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, Bajic, Marko, Maher, Kelsey A., Deal, Roger B. |
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. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 1 | 100% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 1 | 100% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 124 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 35 | 28% |
Researcher | 28 | 23% |
Student > Bachelor | 14 | 11% |
Student > Master | 6 | 5% |
Professor > Associate Professor | 5 | 4% |
Other | 10 | 8% |
Unknown | 26 | 21% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 54 | 44% |
Biochemistry, Genetics and Molecular Biology | 37 | 30% |
Environmental Science | 3 | 2% |
Immunology and Microbiology | 2 | 2% |
Neuroscience | 1 | <1% |
Other | 0 | 0% |
Unknown | 27 | 22% |