Single-cell analysis of cell identity in the Arabidopsis root apical meristem: insights and opportunities

Abstract

A fundamental question in developmental biology is how the progeny of stem cells become differentiated tissues. The Arabidopsis root is a tractable model to address this question due to its simple organization and defined cell lineages. In particular, the zone of dividing cells at the root tip-the root apical meristem-presents an opportunity to map the gene regulatory networks underlying stem cell niche maintenance, tissue patterning, and cell identity acquisition. To identify molecular regulators of these processes, studies over the last 20 years employed global profiling of gene expression patterns. However, these technologies are prone to information loss due to averaging gene expression signatures over multiple cell types and/or developmental stages. Recently developed high-throughput methods to profile gene expression at single-cell resolution have been successfully applied to plants. Here, we review insights from the first published single-cell mRNA sequencing and chromatin accessibility datasets generated from Arabidopsis roots. These studies successfully reconstruct developmental trajectories, phenotype cell identity mutants at unprecedented resolution, and reveal cell type-specific responses to environmental stimuli. The experimental insight gained from Arabidopsis paves the way to profile roots from additional species.

Keywords: Arabidopsis root; cell identity; chromatin accessibility; developmental trajectories; environmental response; single-cell RNA sequencing; transcriptomics.

Fig. 1.

Single-cell transcriptomics and chromatin accessibility experiments provide new insight into root development and environmental response. Single-cell mRNA sequencing (scRNA-seq) of Arabidopsis root protoplasts captures all major cell types and developmental stages. Since scRNA-seq requires cell destruction, developmental trajectories are inferred computationally. In addition to wild-type roots, scRNA-seq has been applied to mutants and roots which have been subjected to abiotic stress. In combination with scRNA-seq, single-cell chromatin accessibility (scATAC-seq) data generated from nuclei can be used to infer gene regulation underlying developmental processes and environmental responses. Beyond Arabidopsis, single-nuclei RNA-seq (snRNA-seq) is a promising approach to profile recalcitrant tissues from species such as maize or rice. The root illustration is modified from the Plant Illustrations repository (Sparks, 2017). All other panels were created with BioRender.com.