Profiling single-cell chromatin accessibility in plants

Alexandre P Marand; Xuan Zhang; Julie Nelson; Pedro Augusto Braga Dos Reis; Robert J Schmitz

doi:10.1016/j.xpro.2021.100737

Profiling single-cell chromatin accessibility in plants

STAR Protoc. 2021 Aug 12;2(3):100737. doi: 10.1016/j.xpro.2021.100737. eCollection 2021 Sep 17.

Authors

Alexandre P Marand¹, Xuan Zhang¹, Julie Nelson², Pedro Augusto Braga Dos Reis^{1

3}, Robert J Schmitz¹

Affiliations

¹ Department of Genetics, University of Georgia, Athens, GA 30602, USA.
² Center for Tropical and Emerging Disease, University of Georgia, Athens, GA 30602, USA.
³ Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, Brazil.

Abstract

Coupling assay for transposase-accessible chromatin sequencing (ATAC-seq) with microfluidic separation and cellular barcoding has emerged as a powerful approach to investigate chromatin accessibility of individual cells. Here, we define a protocol for constructing single-cell ATAC-seq libraries from maize seedling nuclei and the preliminary computational steps for assessing data quality. This protocol can be readily adapted to other plant species or tissues with minor changes to reveal chromatin accessibility variation among individual cells. For complete details on the use and execution of this protocol, please refer to Marand et al. (2021).

Keywords: developmental biology; genomics; molecular biology; plant sciences; sequence analysis; sequencing; single cell.

Publication types

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

MeSH terms

Cell Culture Techniques
Chromatin Immunoprecipitation Sequencing / methods*
Chromatin* / chemistry
Chromatin* / genetics
Plant Cells / chemistry*
Seedlings / cytology
Single-Cell Analysis / methods*
Zea mays / cytology

Substances

Chromatin