Chromatin Methods and Protocols

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 under a Creative Commons Attribution 4.0 International License via link.springer.com.

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

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