Chromatin remodeling : methods and protocols

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