Chromatin Remodeling: Methods and Protocols (Methods in Molecular Biology)

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(TM) 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. 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