ArticleNature communications2024
Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Early detection and genetic insights into salt tolerance in rice by linking physiology and spectral reflectance during seed germination.Plant phenomics (Washington, D.C.) · 2026Article
- Transcriptional activity during seed imbibition is conserved, robust and required for germination.Nature communications · 2026Article
- Advances in mutant characterization for detecting causal mutations in crop plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Two genes, one switch: a bidirectional promoter strategy for inducible plant immunity.Plant physiology · 2026Article
- Replication-independent eviction of the histone variant H2B.8 reveals chromatin reprogramming during seed imbibition.Nature communications · 2026Article
- Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq).Nature protocols · 2026Review
- A four-dimensional spatial transcriptome atlas of barley caryopsis development and germination.The Plant cell · 2026Article
- Advances in seed omics.Journal of experimental botany · 2026Review
- Epitranscriptomics as a Candidate Universal Modulator of Dormancy Transitions.Ecology and evolution · 2026Review
- Identification of Accessible Transcription Factor Binding Sites During the Seed-to-Seedling Transition.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Plant-specific function of H3K9me3 as a permissive chromatin mark during Arabidopsis seed germination.Frontiers in plant science · 2026Article
- Translational and epitranscriptomic regulation of seed germination in Arabidopsis thaliana genotypes with contrasting dormancy phenotypes.Plant molecular biology · 2025Article
- Regulatory Landscapes of Non-Coding RNAs During Drought Stress in Plants.International journal of molecular sciences · 2025Review
- Long Noncoding RNAs as Emerging Regulators of Seed Development, Germination, and Senescence.International journal of molecular sciences · 2025Review
- Polycomb repressive complex 2 facilitates the transition from heterotrophy to photoautotrophy during seedling emergence.The Plant cell · 2025Article
- How chromatin senses plant hormones.Current opinion in plant biology · 2024Review
- Enhancers associated with unstable RNAs are rare in plants.Nature plants · 2024Article
- Voice from both sides: a molecular dialogue between transcriptional activators and repressors in seed-to-seedling transition and crop adaptation.Frontiers in plant science · 2024Review
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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