Multiome in the same cell revealed the impact of osmotic stress on Arabidopsis root tip development at single-cell level

Cell-specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single-cell mono-omics techniques are unable to fully capture the relationships and dynamics of molecular information within cells. While data integration algorithm facilitates the merging of single-cell RNA-seq and single-cell ATAC-seq data, ensuring the accuracy of the integration process remains a challenge, particularly when investigating cell-type-specific TRNs. In this study, we aimed to elucidate the TRNs of Arabidopsis under osmotic stress at the single-cell level by employing single-cell multi-omics technology to simultaneously examine gene expression and chromatin accessibility of 16,670 Arabidopsis root tip nuclei. We performed 12,968 peak-to-gene linkage at bona fide single-cell level, instead of previous computational integration at cell type level, which enabled us to obtain an unprecedented resolution to reconstruct transcriptional regulation. Pseudotime developmental trajectories revealed that osmotic stress led to shift the developmental status of Suberin synthetic endodermis (Suberin-endo) and trichoblast cells. We identified candidate stress-related cell-specific enhancers and cis-regulatory elements as well as potential target genes, and uncovered large cellular heterogeneity. We also found that cis-regulatory elements became accessible prior to gene expression and these cis-regulatory elements could form a positive feedback loop with epigenetic modification H3K4me3 in response to osmotic stress in columella cells.