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

Benjamin J. M. Tremblay, Cristina P. Santini, Yajiao Cheng, Xue Zhang, Stefanie Rosa and Julia I. Qüesta ()
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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

Nature Communications, 2024, vol. 15, issue 1, 1-21

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-46082-5

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