In vitro histone demethylase assays / Lirong Peng, Zhigang Yuan, and Edward Seto -- 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 / Hélène Gaillard, Ralf Erik Wellinger, and Andrés Aguilera -- Methods to study transcription-coupled repair in chromatin / 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 -- Methods to study histone chaperone function in nucleosome assembly and chromatin transcription / Parijat Senapati ... [et al.] -- 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.] -- ChIP-on-Chip analysis methods for affymetrix tiling arrays / Sean J. Yoder. 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.
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.
Series:
Methods in molecular biology, 1064-3745 ; 1288 Springer protocols, 1949-2448
This resource is supported by the Institute of Museum and Library Services under the provisions of the Library Services and Technology Act as administered by State Library of Iowa.