ArticleNature communications2021
The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
97 citing papers in PubMed.
- Advances in single-cell and spatial multi-omics for plant development and stress responses.Plant diversity · 2026Review
- Integrating single-cell omic techniques to resolve the spatio-temporal complexity of arbuscular mycorrhizal symbiosis.Journal of experimental botany · 2026Review
- Single-Cell and Spatial Omics Technologies in Rice Abiotic Stress Biology: A Methodological Review.International journal of molecular sciences · 2026Review
- Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants.Nature communications · 2026Article
- Single-nucleus RNA-seq and ATAC-seq analyses provide molecular insights into cadmium-stress response in alfalfa roots.Horticulture research · 2026Article
- OsNAC10 negatively regulates salt tolerance by repressing OsHKT1;5 expression and reducing shoot-to-root NaPlant communications · 2026Article
- Divergent Roles ofPlants (Basel, Switzerland) · 2026Article
- Single-cell chromatin accessibility and cis-regulatory element analyses in plants using the scPlantReg platform.Nature plants · 2026Article
- Lineage-specific evolution of regulatory landscapes in a polyploid plant and its diploid progenitors.bioRxiv : the preprint server for biology · 2026Article
- Integrating Single-Cell and Spatial Multi-Omics to Decode Plant-Microbe Interactions at Cellular Resolution.Microorganisms · 2026Review
- Big data approaches to understanding gene regulatory networks in the shoot apical meristem andFrontiers in plant science · 2026Review
- How to improve crop pathogen resistance with epigenetics.Phytopathology research · 2026Review
- Integrated single cell transcriptomics analysis for unraveling heterogeneity and plasticity of root cells for sustainable and regenerative agriculture.Frontiers in plant science · 2026Review
- Single-Cell Omics in Legumes: Research Trends and Applications.Plants (Basel, Switzerland) · 2025Review
- Motif-based models accurately predict cell type-specific distal regulatory elements.Nature communications · 2025Article
- Molecular Network Analysis in Model and Non-Model Legumes: Challenges in Omics Data Interpretation Across Species, with a Focus onPlants (Basel, Switzerland) · 2025Review
- Organ-level gene-regulatory networks inferred from transcriptomic data reveal context-specific regulation and highlight novel regulators of ripening and ABA-mediated responses in tomato.Plant communications · 2025Article
- DNA methylation in plant heterosis: mechanisms and prospects.Functional & integrative genomics · 2025Review
- Single-cell transcriptome atlas unveils transcriptional regulation networks of banana root tips in response toHorticulture research · 2025Article
- Single-nucleus RNA-sequencing reveals the cellular programs driving nematode-induced giant cell formation in tomato.Horticulture research · 2025Article
37 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.