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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 In Vitro Cell Differentiation Systems
Profiling Accessible Chromatin and Nucleosomes in the Mammalian Genome
Dissecting Locus-Specific Chromatin Interactions by CRISPR CAPTURE
CUT &amp 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
Investigating Tissue Regeneration Using the DUAL Control Genetic Ablation System
Fishing for Developmental Regulatory Regions: Zebrafish Tissue-Specific ATAC-seq