MethylationEPIC BeadChip Microarrays

Bioinformatic Estimation of DNA Methylation and Hydroxymethylation Proportions

TAB-seq and ACE-seq Data Processing for Genome-Wide DNA Hydroxymethylation Profiling

Genomic Targeting of TET Activity for Targeted Demethylation using CRISPR/Cas9

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

Identifying Protein-(hydroxy)methylated DNA Interactions using Quantitative Interaction Proteomics

Purification of TET Proteins

Uncovering Sequence Specific Transcription Factors Interacting with TET2

ChIP-Sequencing of TET Proteins

Harnessing Alternative Substrates to Probe TET Family Enzymes

Generation and Molecular Characterization of Transient tet1/2/3 Zebrafish Knockouts.

Other Format:

Printed edition:

ISBN:

978-1-0716-1294-1

9781071612941

Access Restriction:

Restricted for use by site license.