Regulation of seed dormancy by histone post-translational modifications in the model plant Arabidopsis thaliana.

Plants synchronize their growth and development with environmental changes, which is critical for their survival. Among their life cycle transitions, seed germination is key for ensuring the survival and optimal growth of the next generation. However, even under favorable conditions, oftentimes germination can be blocked by seed dormancy, a regulatory multilayered checkpoint integrating internal and external signals. Intricate genetic and epigenetic mechanisms underlie seed dormancy establishment, maintenance, and release. In this review, we focus on recent advances that shed light on the complex mechanisms associated with physiological dormancy, prevalent in seed plants, with Arabidopsis thaliana serving as a model. Here, we summarize the role of multiple epigenetic regulators, but with a focus on histone modifications like acetylation and methylation, that finely tune dormancy responses and influence dormancy-associated gene expression. Understanding these mechanisms can lead to a better understanding of seed biology in general, as well as result in the identification of possible targets for breeding climate-resilient plants.

Alternative splicing in plants: current knowledge and future directions for assessing the biological relevance of splice variants.

Alternative splicing is an important regulatory process that produces multiple transcripts from a single gene, significantly modulating the transcriptome and potentially the proteome, during development and in response to environmental cues. In the first part of this review, we summarize recent advances and highlight the accumulated knowledge on the biological roles of alternative splicing isoforms that are key for different plant responses and during development. Remarkably, we found that many of the studies in this area use similar methodological approaches that need to be improved to gain more accurate conclusions, since they generally presume that stable isoforms undoubtedly have coding capacities. This is mostly done without data indicating that a particular RNA isoform is in fact translated. So, in the latter part of the review, we propose a thorough strategy to analyze, evaluate, and characterize putative functions for alternative splicing isoforms of interest.

Light in the transcription landscape: chromatin, RNA polymerase II and splicing throughout Arabidopsis thaliana's life cycle.

Plants have a high level of developmental plasticity that allows them to respond and adapt to changes in the environment. Among the environmental cues, light controls almost every aspect of A. thaliana's life cycle, including seed maturation, seed germination, seedling de-etiolation and flowering time. Light signals induce massive reprogramming of gene expression, producing changes in RNA polymerase II transcription, alternative splicing, and chromatin state. Since splicing reactions occur mainly while transcription takes place, the regulation of RNAPII transcription has repercussions in the splicing outcomes. This cotranscriptional nature allows a functional coupling between transcription and splicing, in which properties of the splicing reactions are affected by the transcriptional process. Chromatin landscapes influence both transcription and splicing. In this review, we highlight, summarize and discuss recent progress in the field to gain a comprehensive insight on the cross-regulation between chromatin state, RNAPII transcription and splicing decisions in plants, with a special focus on light-triggered responses. We also introduce several examples of transcription and splicing factors that could be acting as coupling factors in plants. Unravelling how these connected regulatory networks operate, can help in the design of better crops with higher productivity and tolerance.

Molecular mechanisms underlying the entrance in secondary dormancy of Arabidopsis seeds.

As seasons change, dormant seeds cycle through dormant states until the environmental conditions are favourable for seedling establishment. Dormancy cycle is widespread in the plant kingdom allowing the seeds to display primary and secondary dormancy. Several reports in the last decade have focused on understanding the molecular mechanisms of primary dormancy, but our knowledge regarding secondary dormancy is limited. Here, we studied secondary dormancy induced in Arabidopsis thaliana by incubating seeds at 25 °C in darkness for 4 d. By physiological, pharmacological, expression and genetics approaches, we demonstrate that (1) the entrance in secondary dormancy involves changes in the content and sensitivity to GA, but the content and sensitivity to ABA do not change, albeit ABA is required; (2) RGL2 promotes the entrance in secondary dormancy through ABI5 action; and (3) multivariate analysis with 18 geographical and environmental parameters of accession collection place suggests that temperature is an important variable influencing the induction of secondary dormancy in nature.