Establishment of single-cell transcriptional states during seed germination

Liew, LC; You, Y; Auroux, L; Oliva, M; Peirats-Llobet, M; Ng, S; Tamiru-Oli, M; Berkowitz, O; Hong, UVT; Haslem, A; Stuart, T; Ritchie, ME; Bassel, GW; Lister, R; Whelan, J; Gouil, Q; Lewsey, MG

Author(s): Liew, LC; You, Y; Auroux, L; Oliva, M; Peirats-Llobet, M; Ng, S; Tamiru-Oli, M; Berkowitz, O; Hong, UVT; Haslem, A; Stuart, T; Ritchie, ME; Bassel, GW; Lister, R; Whelan, J; Gouil, Q; Lewsey, MG;
Details: Publication Year 2024-09,Volume 10,Issue #9,Page 1418-1434
Journal Title: Nature Plants
Abstract: Germination involves highly dynamic transcriptional programs as the cells of seeds reactivate and express the functions necessary for establishment in the environment. Individual cell types have distinct roles within the embryo, so must therefore have cell type-specific gene expression and gene regulatory networks. We can better understand how the functions of different cell types are established and contribute to the embryo by determining how cell type-specific transcription begins and changes through germination. Here we describe a temporal analysis of the germinating Arabidopsis thaliana embryo at single-cell resolution. We define the highly dynamic cell type-specific patterns of gene expression and how these relate to changing cellular function as germination progresses. Underlying these are unique gene regulatory networks and transcription factor activity. We unexpectedly discover that most embryo cells transition through the same initial transcriptional state early in germination, even though cell identity has already been established during embryogenesis. Cells later transition to cell type-specific gene expression patterns. Furthermore, our analyses support previous findings that the earliest events leading to the induction of seed germination take place in the vasculature. Overall, our study constitutes a general framework with which to characterize Arabidopsis cell transcriptional states through seed germination, allowing investigation of different genotypes and other plant species whose seed strategies may differ.
Publisher: Springer Nature
Keywords: *Germination/genetics; *Arabidopsis/genetics/growth & development; *Seeds/genetics/growth & development; *Gene Expression Regulation, Plant; Single-Cell Analysis; Gene Regulatory Networks; Transcription Factors/genetics/metabolism; Arabidopsis Proteins/genetics/metabolism
Research Division(s): Epigenetics And Development
PubMed ID: 39256563
Publisher's Version: https://doi.org/10.1038/s41477-024-01771-3
Open Access at Publisher's Site: https://doi.org/10.1038/s41477-024-01771-3
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2024-10-04 10:45:05

Last Modified: 2024-10-04 10:51:24