Bookedited by Srikumar P. Chellappan.
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.
Contents:
Beads-on-a-string on a bead : reconstitution and analysis of chromatin on a solid support / Raphael Sandaltzopoulos and Peter B. Becker
Preparation and analysis of positioned mononucleosomes / Olga I. Kulaevaand Vasily M. Studitsky
Chromatin imaging with time-lapse atomic force microscopy / Yuri L. Lyubchenko and Luda S. Shlyakhtenko
Isolation of specific genomic regions and ifentification of associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR / Toshitsugu Fujita and Hodaka Fujii
Drug-induced premature chromosome condensation (PCC) protocols : cytogenetic approaches in mitotic chromosome and interphase chromatin / Eisuke Gotoh
Analysis of genomic aberrations using comparative genomic hybridization of metaphase chromosomes / Melanie A. Carless
Histone deacetylase activity assay / Lirong Peng, Zhigang Yuan, and Edward Seto
In vitro histone demethylase assays / Kenji Kokura, Lidong Sun, and Jia Fang
Integrated DNA methylation and chromatin structural analysis at single-molecule resolution / Carolina E. Pardo ... [et al.]
Determination of DNA methylation levels using illumina HumanMethylation450 BeadChips / Melanie A. Carless
Investigation of genomic methylation status using methylation-specific and bisulfite sequencing polymerase chain reaction / Melanie A. Carless
In vitro and in vivo assays for studying histone ubiquitination and deubiquitination / Heui-Yun Joo ... [et al.]
Immunostaining analysis of tissue cultured cells and tissue sections using phospho-histone H3 (Serine 10) antibody / Jaya Padmanabhan
Identification and characterization of nonhistone chromatin proteins : human positive coactivator 4 as a candidate / Sujata Kumari ... [et al.]
Methods to study transcription-coupled repair in chromatin / / Hélène Gaillard, Ralf Erik Wellinger, and Andrés Aguilera
Analysis of DNA replication associated chromatin decondensation : in vivo assay for understanding chromatin remodeling mechanisms of selected proteins / Sergiy Borysov, Victoria L. Bryant, and Mark G. Alexandrow
Non-radioactive assay methods for the assessment of telomerase activity and telomere length / Partha P. Banerjee and Shankar Jagadeesh
Detecting ATM-dependent chromatin modification in DNA damage response / Durga Udayakumar ... [et al.]
Imaging local deposition of newly synthesized histones in UVC-damaged chromatin / Salomé Adam ... [et al.]
In vitro replication assay with mammalian cell extracts / Wasia Rizwani and Srikumar P. Chellappan
Fluorescent in situ hybridization on comets : FISH comet / Sergey Shaposhnikov, Naouale El Yamani, and Andrew R. Collins
Methods to study histone chaperone function in nucleosome assembly and chromatin transcription / Parijat Senapati ... [et al.]
Preparation of mononucleosomal templates for analysis of transcription with RNA polymerase using spFRET / Kseniya S. Kudryashova ... [et al.]
Transcriptome-wide identification of in vivo interactions between RNAs and RNA-binding proteins by RIP and PAR- CLIP assays / Edgar González-Buendía ... [et al.]
Chromatin immunoprecipitation assays : analyzing transcription factor binding and histone modifications in vivo / Smitha Pillai, Piyali Dasgupta, and Srikumar P. Chellappan
ChIP on chip and ChIP-Seq assays : genome-wide analysis of transcription factor binding and histone modifications / Smitha Pillai and Srikumar P. Chellappan
ChIP-on-Chip analysis methods for affymetrix tiling arrays / Sean J. Yoder.