Chromatin Remodeling: Methods and Protocols

ISBN-13: 9781493962136 / Angielski / Miękka / 2016 / 456 str.

Randall H. Morse

Opis

This Methods in Molecular Biology (TM) volume offers methods for investigating chromatin remodeling in vitro and in vivo, in yeast, plants and mammalian cells, and at local and global levels. Includes materials lists, protocols, troubleshooting tips and more.

Recenzje

From the reviews:

"This is an outstanding and timely collection of methods concerning how one can investigate chromatin remodelling. ... There are detailed laboratory procedures and notes attached to all chapters, and this enable readers to use the volume as a laboratory manual. ... The editor, Randall Morse, has to be congratulated on producing such an excellent book; a book that I recommend most highly to researchers in this arena." (Raymond Waters, Human Genetics, Vol. 131, 2012)

Spis treści

1. Strain Construction and Screening Methods for a Yeast Histone H3/H4 Mutant Library

            Junbiao Dai and Jef D. Boeke

 

2. Measuring Dynamic Changes in Histone Modifications and Nucleosome Density during Activated Transcription in Budding Yeast

            Chhabi K. Govind, Daniel Ginsburg, and Alan G. Hinnebusch

 

3. Monitoring the Effects of Chromatin Remodelers on Long-Range Interactions In Vivo

            Christine M. Kiefer and Ann Dean

 

4. Measuring Nucleosome Occupancy In Vivo by Micrococcal Nuclease

            Gene O. Bryant

 

5. Analysis of Nucleosome Positioning Using a Nucleosome-Scanning Assay (NuSA)

            Juan Jose Infante, G. Lynn Law, and Elton T. Young

 

6. Assaying Chromatin Structure and Remodeling by Restriction Enzyme Accessibility

            Kevin W. Trotter and Trevor K. Archer

 

7. Generation of DNA Circles in Yeast by Inducible Site-Specific Recombination

            Marc R. Gartenberg

 

8. An Efficient Purification System for Native Minichromosome from S. cerevisiae

            Ashwin Unnikrishnan, Bungo Akiyoshi, Sue Biggins, and Toshio Tsukiyama

 

9. Simultaneous, Single-Molecule Detection of Endogenous C-5 DNA Methylation and Chromatin Accessibility Using MAPit

            Russell P. Darst, Carolina E. Pardo, Santhi Pondugula, Vamsi K. Gangaraju, Nancy H. Nabilsi, Blaine Bartholomew, and Michael P. Kladde

 

10. Analysis of Stable and Transient Protein-Protein Interactions

            Stephanie Byrum, Sherri K. Smart, Signe Larson, and Alan J. Tackett

 

11. Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Fluorescence Recovery after Photobleaching (FRAP)

            Florian Mueller, Tatiana S. Karpova, Davide Mazza, and James G. McNally

 

12. Monitoring Dynamic Binding of Chromatin Proteins In Vivo by Fluorescence Correlation Spectroscopy (FCS) and Temporal Image Correlation Spectroscopy (TICS)

            Davide Mazza, Timothy J. Stasevich, Tatiana S. Karpova, and James G. McNally

 

13. Analysis of Chromatin Structure in Plant Cells

            Mala Singh, Amol Ranjan, Krishan Mohan Rai, Sunil Kumar Singh, Verandra Kumar, Ila Trivedi, Niraj Lodhi, and Samir V. Sawant

 

14. Analysis of Histones and Histone Variants in Plants

            Ila Trivedi, Krishan Mohan Rai, Sunil Kumar Singh, Verandra Kumar, Mala Singh, Amol Ranjan, Niraj Lodhi, and Samir V. Sawant

 

15. Reconstitution of Modified Chromatin Templates for In Vitro Functional Assays

            Miyong Yun, Chun Ruan, Jae-Wan Huh, and Bing Li

 

16. A Defined In Vitro System to Study ATP-Dependent Remodeling of Short Chromatin Fibers

            Verena K. Maier and Peter B. Becker

 

17. In Vitro Reconstitution of In Vivo-Like Nucleosome Positioning on Yeast DNA

            Christian J. Wippo and Philipp Korber

 

18. Activator-Dependent Acetylation of Chromatin Model Systems

            Heather J. Szerlong and Jeffrey C. Hansen

 

19. Mapping Assembly-Favored and Remodeled Nucleosome Positions on Polynucleosomal Templates

            Hillel I. Sims, Chuong Pham, and Gavin R. Schnitzler

 

20. Analysis of Changes in Nucleosome Conformation Using Fluorescence Resonance Energy Transfer (FRET)

            Tina Shahian and Geeta J. Narlikar

 

21. Preparation of Nucleosomes Containing a Specific H2A-H2A Crosslink Forming a DNA-Constraining Loop Structure

            Ning Liu and Jeffrey J. Hayes

 

22. Sulfyhydryl Reactive Site-Directed Crosslinking as a Method for Probing the Tetrameric Structure of Histones H3 and H4

            Andrew Bowman and Tom Owen-Hughes

 

23. Genomic Approaches for Determining Nucleosome Occupancy in Yeast

            Kyle Tsui, Tanja Durbic, Marinella Gebbia, and Corey Nislow

 

24. Genome-Wide Approaches to Determining Nucleosome Occupancy in Metazoans Using MNase-Seq

            Kairong Cui and Keji Zhao

 

25. Salt Fractionation of Nucleosomes for Genome-Wide Profiling

            Sheila S. Teves and Steven Henikoff

 

26. Quantitative Analysis of Genome-Wide Chromatin Remodeling

            Songjoon Baek, Myong-Hee Sung, and Gordon L. Hager

 

27. Computational Analysis of Nucleosome Positioning

            Itay Tirosh

Blurb

Chromatin is of central importance to gene regulation in eukaryotes.  Reflecting this singular role for chromatin, numerous approaches have evolved in the laboratory over the past three decades to study chromatin structure and its alterations. Methods of investigating chromatin remodeling, whether in changes in nucleosome structure or position with respect to the incorporated DNA or in histone modifications, have progressed rapidly over the recent years.  In Chromatin Remodeling: Methods and Protocols, expert researchers contribute chapters which include methods for investigating chromatin remodeling in vitro and in vivo, in yeast, plants, and mammalian cells, and at local and global levels.  Both gene-specific and genome-wide approaches are covered, and in recognition of the increasing prevalence of the latter type of study, the final two chapters focus on bioinformatic/computational approaches to analyzing genome-wide data on chromatin structure. Written in the highly successful Methods in Molecular Biology™ series format, the chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

 

Comprehensive and essential, Chromatin Remodeling: Methods and Protocols serves as a key source of clear techniques as well as a collection of chapters that can inspire future techniques in this vital field of study.