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Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition

Author

Listed:
  • Benjamin J. M. Tremblay

    (Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra)

  • Cristina P. Santini

    (Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra)

  • Yajiao Cheng

    (Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra)

  • Xue Zhang

    (Swedish University of Agricultural Sciences (SLU))

  • Stefanie Rosa

    (Swedish University of Agricultural Sciences (SLU))

  • Julia I. Qüesta

    (Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra)

Abstract

Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in Arabidopsis thaliana we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.

Suggested Citation

  • Benjamin J. M. Tremblay & Cristina P. Santini & Yajiao Cheng & Xue Zhang & Stefanie Rosa & Julia I. Qüesta, 2024. "Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46082-5
    DOI: 10.1038/s41467-024-46082-5
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