Uncovering the regulatory landscape of Arabidopsis thaliana responses to cold temperatures

ended

Plants, as sessile organisms, must constantly adapt to variable environmental conditions, among which temperature is of paramount importance in the context of climate change. Indeed, in future years, despite an expected rise in temperatures due to global warming, we can also expect an increase in the frequency of severe cold periods for which plants are not prepared. Therefore, understanding the molecular processes that allow plants to react and adapt to cold is essential for developing cold-resistant plants, which is ultimately indispensable for global food security. In recent decades many studies have embarked in addressing this issue. However, the global regulatory landscape underlying cold acclimation and adaption of plants to noisy and fluctuating natural cold conditions remain poorly investigated. Low temperatures are known to have a direct effect on chromatin accessibility which is directly linked to gene expression. Therefore, the aim of this project is to investigate the dynamics of the coding and non-coding Arabidopsis thaliana transcriptome, as well as changes in chromatin accessible sites, in response to regimes of decreasing temperatures. To this end, a comparative analysis of deep-coverage RNA-seq (transcriptome) and ATAC-seq (chromatin accessibility) will be performed on A. thaliana plants grown over weeks of fluctuating temperatures, mimicking natural cold conditions of autumn and early winter. The proposed experimental design will reveal novel coding genes, long non-coding RNAs (lncRNAs) and potential distal regulatory elements involved in Arabidopsis responses to cold. Thus, by combining interdisciplinary and mutually reinforcing approaches including (epi)genomics, (epi)genetics, transcriptomics and bioinformatics, the proposed project will significantly improve our understanding of the molecular mechanisms required for plant adaptation to cold temperatures likely delivering valuable tools for future breeding of cold resilient crop species.