Chromatin Protocols
(Sprache: Englisch)
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,...
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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.
Inhaltsverzeichnis zu „Chromatin Protocols “
1. Beads-on-a-String on a Bead: Reconstitution and Analysis of Chromatin on a Solid SupportRaphael 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.
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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
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
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Bibliographische Angaben
- 2015, 3. Aufl., XIV, 492 Seiten, 36 farbige Abbildungen, Maße: 18,6 x 26,1 cm, Gebunden, Englisch
- Herausgegeben: Srikumar P. Chellappan
- Verlag: Springer, Berlin
- ISBN-10: 1493924737
- ISBN-13: 9781493924738
Sprache:
Englisch
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