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 undera Creative Commons Attribution 4.0 International License via link.springer.com.

Generating sequencing-based DNA methylation maps from low DNA input samples.- Data analysis of DNA methylation Epigenome-Wide Association Studies (EWAS); A guide to the principles of best practice.- Next-generation bisulfite sequencing for targeted DNA methylation analysis.- Editing of DNA Methylation Patterns Using CRISPR-Based Tools.- Nanopore sequencing and data analysis for base-resolution genome-wide 5-methylcytosine profiling.- Chromatin immunoprecipitation sequencing (ChIP-seq) protocol for small amounts of frozen biobanked cardiac tissue.- A robust protocol for investigating the cohesin complex by ChIP-sequencing.- Epi-Decoder: decoding the local proteome of a genomic locus by massive parallel chromatin immunoprecipitation combined with DNA-barcode sequencing.- A protocol for studying transcription factor dynamics using fast Single-Particle Tracking and Spot-On model-based analysis.- Characterization of mammalian regulatory complexes at single locus resolution using TINC.- Profiling protein-DNA interactions cell-type-specifically with Targeted DamID.- Genome-wide mapping and microscopy visualization of protein-DNA interactions by pA-DamID.- The dCypher approach to interrogate chromatin reader activity against post-translational modification-defined histone peptides and nucleosomes.- High-resolution ATAC-seq analysis of frozen clinical tissues.- Single-molecule multikilobase-scale profiling of chromatin accessibility using m6A-SMAC-seq and m6A-CpG-GpC-SMAC-seq.- Circular chromosome conformation capture sequencing (4C-seq) in primary adherent cells.- Mammalian Micro-C-XL.- In situ HiC.- LncRNA-chromatin pull-down using biotin-conjugated DNA probes.- Super-resolution microscopy for visualization of physical contacts between chromosomes at nanoscale resolution.