Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips

文献类型： 外文期刊

第一作者： Feng, Dan

作者： Feng, Dan;Liang, Zhe;Wang, Yifan;Hu, Guihua;Qu, Ruihong;Xie, Shang;Li, Dongwei;Yang, Liwen;Gu, Xiaofeng;Yao, Jiaying;Yuan, Zan;Zhao, Xinai;Ma, Yanfei;Lohmann, Jan U.

作者机构：

关键词： Rice; Root; Cell type; Chromatin accessibility; scATAC-seq; Developmental trajectory; Environmental stimulus

期刊名称：BMC BIOLOGY （ 影响因子：7.364； 五年影响因子：8.641 ）

ISSN：

年卷期： 2022 年 20 卷 1 期

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收录情况： SCI

摘要： BackgroundRoot 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. ResultsTo 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. ConclusionsWe 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.

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