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Plant Chromatin Dynamics

Overview of attention for book
Cover of 'Plant Chromatin Dynamics'

Table of Contents

  1. Altmetric Badge
    Book Overview
  2. Altmetric Badge
    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
  36. Altmetric Badge
    Chapter 35 Erratum to: Bisulfite Sequencing Using Small DNA Amounts
Attention for Chapter 12: Identification of Open Chromatin Regions in Plant Genomes Using ATAC-Seq
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Citations

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Chapter title
Identification of Open Chromatin Regions in Plant Genomes Using ATAC-Seq
Chapter number 12
Book title
Plant Chromatin Dynamics
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7318-7_12
Pubmed ID
Book ISBNs
978-1-4939-7317-0, 978-1-4939-7318-7
Authors

Marko Bajic, Kelsey A. Maher, Roger B. Deal

Abstract

Identifying and characterizing highly accessible chromatin regions assists in determining the location of genomic regulatory elements and understanding transcriptional regulation. In this chapter, we describe an approach to map accessible chromatin features in plants using the Assay for Transposase-Accessible Chromatin, combined with high-throughput sequencing (ATAC-seq), which was originally developed for cultured animal cells. This technique utilizes a hyperactive Tn5 transposase to cause DNA cleavage and simultaneous insertion of sequencing adapters into open chromatin regions of the input nuclei. The application of ATAC-seq to plant tissue has been challenging due to the difficulty of isolating nuclei sufficiently free of interfering organellar DNA. Here we present two different approaches to purify plant nuclei for ATAC-seq: the INTACT method (Isolation of Nuclei TAgged in specific Cell Types) to isolate nuclei from individual cell types of the plant, and tissue lysis followed by sucrose sedimentation to isolate sufficiently pure total nuclei. We provide detailed instructions for transposase treatment of nuclei isolated using either approach, as well as subsequent preparation of ATAC-seq libraries. Sequencing-ready ATAC-seq libraries can be prepared from plant tissue in as little as one day. The procedures described here are optimized for Arabidopsis thaliana but can also be applied to other plant species.

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 86 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 86 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 26 30%
Researcher 25 29%
Student > Bachelor 7 8%
Professor > Associate Professor 5 6%
Student > Master 4 5%
Other 4 5%
Unknown 15 17%
Readers by discipline Count As %
Agricultural and Biological Sciences 46 53%
Biochemistry, Genetics and Molecular Biology 24 28%
Environmental Science 2 2%
Unknown 14 16%

Attention Score in Context

This research output has an Altmetric Attention Score of 4. 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 09 September 2019.
All research outputs
#4,654,333
of 15,807,159 outputs
Outputs from Methods in molecular biology
#1,334
of 9,234 outputs
Outputs of similar age
#110,329
of 323,004 outputs
Outputs of similar age from Methods in molecular biology
#1
of 1 outputs
Altmetric has tracked 15,807,159 research outputs across all sources so far. This one has received more attention than most of these and is in the 69th percentile.
So far Altmetric has tracked 9,234 research outputs from this source. They receive a mean Attention Score of 2.6. This one has done well, scoring higher than 85% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 323,004 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 65% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them