Abstract
The scarcity of accessible sites that are dynamic or cell type-specific in plants may be due in part to tissue heterogeneity in bulk studies. To assess the effects of tissue heterogeneity, we apply single-cell ATAC-seq to Arabidopsis thaliana roots and identify thousands of differentially accessible sites, sufficient to resolve all major cell types of the root. We find that the entirety of a cell’s regulatory landscape and its transcriptome independently capture cell type identity. We leverage this shared information on cell identity to integrate accessibility and transcriptome data to characterize developmental progression, endoreduplication and cell division. We further use the combined data to characterize cell type-specific motif enrichments of transcription factor families and link the expression of family members to changing accessibility at specific loci, resolving direct and indirect effects that shape expression. Our approach provides an analytical framework to infer the gene regulatory networks that execute plant development.
Highlights
The scarcity of accessible sites that are dynamic or cell type-specific in plants may be due in part to tissue heterogeneity in bulk studies
Studies of chromatin accessibility in samples enriched for specific plant cell types have revealed: (i) the existence of cell type-specific regulatory elements; (ii) the relative scarcity of such elements compared to their prevalence in animals or humans; (iii) the expected enrichment of transcription factor binding sites within these elements; and (iv) a higher frequency of dynamic regulatory elements upstream of environmentally-responsive genes than constitutively expressed genes[7,8]
The correlation between chromatin accessibility and nearby gene expression is generally weak in both plants and animals[9], this correlation improves for regulatory elements that show dynamic changes in chromatin accessibility, for example in response to an environmental stimulus or developmental signal[7,9,10,11]
Summary
The scarcity of accessible sites that are dynamic or cell type-specific in plants may be due in part to tissue heterogeneity in bulk studies. We link individual cells from our scATAC-seq data with their nearest neighbors in scRNA space to define relative developmental progression, level of endoreduplication, and the genes differentially expressed in these nearest neighbors.
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