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<p>Alternative polyadenylation (APA) generates transcript diversity by producing mRNA isoforms with distinct 3’ ends. Despite the critical roles that APA plays in various biological processes, the mechanisms regulating APA in response to stresses have remained poorly understood in plants. Here, we perform comprehensive analysis of APA in tomato, and focus on a phosphate (Pi)- regulated APA gene <i>SlSPX5</i>, encoding a putative Pi sensor protein. SlSPX5 interacts with and sequesters the transcription factor SlPHL1 in the cytosol, thereby inhibiting the expression of Pi starvation inducible genes. We discover that a <i>cis</i>-natural antisense RNA (<i>cis</i>-NAT) is activated from <i>SlSPX5</i> to promote its proximal polyadenylation under Pi-depleted conditions. The transcription of this <i>cis</i>-NAT induces RNA Polymerase II pausing, generating Ser2 phosphorylation signals that recruit polyadenylation machinery to the 5’ end of <i>SlSPX5</i>. Our findings demonstrate that a cis-NAT regulates APA of its cognate gene in response to Pi starvation.</p>

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A cis-natural antisense RNA regulates alternative polyadenylation of SlSPX5 under Pi starvation in tomato

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年8月27日

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  • Shenghong Ge,
  • Jinkai Li,
  • Hui Ma,
  • María Sánchez-Bermúdez,
  • Siqun Wu,
  • Qiuyu Lv,
  • Fengxiao Guo,
  • Jinsong Dong,
  • Guojie Ma,
  • Qingshun Quinn Li,
  • Viswanathan Satheesh,
  • Mingguang Lei

摘要

Alternative polyadenylation (APA) generates transcript diversity by producing mRNA isoforms with distinct 3’ ends. Despite the critical roles that APA plays in various biological processes, the mechanisms regulating APA in response to stresses have remained poorly understood in plants. Here, we perform comprehensive analysis of APA in tomato, and focus on a phosphate (Pi)- regulated APA gene SlSPX5, encoding a putative Pi sensor protein. SlSPX5 interacts with and sequesters the transcription factor SlPHL1 in the cytosol, thereby inhibiting the expression of Pi starvation inducible genes. We discover that a cis-natural antisense RNA (cis-NAT) is activated from SlSPX5 to promote its proximal polyadenylation under Pi-depleted conditions. The transcription of this cis-NAT induces RNA Polymerase II pausing, generating Ser2 phosphorylation signals that recruit polyadenylation machinery to the 5’ end of SlSPX5. Our findings demonstrate that a cis-NAT regulates APA of its cognate gene in response to Pi starvation.