{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Feng D"],"funding":["Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences","European Research Council","The Agricultural Science and Technology Innovation Program","National Transgenic Major Program"],"pagination":["274"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9733338"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["20(1)"],"pubmed_abstract":["<h4>Background</h4>Root development and function have central roles in plant adaptation to the environment. The modification of root traits has additionally been a major driver of crop performance since the green revolution; however, the molecular underpinnings and the regulatory programmes defining root development and response to environmental stress remain largely unknown. Single-cell reconstruction of gene regulatory programmes provides an important tool to understand the cellular phenotypic variation in complex tissues and their response to endogenous and environmental stimuli. While single-cell transcriptomes of several plant organs have been elucidated, the underlying chromatin landscapes associated with cell type-specific gene expression remain largely unexplored.<h4>Results</h4>To comprehensively delineate chromatin accessibility during root development of an important crop, we applied single-cell ATAC-seq (scATAC-seq) to 46,758 cells from rice root tips under normal and heat stress conditions. Our data revealed cell type-specific accessibility variance across most of the major cell types and allowed us to identify sets of transcription factors which associate with accessible chromatin regions (ACRs). Using root hair differentiation as a model, we demonstrate that chromatin and gene expression dynamics during cell type differentiation correlate in pseudotime analyses. In addition to developmental trajectories, we describe chromatin responses to heat and identify cell type-specific accessibility changes to this key environmental stimulus.<h4>Conclusions</h4>We report chromatin landscapes during rice root development at single-cell resolution. Our work provides a framework for the integrative analysis of regulatory dynamics in this important crop organ at single-cell resolution."],"journal":["BMC biology"],"pubmed_title":["Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips."],"pmcid":["PMC9733338"],"funding_grant_id":["810296","2019ZX08010-002","No.Y2020PT06"],"pubmed_authors":["Yao J","Yang L","Gu X","Li D","Liang Z","Ma Y","Feng D","Xie S","Zhao X","Qu R","Lohmann JU","Hu G","Wang Y","Yuan Z"],"additional_accession":[]},"is_claimable":false,"name":"Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips.","description":"<h4>Background</h4>Root development and function have central roles in plant adaptation to the environment. The modification of root traits has additionally been a major driver of crop performance since the green revolution; however, the molecular underpinnings and the regulatory programmes defining root development and response to environmental stress remain largely unknown. Single-cell reconstruction of gene regulatory programmes provides an important tool to understand the cellular phenotypic variation in complex tissues and their response to endogenous and environmental stimuli. While single-cell transcriptomes of several plant organs have been elucidated, the underlying chromatin landscapes associated with cell type-specific gene expression remain largely unexplored.<h4>Results</h4>To comprehensively delineate chromatin accessibility during root development of an important crop, we applied single-cell ATAC-seq (scATAC-seq) to 46,758 cells from rice root tips under normal and heat stress conditions. Our data revealed cell type-specific accessibility variance across most of the major cell types and allowed us to identify sets of transcription factors which associate with accessible chromatin regions (ACRs). Using root hair differentiation as a model, we demonstrate that chromatin and gene expression dynamics during cell type differentiation correlate in pseudotime analyses. In addition to developmental trajectories, we describe chromatin responses to heat and identify cell type-specific accessibility changes to this key environmental stimulus.<h4>Conclusions</h4>We report chromatin landscapes during rice root development at single-cell resolution. Our work provides a framework for the integrative analysis of regulatory dynamics in this important crop organ at single-cell resolution.","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 Dec","modification":"2026-06-20T03:22:23.786Z","creation":"2025-04-05T21:24:54.877Z"},"accession":"S-EPMC9733338","cross_references":{"pubmed":["36482454"],"doi":["10.1186/s12915-022-01473-2"]}}