Protocol for assaying chromatin accessibility using ATAC-seq in plants

Fu-Xiang Wang; Guan-Dong Shang; Lian-Yu Wu; Yan-Xia Mai; Jian Gao; Zhou-Geng Xu; Jia-Wei Wang

doi:10.1016/j.xpro.2020.100289

Protocol for assaying chromatin accessibility using ATAC-seq in plants

STAR Protoc. 2021 Jan 21;2(1):100289. doi: 10.1016/j.xpro.2020.100289. eCollection 2021 Mar 19.

Authors

Fu-Xiang Wang^{1

2}, Guan-Dong Shang^{1

2}, Lian-Yu Wu^{1

3}, Yan-Xia Mai¹, Jian Gao^{1

2}, Zhou-Geng Xu^{1

2}, Jia-Wei Wang^{1

3}

Affiliations

¹ National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS center for Excellence in Molecular Plant Science, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China.
² University of Chinese Academy of Sciences (UCAS), Shanghai 200032, China.
³ ShanghaiTech University, Shanghai 200031, China.

Abstract

Open or accessible regions of the genome are the primary positions of binding sites for transcription factors and chromatin regulators. Transposase-accessible chromatin sequencing (ATAC-seq) can probe chromatin accessibility in the intact nucleus. Here, we describe a protocol to generate ATAC-seq libraries from fresh Arabidopsis thaliana tissues and establish an easy-to-use bioinformatic analysis pipeline. Our method could be applied to other plants and other tissues and allows for the reliable detection of changes in chromatin accessibility throughout plant growth and development. For complete details on the use and execution of this protocol, please refer to Wang et al. (2020).

Keywords: Bioinformatics; Gene Expression; Model Organisms; Sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Arabidopsis / genetics*
Chromatin / genetics*
Chromatin / metabolism
Gene Library*
High-Throughput Nucleotide Sequencing*
Transposases*

Substances

Chromatin
Transposases