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

Author

Listed:
  • Shenghong Ge

    (Hangzhou Normal University)

  • Jinkai Li

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Hui Ma

    (Xiamen University)

  • María Sánchez-Bermúdez

    (Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo)

  • Siqun Wu

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Qiuyu Lv

    (Hangzhou Normal University)

  • Fengxiao Guo

    (Hangzhou Normal University)

  • Jinsong Dong

    (Hangzhou Normal University)

  • Guojie Ma

    (Hangzhou Normal University)

  • Qingshun Quinn Li

    (Xiamen University
    Western University of Health Sciences)

  • Viswanathan Satheesh

    (Iowa State University)

  • Mingguang Lei

    (Hangzhou Normal University)

Abstract

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.

Suggested Citation

  • 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, 2025. "A cis-natural antisense RNA regulates alternative polyadenylation of SlSPX5 under Pi starvation in tomato," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-63406-1
    DOI: 10.1038/s41467-025-63406-1
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