Dynamics of gene expression in single root cells of A. thaliana

First author: Ken Jean-Baptiste; Affiliations: University of Washington (华盛顿大学): Seattle, USA

Corresponding author: Josh Cuperus

Single-cell RNA-seq can yield high-resolution cell-type-specific expression signatures that reveal new cell types and the developmental trajectories of cell lineages. Here, we apply this approach to A. thaliana root cells to capture gene expression in 3,121 root cells. We used Monocle 3, ordering single-cell transcriptomes in an unsupervised manner reconstructing single-cell developmental trajectories. We identify hundreds of genes with cell-type-specific expression, with pseudotime analysis of several cell lineages revealing both known and novel genes that are expressed along a developmental trajectory. We identify transcription factor motifs that are enriched across development, together with the corresponding candidate transcription factors that likely drive the observed expression patterns. We assess and interpret changes in total RNA expression along developmental trajectories and show that trajectory branch points mark developmental decisions. Finally, by applying heat stress to whole seedlings, we address the longstanding question of possible heterogeneity among cell types in the response to an abiotic stress. Although the response of canonical heat shock genes dominates expression across cell types, subtle but significant differences in other genes can be detected among cell types. Taken together, our results demonstrate that single-cell transcriptomics holds promise for studying plant development and plant physiology with unprecedented resolution.

单细胞RNA-seq可以产生高分辨率的细胞类型特异性表达信号，有利于鉴定新的细胞类型和追踪细胞系的发育轨迹。本文，作者通过单细胞RNA-seq对拟南芥根的3121个细胞进行基因表达谱的研究。作者利用Monocle 3对所获得的单细胞转录组进行无监督聚类重建单细胞发育轨迹。作者鉴定了数百个基因具有细胞类型特异性表达，同时对某系细胞系的拟时分析显示了一些已知基因和一些新的基因随着发育轨迹而表达。作者还鉴定了不同发育阶段富集的转录因子基序，这些基序与对应的转录因子一起可能驱动了基因表达模式的建成。作者评估并解释了随着发育轨迹总体RNA表达上的变化，结果显示发育轨迹的分支点标志着细胞的发育决策。最终，通过对整个小苗进行热胁迫处理，作者研究了植物响应非生物胁迫时不同细胞类型是否存在异质性这一长期存在的疑问。尽管响应于高温的热激基因在不同细胞类型中都存在优势表达，但仍有一些其它的基因在不同细胞类型中存在显著的差异。综上，本文的研究结果揭示了单细胞转录组将为植物发育生物学和植物生理学等植物科学领域提供一个前所未有的研究策略。

通讯：Josh Cuperus (http://queitschlab.gs.washington.edu/#people)

个人简介：2005年，俄勒冈州立大学，微生物学学士；2011年，俄勒冈州立大学，分子和细胞生物学博士。

doi: https://doi.org/10.1105/tpc.18.00785

Journal: Plant Cell

First Published: March 28, 2019