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.

Activation of Nucleases, PCD, and Mobilization of Reserves in the Araucaria angustifolia Megagametophyte During Germination.

The megagametophyte of mature seeds of Araucaria angustifolia consists of cells with thin walls, one or more nuclei, a central vacuole storing proteins, and a cytoplasm rich in amyloplasts, mitochondria and lipid bodies. In this study, we describe the process of mobilization of reserves and analyzed the dismantling of the tissue during germination, using a range of well-established markers of programmed cell death (PCD), including: morphological changes in nuclei and amyloplasts, DNA degradation, and changes in nuclease profiles. TUNEL reaction and DNA electrophoresis demonstrate that DNA fragmentation in nuclei occurs at early stages of germination, which correlates with induction of specific nucleases. The results of the present study add knowledge on the dismantling of the megagametophyte of genus Araucaria, a storage tissue that stores starch as the main reserve substance, as well as on the PCD pathway, by revealing new insights into the role of nucleases and the expression patterns of putative nuclease genes during germination.