ArticleGenome biology2017
Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
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97 citing papers in PubMed.
- Replication-independent eviction of the histone variant H2B.8 reveals chromatin reprogramming during seed imbibition.Nature communications · 2026Article
- A four-dimensional spatial transcriptome atlas of barley caryopsis development and germination.The Plant cell · 2026Article
- Holistic overview of regulatory networks governing seed dormancy and germination in plants.Science China. Life sciences · 2026Review
- Advances in seed omics.Journal of experimental botany · 2026Review
- Identification of Accessible Transcription Factor Binding Sites During the Seed-to-Seedling Transition.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Reconfiguration of DNA methylation at growth resumption after winter dormancy in Kiwifruit.Scientific reports · 2025Article
- Stage-Specific Transcriptomic Insights into Seed Germination and Early Development inPlants (Basel, Switzerland) · 2025Article
- DSK2-mediated degradation of F-box protein LAO1 and class I TCPs modulates the nitrogen starvation response.EMBO reports · 2025Article
- Polycomb repressive complex 2 facilitates the transition from heterotrophy to photoautotrophy during seedling emergence.The Plant cell · 2025Article
- Epigenetics in the modern era of crop improvements.Science China. Life sciences · 2025Review
- Diversity of organ-specific plant transcriptomes.Acta biochimica Polonica · 2025Review
- A new conceptual model for seed germination and seedling tillering of winter wheat in the field.Royal Society open science · 2025Article
- GABA does not regulate stomatal CO2 signalling in Arabidopsis.Journal of experimental botany · 2024Article
- Establishment of single-cell transcriptional states during seed germination.Nature plants · 2024Article
- Hints of Biological Activity of Xerosydryle: Preliminary Evidence on the Early Stages of Seedling Development.International journal of molecular sciences · 2024Article
- DNA methylation variations underlie lettuce domestication and divergence.Genome biology · 2024Article
- Population genomics and epigenomics of Spirodela polyrhiza provide insights into the evolution of facultative asexuality.Communications biology · 2024Article
- A commitment for life: Decades of unraveling the molecular mechanisms behind seed dormancy and germination.The Plant cell · 2024Review
- ABA Inhibits Rice Seed Aging by Reducing HPlants (Basel, Switzerland) · 2024Article
- Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition.Nature communications · 2024Article
37 more citing papers are in PubMed but not listed here.
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9 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundSeed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene expression and the dynamic changes in the epigenome and small RNAs during germination is limited. The interactions between genome, transcriptome and epigenome must be revealed in order to identify the regulatory mechanisms that control seed germination.
resultsWe present an integrated analysis of high-resolution RNA sequencing, small RNA sequencing and MethylC sequencing over ten developmental time points in Arabidopsis thaliana seeds, finding extensive transcriptomic and epigenomic transformations associated with seed germination. We identify previously unannotated loci from which messenger RNAs are expressed transiently during germination and find widespread alternative splicing and divergent isoform abundance of genes involved in RNA processing and splicing. We generate the first dynamic transcription factor network model of germination, identifying known and novel regulatory factors. Expression of both microRNA and short interfering RNA loci changes significantly during germination, particularly between the seed and the post-germinative seedling. These are associated with changes in gene expression and large-scale demethylation observed towards the end of germination, as the epigenome transitions from an embryo-like to a vegetative seedling state.
conclusionsThis study reveals the complex dynamics and interactions of the transcriptome and epigenome during seed germination, including the extensive remodelling of the seed DNA methylome from an embryo-like to vegetative-like state during the seed-to-seedling transition. Data are available for exploration in a user-friendly browser at https://jbrowse.latrobe.edu.au/germination_epigenome .
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