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Biology subjects

Tzioutziou, N.

Publications and source records attributed to Tzioutziou, N..

2 recordsLinked to original sources

REVEILLE2 Thermosensitive Splicing: A Molecular Basis for the Integration of Nocturnal Temperature Information by the Arabidopsis Circadian Clock

O_LICold stress is one of the major environmental factors that limit growth and yield of plants. However, it is still not fully understood how plants account for daily temperature fluctuations, nor how these temperature changes are integrated with other regulatory systems such as the circadian clock. C_LIO_LIWe demonstrate that REVEILLE2, a MYB-like transcription factor, exhibits a cold-induced alternative splicing switch from a non-translatable isoform at ambient temperature to a translatable isoform upon cold exposure. We explore the biological function of REVEILLE2 using a combination of molecular genetics, transcriptomics, and physiology. C_LIO_LIDisruption of the REVEILLE2 cooling switch alters regulatory gene expression, impairs circadian timing, and improves photosynthetic capacity. Changes in nuclear gene expression are particularly apparent in the initial hours following chilling, with chloroplast gene expression subsequently up-regulated. C_LIO_LIThe REVEILLE2 cold switch extends our understanding of plants immediate response to cooling. We propose that the circadian component REVEILLE2 restricts plants responses to nocturnal reductions in temperature, thereby enabling appropriate responses to daily environmental changes. C_LI Plain language summaryPlants need to respond appropriately to temperature, accounting for the expected daily patterns of reduced temperatures that occur every night relative to the day. Here, we show that a gene expressed at night fulfils this function.

plant biology↗

3D RNA-seq - a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists

RNA-seq analysis of gene expression and alternative splicing should be routine and robust but is often a bottleneck for biologists because of reliance on specialized bioinformatics skills. Thus, we have developed "3D RNA-seq", an R shiny App and web based service which provides an easy-to-use, flexible and powerful tool for three-component analysis of RNA-seq data: Differential Expression, Differential Alternative Splicing and Differential Transcript Usage. 3D RNA-seq integrates state-of-the-art, highly rated differential expression analysis tools and adopts best practice for RNA-seq analysis. It operates through a user-friendly graphical interface, can handle complex experimental designs, allows setting of statistical parameters, tracks results through graphics and tables, and generates figures and a comprehensive report that will guarantee reproducibility. 3D RNA-seq can be applied to any species and is designed to be run by biologists with no programming skills (or by bioinformaticians) allowing lab scientists to perform rapid and accurate analysis of RNA-seq data.

bioinformatics↗