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Plant Chromatin Dynamics

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Cover of 'Plant Chromatin Dynamics'

Table of Contents

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    Book Overview
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    Chapter 1 Profiling Developmentally and Environmentally Controlled Chromatin Reprogramming
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    Chapter 2 Profiling DNA Methylation Using Bisulfite Sequencing (BS-Seq)
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    Chapter 3 Bisulfite Sequencing Using Small DNA Amounts
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    Chapter 4 Identification of Differentially Methylated Regions in the Genome of Arabidopsis thaliana
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    Chapter 5 A Rapid and Efficient ChIP Protocol to Profile Chromatin Binding Proteins and Epigenetic Modifications in Arabidopsis
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    Chapter 6 Sequential ChIP Protocol for Profiling Bivalent Epigenetic Modifications (ReChIP)
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    Chapter 7 A Method to Identify Nucleolus-Associated Chromatin Domains (NADs)
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    Chapter 8 Cell Type-Specific Profiling of Chromatin Modifications and Associated Proteins
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    Chapter 9 Mapping of Histone Modifications in Plants by Tandem Mass Spectrometry
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    Chapter 10 Histone H1 Purification and Post-Translational Modification Profiling by High–Resolution Mass Spectrometry
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    Chapter 11 Profiling Nucleosome Occupancy by MNase-seq: Experimental Protocol and Computational Analysis
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    Chapter 12 Identification of Open Chromatin Regions in Plant Genomes Using ATAC-Seq
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    Chapter 13 Unraveling the Complex Epigenetic Mechanisms that Regulate Gene Activity
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    Chapter 14 Technical Review: A Hitchhiker’s Guide to Chromosome Conformation Capture
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    Chapter 15 3C in Maize and Arabidopsis
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    Chapter 16 Profiling Histone Modifications in Synchronized Floral Tissues for Quantitative Resolution of Chromatin and Transcriptome Dynamics
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    Chapter 17 De Novo Identification of sRNA Loci and Non-coding RNAs by High-Throughput Sequencing
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    Chapter 18 Identification of In Planta Protein–Protein Interactions Using IP-MS
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    Chapter 19 RNA Immunoprecipitation Protocol to Identify Protein–RNA Interactions in Arabidopsis thaliana
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    Chapter 20 In Vitro Assays to Measure Histone Methyltransferase Activity Using Different Chromatin Substrates
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    Chapter 21 Identification of Parent-of-Origin-Dependent QTLs Using Bulk-Segregant Sequencing (Bulk-Seq)
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    Chapter 22 QTLepi Mapping in Arabidopsis thaliana
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    Chapter 23 A Compendium of Methods to Analyze the Spatial Organization of Plant Chromatin
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    Chapter 24 Localization of Chromatin Marks in Arabidopsis Early Embryos
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    Chapter 25 Cell-Type Specific Chromatin Analysis in Whole-Mount Plant Tissues by Immunostaining
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    Chapter 26 Measuring Dynamics of Histone Proteins by Photobleaching in Arabidopsis Roots
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    Chapter 27 Fluorescence In Situ Hybridization (FISH) and Immunolabeling on 3D Preserved Nuclei
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    Chapter 28 High-Affinity LNA–DNA Mixmer Probes for Detection of Chromosome-Specific Polymorphisms of 5S rDNA Repeats in Arabidopsis thaliana
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    Chapter 29 A Method for Testing Random Spatial Models on Nuclear Object Distributions
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    Chapter 30 Technical Review: Cytogenetic Tools for Studying Mitotic Chromosomes
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    Chapter 31 Technical Review: Microscopy and Image Processing Tools to Analyze Plant Chromatin: Practical Considerations
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    Chapter 32 Automated 3D Gene Position Analysis Using a Customized Imaris Plugin: XTFISHInsideNucleus
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    Chapter 33 Quantitative 3D Analysis of Nuclear Morphology and Heterochromatin Organization from Whole-Mount Plant Tissue Using NucleusJ
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    Chapter 34 Transmission Electron Microscopy Imaging to Analyze Chromatin Density Distribution at the Nanoscale Level
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    Chapter 35 Erratum to: Bisulfite Sequencing Using Small DNA Amounts
Attention for Chapter 8: Cell Type-Specific Profiling of Chromatin Modifications and Associated Proteins
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Chapter title
Cell Type-Specific Profiling of Chromatin Modifications and Associated Proteins
Chapter number 8
Book title
Plant Chromatin Dynamics
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7318-7_8
Pubmed ID
Book ISBNs
978-1-4939-7317-0, 978-1-4939-7318-7
Authors

Ana Karina Morao, Erwann Caillieux, Vincent Colot, François Roudier

Abstract

Progression of a cell along a differentiation path is characterized by changes in gene expression profiles. Alterations of these transcriptional programs result from cell type-specific transcription factors that act in a dynamic chromatin environment. Understanding the precise contribution of these molecular factors during the differentiation process requires accessing specific cell types within a developing organ. This chapter describes a streamlined and alternative version of INTACT, a method enabling the isolation of specific cell populations by affinity-purification of tagged nuclei and the subsequent analysis of gene expression, transcription factor binding profiles, as well as chromatin state at a genome-wide scale. In particular, modifications of the nuclei isolation, capture, and purification procedures are proposed that improve time scale, yield, and purity. In addition, the combination of different tags enables the analysis of distinct cell populations from a single transgenic line and the subtractive purification of subpopulations of cells, including those for which no specific promoter is available. Finally, we describe a chromatin immunoprecipitation protocol that has been successfully used to profile histone modifications and other chromatin-associated proteins such as RNA Polymerase II in different cell populations of the Arabidopsis root, including the quiescent center of the stem cell niche.

Twitter Demographics

The data shown below were collected from the profile of 1 tweeter who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 7 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 7 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 2 29%
Student > Ph. D. Student 1 14%
Professor > Associate Professor 1 14%
Student > Master 1 14%
Unknown 2 29%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 2 29%
Agricultural and Biological Sciences 2 29%
Neuroscience 1 14%
Unknown 2 29%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 21 October 2017.
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#10,662,429
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#5,586
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Outputs of similar age from Methods in molecular biology
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