Overview

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 mapping 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 link.springer.com.

Full Product Details

Author:   Julia Horsfield ,  Judith Marsman
Publisher:   Springer-Verlag New York Inc.
Imprint:   Springer-Verlag New York Inc.
Edition:   1st ed. 2022
Volume:   2458
Weight:   0.932kg
ISBN:  

9781071621394

ISBN 10:   1071621394
Pages:   379
Publication Date:   02 February 2022
Audience:   Professional and scholarly ,  Professional & Vocational
Format:   Hardback
Publisher's Status:   Active
Availability:   Manufactured on demand  
We will order this item for you from a manufactured on demand supplier.

Table of Contents

Part I: DNA Methylation   1.Generating sequencing-based DNA methylation maps from low DNA input samples Suzan Al Momani, Euan J. Rodger, Peter A. Stockwell, Michael R. Eccles and Aniruddha Chatterjee   2.Data analysis of DNA methylation Epigenome-Wide Association Studies (EWAS); A guide to the principles of best practice Basharat Bhat and Gregory T. Jones   3.Next-generation bisulfite sequencing for targeted DNA methylation analysis Jim Smith, Robert Day and Robert J. Weeks   4.Editing of DNA Methylation Patterns Using CRISPR-Based Tools Jim Smith, Rakesh Banerjee, Robert J. Weeks and Aniruddha Chatterjee   5.Nanopore sequencing and data analysis for base-resolution genome-wide 5-methylcytosine profiling  Allegra Angeloni, James Ferguson and Ozren Bogdanovic     Part II: Protein-DNA interactions   6.Chromatin immunoprecipitation sequencing (ChIP-seq) protocol for small amounts of frozen biobanked cardiac tissue Jiayi Pei, Noortje AM van den Dungen, Folkert W Asselbergs, Michal Mokry and Magdalena Harakalova   7.A robust protocol for investigating the cohesin complex by ChIP-sequencing  Macarena Moronta Gines and Kerstin S. Wendt   8.Epi-Decoder: decoding the local proteome of a genomic locus by massive parallel chromatin immunoprecipitation combined with DNA-barcode sequencing Maria Elize van Breugel and Fred van Leeuwen   9.A protocol for studying transcription factor dynamics using fast Single-Particle Tracking and Spot-On model-based analysis Asmita Jha and Anders S. Hansen   10.Characterization of mammalian regulatory complexes at single locus resolution using TINC Anja S. Knaupp, Ralf B.Schittenhelm and Jose M. Polo   11.Profiling protein-DNA interactions cell-type-specifically with Targeted DamID Owen J. Marshall and Caroline Delandre   12.Genome-wide mapping and microscopy visualization of protein-DNA interactions by pA-DamID Tom van Schaik, Stefano G. Manzo and Bas van Steensel   13.The dCypher approach to interrogate chromatin reader activity against post-translational modification-defined histone peptides and nucleosomes Matthew R. Marunde, Irina K. Popova, Ellen N. Weinzapfel, and Michael C. Keogh     Part III: Chromatin accessibility   14High-resolution ATAC-seq analysis of frozen clinical tissues  Paloma Cejas and Henry W. Long   15 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, and William J. Greenleaf     Part IV: Genome structure and organisation   16 Circular chromosome conformation capture sequencing (4C-seq) in primary adherent cells Judith Marsman, Robert C. Day and Gregory Gimenez   17 Mammalian Micro-C-XL Nils Krietenstein and Oliver J. Rando   18 In situ HiC Timothy M. Johanson and Rhys S. Allan   19 LncRNA-chromatin pull-down using biotin-conjugated DNA probes Debina Sarkar and Sarah D. Diermeier   20 Super-resolution microscopy for visualization of physical contacts between chromosomes at nanoscale resolution Zulin Yu and Tamara A. Potapova        

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