Methods for Plant Nucleus and Chromatin Studies Methods and Protocols

This volume provides a comprehensive collection of protocols that can be used to study plant chromatin structure and composition. Chapters divided into five 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 key tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Methods for Plant Nucleus and Chromatin Studies: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Whole-Genome Bisulfite Sequencing with a Small Amount of DNA.- Quantitative profiling of Histone variants and post-translational modifications by Tandem Mass Spectrometry in Arabidopsis.- Hi-ChIP for plant tissues.- A practical approach to high-throughput and accurate mapping-by-sequencing in Arabidopsis.- ChIP-Rx: Arabidopsis chromatin profiling using quantitative ChIP-seq.- Chromatin Immunoprecipitation for standard, rare or weakly-binding proteins.- Isolation and identification of Nuclear Protein Complexes Using GFP-tagged Arabidopsis Lines and IP-MS Approach.- Identification of Plant Chromatin Interaction Networks Using IP-MS and co-IP.- Unraveling Plant Nuclear Envelope Composition Using Proximity Labeling Proteomics.- A method for characterizing protein-histone peptide interactions in vitro.- Detection and automated quantification of nucleocytoplasmic RNA fractions in Arabidopsis using smFISH.- Simultaneous visualization of protein and genomic regions in plant nuclei.- Microfluidics to follow spatio-temporal dynamics at the nucleo-cytoplasmic interface during plant root growth.- Characterizations of nuclear organization and chromatin modifications in mature embryos from Arabidopsis dry seeds.- 3D STED Imaging of Isolated Arabidopsis thaliana Nuclei.- Understanding and simulating the dynamics of a polymer like chromatin.- Technical Mini-Review: dCas-based tools to visualize chromatin or modify epigenetic marks at specific plant genomic loci.- Using Callus as an Ex-Vivo System for Chromatin Analysis.