Chromatin Remodeling: Methods and Protocols by Randall H. MorseChromatin Remodeling: Methods and Protocols by Randall H. Morse

Chromatin Remodeling: Methods and Protocols

EditorRandall H. Morse

Hardcover | December 21, 2011

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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 BiologyT 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.

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Title:Chromatin Remodeling: Methods and ProtocolsFormat:HardcoverDimensions:465 pagesPublished:December 21, 2011Publisher:Humana PressLanguage:English

The following ISBNs are associated with this title:

ISBN - 10:1617794767

ISBN - 13:9781617794766

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Table of Contents

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