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Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level

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Farmer, Andrew, Thibivilliers, Sandra, Ryu, Kook Hui, Schiefelbein, John, Libault, Marc·2021·Molecular Plant
DOI 10.1016/j.molp.2021.01.001
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Abstract

Similar to other complex organisms, plants consist of diverse and specialized cell types. The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-type-specific transcriptional programs. As a necessary step in gaining a deeper understanding of the regulatory mechanisms controlling plant gene expression, we report the use of single-nucleus RNA sequencing (sNucRNA-seq) and single-nucleus assay for transposase accessible chromatin sequencing (sNucATAC-seq) technologies on Arabidopsis roots. The comparison of our single-nucleus transcriptomes to the published protoplast transcriptomes validated the use of nuclei as biological entities to establish plant cell-type-specific transcriptomes. Furthermore, our sNucRNA-seq results uncovered the transcriptomes of additional cell subtypes not identified by single-cell RNA-seq. Similar to our transcriptomic approach, the sNucATAC-seq approach led to the distribution of the Arabidopsis nuclei into distinct clusters, suggesting the differential accessibility of chromatin between groups of cells according to their identity. To reveal the impact of chromatin accessibility on gene expression, we integrated sNucRNA-seq and sNucATAC-seq data and demonstrated that cell-type-specific marker genes display cell-type-specific patterns of chromatin accessibility. Our data suggest that the differential chromatin accessibility is a critical mechanism to regulate gene activity at the cell-type level.

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Metadata

Authors
Farmer, A., Thibivilliers, S., Ryu, K. H., Schiefelbein, J., & Libault, M.
Venue
Molecular Plant
Publisher
Elsevier BV
Published
2021-03
Volume
14
Issue
3
Pages
372-383
ISSN
1674-2052 (ISSN-L)
DOI
10.1016/j.molp.2021.01.001
OpenAlex
W3119669192
Cited by
317
References
8
FWCI
15.03
Type
journal article
Language
en
Open access
hybrid
Licence
Funders
  • National Science Foundation (IOS #1339194, IOS #1923589, 1854326)
  • U.S. Department of Energy (DE-SC0020358)

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CoChat. (2026). Citation check: Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level. https://app.cochat.ai/papers/10.1016/j.molp.2021.01.001
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Farmer, A., Thibivilliers, S., Ryu, K. H., Schiefelbein, J., & Libault, M. (2021). Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level. Molecular Plant. https://doi.org/10.1016/j.molp.2021.01.001

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