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. 

1. A DNA pull-down assay with diversity forms of competitor for detecting or evaluating protein-DNA interactions

Hongyan Sui and Tomozumi Imamichi

2. Enhanced yeast one-hybrid assays to study protein-DNA interactions

Anna Berenson, Juan Ignacio, and Fuxman Bass

3. Chromatin Immunoprecipitation on Fixed Tissues and Cell Lines

Dimitrius Pramio and Deborah Schechtman

4. The ChIP-exo method to identify genomic locations of DNA-binding Proteins at Near Single Base-Pair Resolution

Ssu-Yu Yeh and Ho Sung Rhee

5. ChIP-seq Protocol for invVitro Cell Differentiation Systems

6. Profiling Accessible Chromatin and Nucleosomes in the Mammalian Genome

Hee Woong Lim and Makiko Iwafuchi

7. Dissecting Locus-Specific Chromatin Interactions by CRISPR Capture

Giovanni A. Botten, Michael Lee Jr., and Jian Xu

8. CUT&RUN to Profile Chromatin-Bound Proteins in Primary Mouse Neural Progenitor Cells

Yurika Matsui and Jamy C. Peng

9. Easy Hi-C: A Low Input Method for Capturing Genome Organization

Leina Lu and Fulai Jin

10. Single Molecule Imaging of DNA Protein Interactions Using DNA Curtains

J. Brooks Crickard

11. Quantifying the Binding and Target-Search Kinetics of Transcriptional Regulatory Factors by Live-Cell Single-Molecule Tracking

Steven Ingersoll, Kyle Brown, Brian Ma, and Xiaojun Ren

12. Preparation of Recombinant Histones and Widom 601 DNA for Reconstitution of Nucleosome Core Particles

Emeleeta A. Paintsil and Emma A. Morrison

13. Nucleosome Core Particle Reconstitution with Recombinant Histones and Widom 601 DNA

Erin F. Hammonds and Emma A. Morrison

Karmella A. Haynes and J. Harrison Priode

15. Mapping Transcription Regulation with Run-on and Sequencing Data Using The Web-Based tfTarget Gateway

17. In situ Hybridization as a Method to Examine Gene Regulatory Activity in vivo

Rhea R Datta and Pinar Onal

18. In situ Hybridization as a Method to Examine Gene Regulatory Activity in vivo

Rhea R Datta and Pinar Onal

19. Fishing for developmental regulatory regions: Zebrafish tissue-specific ATAC-seq

Rekha M. Dhillon-Richardson, Alexandra K. Haugan, and Megan L. Martik