Most plant species rely on seeds for their dispersal and survival under unfavorable environmental conditions. Seeds are characterized by their low moisture content and significantly reduced metabolic activities. During the maturation phase, seeds accumulate storage reserves and become desiccation-tolerant and dormant. Growth is resumed after release of dormancy and the occurrence of favorable environmental conditions. Here we show that embryonic cotyledon nuclei of Arabidopsis thaliana seeds have a significantly reduced nuclear size, which is established at the beginning of seed maturation. In addition, the chromatin of embryonic cotyledon nuclei from mature seeds is highly condensed. Nuclei regain their size and chromatin condensation level during germination. The reduction in nuclear size is controlled by the seed maturation regulator ABSCISIC ACID-INSENSITIVE 3, and the increase during germination requires two predicted nuclear matrix proteins, LITTLE NUCLEI 1 and LITTLE NUCLEI 2. Our results suggest that the specific properties of nuclei in ripe seeds are an adaptation to desiccation, independent of dormancy. We conclude that the changes in nuclear size and chromatin condensation in seeds are independent, developmentally controlled processes.seed development | seed imbibition | seed germination | chromatin organization P lant seeds represent a quiescent dehydrated state with significantly reduced metabolic activities, which renders them resistant to abiotic stresses and viable for years. Germination occurs when nondormant seeds meet permissive environmental conditions for humidity, light, and temperature. Seed dormancy evolved to postpone germination during unfavorable seasons (1-3). The moisture content of ripe seeds from the model plant Arabidopsis thaliana is <10% (4). Low humidity levels can cause cellular damage due to protein unfolding and membrane disturbance. Sugars, late embryogenesis abundant proteins, and heat shock proteins play important roles in preventing this damage in seeds (5).Dehydration, accumulation of storage reserves, and induction of dormancy occur during the seed maturation phase, which is initiated after the embryo has fully developed (4). In Arabidopsis, seed maturation is tightly controlled by at least four central regulators, ABSCISIC ACID-INSENSITIVE 3 (ABI3), LEAFY COTYLEDON 1 (LEC1), LEC2, and FUSCA 3 (FUS3) (3, 6, 7). Other proteins have more dedicated roles in one of these processes; for instance, DELAY OF GERMINATION 1 (DOG1) and HISTONE MONOUBIQUITINATION 1 (HUB1) are required only for the establishment of seed dormancy (8, 9).Dry seeds represent a transitional state between embryo and seedling. During a phase transition, genes that control the "new" state need to be activated, whereas genes required for the "old" state must be repressed. Chromatin compaction in the cell nucleus has been proposed to contribute to gene regulation by allowing differential accessibility of DNA for the transcription machinery (10, 11). Accordingly, developmental changes in the plant are often ...

The life of a plant is characterized by major phase transitions. This includes the agriculturally important transitions from seed to seedling (germination) and from vegetative to generative growth (flowering induction). In many plant species, including Arabidopsis thaliana, freshly harvested seeds are dormant and incapable of germinating. Germination can occur after the release of dormancy and the occurrence of favourable environmental conditions. Although the hormonal control of seed dormancy is well studied, the molecular mechanisms underlying the induction and release of dormancy are not yet understood.In this study, we report the cloning and characterization of the mutant reduced dormancy 2-1 (rdo2-1). We found that RDO2 is allelic to the recently identified dormancy gene TFIIS, which is a transcription elongation factor. HUB1, which was previously called RDO4, was identified in the same mutagenesis screen for reduced dormancy as rdo2-1 and was also shown to be involved in transcription elongation. The human homologues of RDO2 and HUB1 interact with the RNA Polymerase II Associated Factor 1 Complex (PAF1C). Therefore, we investigated the effect of other Arabidopsis PAF1C related factors; VIP4, VIP5, ELF7, ELF8 and ATXR7 on seed dormancy. Mutations in these genes resulted in reduced dormancy, similar to hub1-2 and rdo2-1. Consistent with a role at the end of seed maturation, we found that HUB1, RDO2 and VIP5 are upregulated during this developmental phase. Since mutants in PAF1C related factors are also described to be early flowering, we conclude that these components are involved in the regulation of both major developmental transitions in the plant.

The chromatin structure determines gene expression and thereby regulates developmental processes in the plant. The molecular mechanisms regulating the induction and release of seed dormancy are still largely unknown and the underlying changes in chromatin organization have hardly been analyzed. Most chromatin studies in plants have been performed on vegetative tissues and have focused on seedlings. The composition of seeds hampers molecular analyses and requires adaptation of the methods that are used for other tissues. Here, we give an overview of the current methods that are used to study different aspects of chromatin organization in seeds. Cytogenetic methods, like fluorescence in situ hybridization and immunolocalization, are used to study chromatin at the microscopic level. Changes in DNA methylation and histone modifications can be studied with molecular methods, like bisulfite sequencing, immunoblotting, and chromatin immunoprecipitation.