Updated and revised, this thorough volume is organized such that it begins with techniques related to the study of chromatin structure. Protocols for reconstitution of chromatin on solid supports for analysis, preparation of positioned mononucleosomes, techniques to study premature chromatin condensation and the use of comparative genomic hybridization to assess genomic aberration are included as well. Novel techniques for imaging chromatin using atomic force microscopy and the isolation of specific genomic regions using engineered DNA binding molecules generated by CRISPR are then examined. That section is followed by protocols to analyze DNA and histone modifications, while the third section includes methods to study DNA replication and repair, in the context of chromatin. Last but not least, protocols for studying chromatin and its relation with transcriptional regulation are presented in a fourth section. Written in the highly successful Methods in Molecular Biology series format, 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.Authoritative and up-to-date, Chromatin Protocols, Third Edition aims to help researchers in facilitating in-depth molecular analysis of various aspects of chromatin structure and function.

1. Beads-on-a-String on a Bead: Reconstitution and Analysis of Chromatin on a Solid Support

            Raphael Sandaltzopoulos and Peter B. Becker

2. Preparation and Analysis of Positioned Mononucleosomes

            Olga Kulaeva and Vasily M. Studitsky

3. Chromatin Imaging with Time-Lapse Atomic Force Microscopy

            Yuri L. Lyubchenko and Luda S. Shlyakhtenko

4. Isolation of Specific Genomic Regions and Identification of Associated Molecules by Engineered DNA-Binding Molecule-Mediated Chromatin Immunoprecipitation (enChIP) Using CRISPR

            Toshitsugu Fujita and Hodaka Fujii

5. Drug-Induced Premature Chromosome Condensation (PCC) Protocols: Cytogenetic Approaches in Mitotic Chromosome and Interphase Chromatin

            Eisuke Gotoh

6. Analysis of Genomic Aberrations Using Comparative Genomic Hybridization of Metaphase Chromosomes

            Melanie Carless

7. Histone Deacetylase Activity Assay

            Lirong Peng, Zhigang Yuan, and Edward Seto

8. In Vitro Histone Demethylase Assays

            Kenji Kokura, Lidong Sun, and Jia Fang

9. Integrated DNA Methylation and Chromatin Structural Analysis at Single-Molecule Resolution

            Carolina E. Pardo, Nancy H. Nabilsi, Russell P. Darst, and Michael P. Kladde

10. Determination of DNA Methylation Levels Using Illumina HumanMethylation450 BeadChips

            Melanie Carless

11. Investigation of Genomic Methylation Status Using Methylation Specific and Bisulfite Sequencing Polymerase Chain Reaction

            Melanie Carless

12. In Vitro and In Vivo Assays for Studying Histone Ubiquitination and Deubiquitination

            Heui-Yun Joo, Qian Dai, Amanda E. Jones, Ling Zhai, and Hengbin Wang

13. Immunostaining Analysis of Tissue Cultured Cells and Tissue Sections Using Phospho-Histone H3 (Serine 10) Antibody

            Jaya Padmanabhan

14. Identification and Characterization of Nonhistone Chromatin Proteins: Human Positive Coactivator 4 as a Candidate

            Sujata Kumari, Chandrima Das, Sweta Sikder, Manoj Kumar, Mahesh Bachu, Udaykumar Ranga, and Tapas K. Kundu

15. Methods to Study Transcription-Coupled Repair in Chromatin

            Hélène Gaillard, Ralf Erik Wellinger, and Andrés Aguilera

16. Analysis of DNA Replication Associated Chromatin Decondensation: In Vivo Assay for Understanding Chromatin Remodeling Mechanisms of Selected Proteins

            Sergiy Borysov, Reeti Behera, and Mark G. Alexandrow

17. Non-Radioactive Assay Methods for the Assessment of Telomerase Activity and Telomere Length

            Partha P. Banerjee and Shankar Jagadeesh

18. Detecting ATM Dependent Chromatin Modification in DNA Damage Response

            Durga Udayakumar, Nobou Horikoshi, Lopa Mishra, Clayton Hunt, and Tej K. Pandita

19. Imaging Local Deposition of Newly Synthesized Histones in UVC-Damaged Chromatin

            Salomé Adam, Juliette Dabin, Siau-Kun Bai, and Sophie E. Polo

20. In Vitro Replication Assay with Mammalian Cell Extracts

            Wasia Rizwani and Srikumar Chellappan

21. Fluorescent In Situ Hybridization on Comets: FISH Comet

            Sergey Shaposhnikov, Naouale El Yamani, and Andrew R. Collins

22. Methods to Study Histone Chaperone Function in Nucleosome Assembly and Chromatin Transcription

            Parijat Senapati, Deepthi Sudarshan, Shrikanth S. Gadad, Jayasha Shandilya, Venkatesh Swaminathan, and Tapas K. Kundu

23. Preparation of Mononucleosomal Templates for Analysis of Transcription with RNA Polymerase Using spFRET

            Kseniya S. Kudryashova, Oleg V. Chertkov, Dmitry V. Nikitin, Nikolai ¿. Pestov, Olga I. Kulaeva, Anastasija V. Efremenko, Alexander S. Solonin, Mikhail P. Kirpichnikov, Vasily ¿. Studitsky, and Alexey V. Feofanov

24. Transcriptome-Wide Identification of In Vivo Interactions Between RNAs and RNA-Binding Proteins by RIP and PAR-CLIP Assays

            Edgar González-Buendía, Ricardo Saldaña-Meyer, Karin Meier, and Félix Recillas-Targa

25. Chromatin Immunoprecipitation Assays: Analyzing Transcription Factor Binding and Histone Modifications In Vivo

            Smitha Pillai, Piyali Dasgupta, and Srikumar P. Chellappan

26. ChIP on Chip and ChIP-Seq Assays: Genome-Wide Analysis of Transcription Factor Binding and Histone Modifications

            Smitha Pillai and Srikumar Chellappan

27. ChIP-on-Chip Analysis Methods for Affymetrix Tiling Arrays

            Sean J. Yoder