DNA-protein interactions : methods and protocols
著者
書誌事項
DNA-protein interactions : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 2599）
Humana Press, c2023
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注記
Includes bibliographical references and index
内容説明・目次
内容説明
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.
目次
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
Jacqueline Copeland, Fjodor Merkuri, and Marcos Simoes-Costa
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
14. Rapid Single-Pot Assembly of Modular Chromatin Proteins for Epigenetic Engineering
Karmella A. Haynes and J. Harrison Priode
15. Mapping Transcription Regulation with Run-on and Sequencing Data Using The Web-Based tfTarget Gateway
Nating Wang, Zhong Wang, Charles G. Danko, and Tinyi Chu
16. In embryo Gene Reporter Assays for Evaluation of Cis-Regulatory Regions Carolina Purcell Goes, Tatiane Y. Kanno, and C.Y. Irene Yan
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
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