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<p>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.</p>

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Single-cell chromatin accessibility and cis-regulatory element analyses in plants using the scPlantReg platform

  • 期刊论文

  • 发表日期：

    2026年4月28日

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  • 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

摘要

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.