The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution

Abstract

In plants, chromatin accessibility – the primary mark of regulatory DNA – is relatively static across tissues and conditions. This scarcity of accessible sites that are dynamic or tissue-specific may be due in part to tissue heterogeneity in previous bulk studies. To assess the effects of tissue heterogeneity, we apply single-cell ATAC-seq to A. thaliana roots and identify thousands of differentially accessible sites, sufficient to resolve all major cell types of the root. However, even this vast increase relative to bulk studies in the number of dynamic sites does not resolve the poor correlation at individual loci between accessibility and expression. Instead, we find that the entirety of a cell’s regulatory landscape and its transcriptome each capture cell type identity independently. We leverage this shared information on cell identity to integrate accessibility and transcriptome data in order to characterize developmental progression, endoreduplication and cell division in the root. We further use the combined data to characterize cell type-specific motif enrichments of large transcription factor families and to link the expression of individual family members to changing accessibility at specific loci, taking the first steps toward resolving the direct and indirect effects that shape gene expression. Our approach provides an analytical framework to infer the gene regulatory networks that execute plant development.

Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis

“…In parallel, H3K27me3 removal in sperm exposes cis -regulatory regions at developmental genes required to initiate transition back to diploid life after fertilisation. While substantial differences in ACRs have been observed across sporophytic Arabidopsis tissues ( Sullivan et al, 2014 ), more closely related cell types appear to show few specific open chromatin sites ( Dorrity et al, 2020 ; Maher et al, 2018 ). Despite being separated by a single cell division, thousands of differential ACRs distinguish the SN and VN, which is the result of the epigenetic reprogramming that occur across the male sporophyte-to-gametophyte transition.…”

A robust method of nuclei isolation for single-cell RNA sequencing of solid tissues from the plant genus Populus

“…Triton X-100, a non-ionic detergent commonly used to permeabilize cell membranes during nuclei isolation, was removed because it may contribute to RNA leakage [ 19 , 20 ]. MgCl 2 (3mM) was included in all buffers to protect the nuclear membrane [ 21 ]. Finally, 0.2 U/μl of Protector RNase Inhibitor was added to reduce the activity of ribonucleases.…”

Single cell gene regulatory networks in plants: Opportunities for enhancing climate change stress resilience

“…Single cell Assay for Transposase Accessible Chromatin (scATACseq) has been used to show that regions of accessible regulatory chromatin vary between classes of Arabidopsis root cells, thereby indicating a distinct cell type specific regulatory logic (Dorrity et al, 2020).…”