Chromatin Accessibility: Methods and Protocols

ISBN-13: 9781071628980 / Angielski / Twarda / 2023 / 341 str.

Georgi K. Marinov; William J. Greenleaf

Opis

This detailed volume provides a comprehensive resource covering the existing and state-of-the-art tools in the field of profiling chromatin accessibility and its dynamics. Beginning with a section on bulk-cell methods for profiling chromatin accessibility and nucleosome positioning that rely on enzymatic cleavage of accessible DNA and produce information about relative accessibility, the book continues with methods that use single-molecule and enzymatic approaches to solving the problem of mapping absolute occupancy/accessibility, emerging tools for mapping DNA accessibility and nucleosome positioning in single cells, imaging-based methods for visualizing accessible chromatin in its nuclear context, as well as computational methods for the processing and analysis of chromatin accessibility datasets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and up-to-date, Chromatin Accessibility: Methods and Protocols serves as an extensive and useful reference for researchers studying different facets of chromatin accessibility in a wide variety of biological contexts. 

Chapter 6 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Spis treści

Part I: Bulk Cleavage-Based Methods

 

1. Genome-Wide Mapping of Active Regulatory Elements Using ATAC-Seq

            Georgi K. Marinov, Zohar Shipony, Anshul Kundaje, and William J. Greenleaf

 

2. Mapping Nucleosome Location Using FS-Seq

            Barry Milavetz, Brenna Hanson, Kincaid Rowbotham, and Jacob Haugen

 

3. NicE-Seq: A Simple and Quick Method for Accessible Chromatin Detection in Fixed Cells

            Hang Gyeong Chin, Udayakumar S. Vishnu, Zhiyi Sun, V.K. Chaithanya Ponnaluri, Guoqiang Zhang, Shuang-yong Xu, Touati Benoukraf, Paloma Cejas, George Spracklin, Pierre-Olivier Estève, Henry W. Long, and Sriharsa Pradhan

 

4. Measuring Inaccessible Chromatin Genome-Wide Using Protect-Seq

            George Spracklin, Liyan Yang, Sriharsa Pradhan, and Job Dekker

 

5. Determination of the Chromatin Openness in Bacterial Genomes

            Mahmoud M. Al-Bassam and Karsten Zengler

 

6. Profiling Chromatin Accessibility on Replicated DNA with Repli-ATAC-Seq

            Kathleen R. Stewart-Morgan and Anja Groth

 

7. Analysis of Chromatin Interaction and Accessibility by Trac-Looping

            Shuai Liu, Qingsong Tang, and Keji Zhao

 

Part II: Methods for Measuring the Absolute Levels of Occupancy/Accessibility

 

8. Single-Molecule Mapping of Chromatin Accessiility Using NOMe-Seq/dSMF

            Michaela Hinks, Georgi K. Marinov, Anshul Kundaje, Lacramioara Bintu, and William J. Greenleaf

 

9. ORE-Seq: Genome-Wide Absolute Occupancy Measurement by Restriction Enzyme Accessibilities

            Elisa Oberbeckmann, Michael Roland Wolff, Nils Krietenstein, Mark Heron, Andrea Schmid, Tobias Straub, Ulrich Gerland, and Philipp Korber

 

Part III: Methods for Profiling Chromatin Accessibility at the Single-Cell Level

 

10. Single-Cell Joint Profiling of Open Chromatin and Transcriptome by Paired-Seq

            Chenxu Zhu, Zhaoning Wang, and Bing Ren

 

11. Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-Seq

            Samuel H. Kim, Georgi K. Marinov, S. Tansu Bagdatli, Soon Il Higashino, Zohar Shipony, Anshul Kundaje, and William J. Greenleaf

 

12. Simultaneous Measurement of DNA Methylation and Nucleosome Occupancy in Single Cells Using scNOMe-Seq

            Michael Wasney and Sebastian Pott

 

13. Massively Parallel Profiling of Accessible Chromatin and Proteins with ASAP-Seq

            Eleni Mimitou, Peter Smibert, and Caleb A. Lareau

 

14. Concomitant Sequencing of Accessible Chromatin and Mitochondrial Genomes in Single Cells Using mtscATAC-Seq

            Leif S. Ludwig and Caleb A. Lareau

 

Part IV: Imaging Methods for Visualization of Accessible DNA

 

15. ATAC-See: A Tn5 Transposase-Mediated Assay for Detection of Chromatin Accessibility with Imaging

            Yonglong Dang, Ram Prakash Yadav, and Xingqi Chen

 

16. NicE-viewSeq: An Integrative Visualization and Genomics Method to Detect Accessible Chromatin in Fixed Cells

            Pierre-Olivier Estève, Udayakumar S. Vishnu, Hang Gyeong Chin, and Sriharsa Pradhan

 

Part V: Computational Analysis of Chromatin Accessibility Datasets

 

17. ATAC-Seq Data Processing

            Daniel Kim

 

18. Deep Learning on Chromatin Accessibility

            Daniel Kim