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<p>DNA methylation plays critical roles in eukaryotic gene silencing, genome imprinting, viral defense, and suppression of transposable elements. In plants, RNA Polymerase V (Pol V)-generated non-coding RNA guides DNA methylation through the RNA-directed DNA methylation (RdDM) pathway; however, how these RNAs are selected is unknown. Here, we show that the 3’-ends of Pol V transcripts are enriched at A-rich template DNA (A-rich-DNA<sub>T</sub>). Arabidopsis RdDM regions possess AT-rich boundaries genome-wide, suggesting that Pol V likely terminates at A-rich-DNA<sub>T</sub>, which subsequently defines the DNA methylation landscape in plants. A-rich-DNA<sub>T</sub> successfully stops Pol V transcription in vitro. Structural snapshots of Pol V transcribing A-rich-DNA<sub>T</sub> show that accumulation of unstable rU:dA pairs in the RNA-DNA hybrid promotes transcription bubble collapse and spontaneous transcription termination. These findings identify an intrinsic Pol V termination signal that shapes genomic DNA methylation patterning in plants and reveals a common mechanism for spontaneous transcription termination.</p>

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A spontaneous termination mechanism of RNA polymerase V shapes the DNA methylation landscape in plants

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年4月2日

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  • Guohui Xie,
  • Xuan Du,
  • Yifang Tan,
  • Yuxing Zhou,
  • Cheng Chi,
  • Sixian Zhou,
  • Colette L Picard,
  • Songge Chai,
  • Lei Wu,
  • Danling Zhu,
  • Jun Zhao,
  • Yan Xue,
  • Sisi Li,
  • Steven E Jacobsen,
  • Zhe Wu,
  • Jiamu Du

摘要

DNA methylation plays critical roles in eukaryotic gene silencing, genome imprinting, viral defense, and suppression of transposable elements. In plants, RNA Polymerase V (Pol V)-generated non-coding RNA guides DNA methylation through the RNA-directed DNA methylation (RdDM) pathway; however, how these RNAs are selected is unknown. Here, we show that the 3’-ends of Pol V transcripts are enriched at A-rich template DNA (A-rich-DNAT). Arabidopsis RdDM regions possess AT-rich boundaries genome-wide, suggesting that Pol V likely terminates at A-rich-DNAT, which subsequently defines the DNA methylation landscape in plants. A-rich-DNAT successfully stops Pol V transcription in vitro. Structural snapshots of Pol V transcribing A-rich-DNAT show that accumulation of unstable rU:dA pairs in the RNA-DNA hybrid promotes transcription bubble collapse and spontaneous transcription termination. These findings identify an intrinsic Pol V termination signal that shapes genomic DNA methylation patterning in plants and reveals a common mechanism for spontaneous transcription termination.