Transmission electron microscopy imaging to analyze chromatin density distribution at the nanoscale level / Tohnyui Ndinyanka Fabrice, Lusik Cherkezyan, Christoph Ringli, and Celia Baroux. Profiling DNA methylation using bisulfite sequencing (BS-Seq) / Yun-Ru Chen, Sheng Yu, and Silin Zhong -- Bisulfite sequencing using small DNA amounts / Susanne Edelmann and Stefan Scholten -- Identification of differentially methylated regions in the genome of Arabidopsis thaliana / Kamal Kishore and Mattia Pelizzola -- Rapid and efficient ChIP protocol to profile chromatin binding proteins and epigenetic modifications in Arabidopsis / Benedicte Desvoyes, Zaida Vergara, Joana Sequeira-Mendes, Sofia Madeira, and Crisanto Gutierrez -- Sequential ChIP protocol for profiling bivalent epigenetic modifications (ReChIP) / Benedicte Desvoyes, Joana Sequeira-Mendes, Zaida Vergara, Sofia Madeira, and Crisanto Gutierrez -- Method to identify nucleolus-associated chromatin domains (NADs) / Marie-Christine Carpentier, Ariadna Picart-Picolo, and Frederic Pontvianne -- Cell type-specific profiling of chromatin modifications and associated proteins / Ana Karina Morao, Erwann Caillieux, Vincent Colot, and Francois Roudier -- Mapping of histone modifications in plants by tandem mass spectrometry / Walid Mahrez and Lars Hennig -- Histone H1 purification and post-translational modification profiling by high-resolution mass spectrometry / Maciej Kotlinski and Andrzej Jerzmanowski -- Profiling nucleosome occupancy by MNase-seq : experimental protocol and computational analysis / Alice Pajoro, Jose M. Muino, Gerco C. Angenent, and Kerstin Kaufmann -- Identification of open chromatin regions in plant genomes using ATAC-Seq / Marko Bajic, Kelsey A. Maher, and Roger B. Deal -- Unraveling the complex epigenetic mechanisms that regulate gene activity / Marian Bemer -- Technical review : a hitchhiker's guide to chromosome conformation capture / Stefan Grob and Giacomo Cavalli -- 3C in maize and Arabidopsis / Blaise Weber, Suraj Jamge, and Maike Stam -- Profiling histone modifications in synchronized floral tissues for quantitative resolution of chromatin and transcriptome dynamics / Julia Engelhorn, Frank Wellmer, and Cristel C. Carles -- De novo identification of sRNA loci and non-coding RNAs by high-throughput sequencing / Alice Lunardon, Cristian Forestan, Silvia Farinati, and Serena Varotto -- Identification of in planta protein-protein interactions using IP-MS / Suraj Jamge, Gerco C. Angenent, and Marian Bemer -- RNA immunoprecipitation protocol to identify protein-RNA interactions in Arabidopsis thaliana / Benoit Mermaz, Fuquan Liu, and Jie Song -- In vitro assays to measure histone methyltransferase activity using different chromatin substrates / Yannick Jacob and Philipp Voigt -- Identification of parent-of-origin-dependent QTLs using bulk-segregant sequencing (bulk-seq) / Nuno D. Pires and Ueli Grossniklaus -- QTLepi mapping in Arabidopsis thaliana / Kathrin Lauss and Joost J.B. Keurentjes -- Compendium of methods to analyze the spatial organization of plant chromatin / Aline V. Probst -- Localization of chromatin marks in Arabidopsis early embryos / Marcelina Garcıa-Aguilar and Daphne Autran -- Cell-type specific chromatin analysis in whole-mount plant tissues by immunostaining / Wenjing She, Celia Baroux, and Ueli Grossniklaus -- Measuring dynamics of histone proteins by photobleaching in Arabidopsis roots / Stefanie Rosa -- Fluorescence in situ hybridization (FISH) and immunolabeling on 3D preserved nuclei / Till David Bey, Maria Koini, and Paul Fransz -- High-affinity LNA-DNA mixmer probes for detection of chromosome-specific polymorphisms of 5S rDNA repeats in Arabidopsis thaliana / Lauriane Simon and Aline V. Probst -- Method for testing random spatial models on nuclear object distributions / Javier Arpon, Valerie Gaudin, and Philippe Andrey -- Technical review : cytogenetic tools for studying mitotic chromosomes / Vaclav Bacovsky, Roman Hobza, and Boris Vyskot -- Technical review : microscopy and image processing tools to analyze plant chromatin : practical considerations / Celia Baroux and Veit Schubert -- Automated 3D gene position analysis using a customized imaris plugin : XTFISHInsideNucleus / Mariamawit S. Ashenafi and Celia Baroux -- Quantitative 3D analysis of nuclear morphology and heterochromatin organization from whole-mount plant tissue using nucleusJ / Sophie Desset, Axel Poulet, and Christophe Tatout -- Transmission electron microscopy imaging to analyze chromatin density distribution at the nanoscale level / Tohnyui Ndinyanka Fabrice, Lusik Cherkezyan, Christoph Ringli, and Celia Baroux.
Summary:
This volume provides a comprehensive collection of protocols that can be used to study plant chromatin structure and composition. Chapters divided into three sections detail the profiling of chromatin features in relation to epigenetic regulation, investigate the interaction between chromatin modifications and gene regulation, and explore the 3D spatial organization of the chromatin inside the nucleus. 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 cutting-edge, Plant Chromatin Dynamics: Methods and Protocols aims to ensure successful results in the further study of this vital field.--Publisher's website.
Series:
Methods in molecular biology, 1064-3745 ; 1675 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.