DNA-Protein Interactions Methods and Protocols

This volume details protocols emphasizing systems-level approaches that can be applied to genomic analyses. Chapters detail techniques for optimized application in in vivo systems, spatial, physiological, environmental contexts, imaging-based techniques, single-molecule approaches, CRISPR systems, new genomic approaches, and measurements of kinetics governing. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

Authoritative and cutting-edge, DNA-Protein Interactions: Methods and Protocols aims to present genome-wide techniques that will complement the biochemistry-based protocols to aid researchers in their studies. 

 A DNA pull-down assay with diversity forms of competitor for detecting or evaluating protein-DNA interactions.- Enhanced yeast one-hybrid assays to study protein-DNA interactions.- Chromatin Immunoprecipitation on Fixed Tissues and Cell Lines.- The ChIP-exo method to identify genomic locations of DNA-binding Proteins at Near Single Base-Pair Resolution.- ChIP-seq Protocol for invVitro Cell Differentiation Systems.- Profiling Accessible Chromatin and Nucleosomes in the Mammalian Genome.- Dissecting Locus-Specific Chromatin Interactions by CRISPR Capture.- CUT&RUN to Profile Chromatin-Bound Proteins in Primary Mouse Neural Progenitor Cells.- Easy Hi-C: A Low Input Method for Capturing Genome Organization.- Single Molecule Imaging of DNA Protein Interactions Using DNA Curtains.- Quantifying the Binding and Target-Search Kinetics of Transcriptional Regulatory Factors by Live-Cell Single-Molecule Tracking.- Preparation of Recombinant Histones and Widom 601 DNA for Reconstitution of Nucleosome Core Particles.- Nucleosome Core Particle Reconstitution with Recombinant Histones and Widom 601 DNA.- Rapid Single-Pot Assembly of Modular Chromatin Proteins for Epigenetic Engineering.- Mapping Transcription Regulation with Run-on and Sequencing Data Using The Web-Based tfTarget Gateway.- In embryo Gene Reporter Assays for Evaluation of Cis-Regulatory Regions.- In situ Hybridization as a Method to Examine Gene Regulatory Activity in vivo.- In situ Hybridization as a Method to Examine Gene Regulatory Activity in vivo.- Fishing for developmental regulatory regions: Zebrafish tissue-specific ATAC-seq.