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TitleChromatin Protocols [electronic resource]
Author edited by Srikumar P. Chellappan
ImprintNew York, NY : Springer New York : Imprint: Humana Press, 2015
Edition 3rd ed. 2015
Connect tohttp://dx.doi.org/10.1007/978-1-4939-2474-5
Descript XIV, 492 p. 74 illus., 36 illus. in color. online resource

SUMMARY

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


CONTENT

Beads-on-a-String on a Bead: Reconstitution and Analysis of Chromatin on a Solid Support -- Preparation and Analysis of Positioned Mononucleosomes -- Chromatin Imaging with Time-Lapse Atomic Force Microscopy -- Isolation of Specific Genomic Regions and Identification of Associated Molecules by Engineered DNA-Binding Molecule-Mediated Chromatin Immunoprecipitation (enChIP) Using CRISPR -- Drug-Induced Premature Chromosome Condensation (PCC) Protocols: Cytogenetic Approaches in Mitotic Chromosome and Interphase Chromatin -- Analysis of Genomic Aberrations Using Comparative Genomic Hybridization of Metaphase Chromosomes -- Histone Deacetylase Activity Assay -- In Vitro Histone Demethylase Assays -- Integrated DNA Methylation and Chromatin Structural Analysis at Single-Molecule Resolution -- Determination of DNA Methylation Levels Using Illumina HumanMethylation450 BeadChips -- Investigation of Genomic Methylation Status Using Methylation Specific and Bisulfite Sequencing Polymerase Chain Reaction -- In Vitro and In Vivo Assays for Studying Histone Ubiquitination and Deubiquitination -- Immunostaining Analysis of Tissue Cultured Cells and Tissue Sections Using Phospho-Histone H3 (Serine 10) Antibody -- Identification and Characterization of Nonhistone Chromatin Proteins: Human Positive Coactivator 4 as a Candidate -- Methods to Study Transcription-Coupled Repair in Chromatin -- Analysis of DNA Replication Associated Chromatin Decondensation: In Vivo Assay for Understanding Chromatin Remodeling Mechanisms of Selected Proteins -- Non-Radioactive Assay Methods for the Assessment of Telomerase Activity and Telomere Length -- Detecting ATM Dependent Chromatin Modification in DNA Damage Response -- Imaging Local Deposition of Newly Synthesized Histones in UVC-Damaged Chromatin -- In Vitro Replication Assay with Mammalian Cell Extracts -- Fluorescent In Situ Hybridization on Comets: FISH Comet -- Methods to Study Histone Chaperone Function in Nucleosome Assembly and Chromatin Transcription -- Preparation of Mononucleosomal Templates for Analysis of Transcription with RNA Polymerase Using spFRET -- Transcriptome-Wide Identification of In Vivo Interactions Between RNAs and RNA-Binding Proteins by RIP and PAR-CLIP Assays -- Chromatin Immunoprecipitation Assays: Analyzing Transcription Factor Binding and Histone Modifications In Vivo -- ChIP on Chip and ChIP-Seq Assays: Genome-Wide Analysis of Transcription Factor Binding and Histone Modifications -- ChIP-on-Chip Analysis Methods for Affymetrix Tiling Arrays


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