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Research article2024Peer reviewedOpen access

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

Tremblay, Benjamin J. M.; Santini, Cristina P.; Cheng, Yajiao; et al.

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.

Published in

Nature Communications
2024, Volume: 15, number: 1, article number: 1724

      SLU Authors

      • UKÄ Subject classification

      Plant Biotechnology

      Publication identifier

      DOI: https://doi.org/10.1038/s41467-024-46082-5

      Permanent link to this page (URI)

      https://res.slu.se/id/publ/131406