The Regulatory Landscape of Arabidopsis Thaliana Roots at Single-Cell Resolution

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.

Dr. Josh Cuperus
Research Assistant Professor
Department of Genome Sciences, University of Washington

Dr. Josh Cuperus is a Research Assistant Professor at University of Washington in the Department of Genome Sciences. Josh has degrees of Microbiology and Cell & Molecular Biology both from Oregon State University. He has been applying sequencing-based technologies to plants for 15 years, with focuses on small RNA biology, gene regulation and the chromatin landscape.

Steve Hoffman, PhD
Segment Marketing Manager for Single Cell Sequencing
Illumina

Adriana Suarez, PhD
Science and Technology Advisor
10x Genomics