Chromatin accessibility map of rice root tips at single-cell resolution [bulkATAC-seq]

Background: Single-cell reconstruction of gene regulatory programs provides an important tool to understand the cellular phenotypic variation in complex tissues and their response to endogenous and environmental stimuli. While the single-cell transcriptomes of several plant organs have been elucidated, the underlying chromatin landscapes remain largely unknown. Results: To comprehensively delineate chromatin accessibility during root development of an important crop, we applied single-cell ATAC-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 dynamics 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. Conclusions: Our work provides a framework for the integrative analysis of regulatory dynamics in an important plant organ at single-cell resolution. Single-cell ATACseq of rice root tips

研究背景：基因调控程序的单细胞重构，是解析复杂组织内细胞表型变异及其对内源性、环境性刺激响应的重要工具。当前虽已阐明多种植物器官的单细胞转录组，但其对应的染色质景观仍在很大程度上未被明确。
研究结果：为全面刻画重要农作物根系发育过程中的染色质可及性，我们针对正常及热胁迫条件下的水稻根尖细胞开展单细胞ATAC测序（single-cell ATAC-seq）分析，共纳入46758个细胞。本研究数据揭示了绝大多数主要细胞类型的细胞特异性染色质可及性差异，并鉴定出一批结合可及染色质区域（ACRs）的转录因子。以根毛分化为模型，通过伪时间分析我们证实，细胞类型分化过程中的染色质动态变化与基因表达动态变化显著相关。除发育轨迹外，本研究还描述了染色质对热胁迫的响应，并鉴定出该关键环境刺激下的细胞类型特异性可及性改变。
研究结论：本研究为以单细胞分辨率开展重要植物器官的调控动态整合分析提供了分析框架。水稻根尖单细胞ATAC测序数据集