DOI：10.1038/s41477-026-02289-6

发表期刊：Nature Plants

链接：https://www.nature.com/articles/s41477-026-02289-6

作者：Haidong Yan†*, Yarong Jin†, Chengran Wang†, Xinxin Zhang†, Jiyuan Jia†, Xiaofang Cao†, Alexandre P. Marand, Mao Xia, Xuan Zhang, Yun Zhong, Xin Tang, Qiang Zhai, Tao Liu, Shilin Tian, Xiaoqin Li, Xiang Li, Jie Yao, Robert J. Schmitz*, Zhaoming Wang* & Linkai Huang*

Abstract：Understanding gene regulation is fundamental to plant improvement. However, the lack of plant-specific single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) frameworks and cross-species databases has limited insights into cell-type-specific cellular regulation. Here we present ‘scPlantReg’, an integrated framework and database for plant scATAC-seq data. scPlantReg supports end-to-end analyses from raw data processing to biological interpretation and features ‘scATACtor’, a supervised machine-learning approach that outperforms existing tools for cell-type annotation. We applied scPlantReg to pearl millet to characterize cell-type-specific chromatin accessibility and identify validated activating and repressing accessible chromatin regions (ACRs), revealing WRKY transcription factors as potential regulators of xylem development. Furthermore, we reanalysed scATAC-seq datasets from 8 plant species, spanning 11 tissues and multiple developmental stages, enabling cross-species comparisons. These analyses uncovered conserved regulatory programmes, including AP2/EREBP-associated ACRs linked to cell wall development and cell-type-conserved TFs across grasses. Collectively, scPlantReg provides a general framework and resource for comparative regulatory analysis in plants.

Keywords: scPlantReg, scATAC-seq, scATACtor, pearl millet, WRKY, cross-species analysis