Reading Arabidopsis heat stress epitranscriptome – HEAT-EpiRNA

Due to global climat change, plants undergo increasing environmental variations unfavorable to their growth and development. Resistance to stress involves sensing and signaling networks driving modifications in gene expression to switch on protective mechanisms. These changes are not the mere result of genetically based alterations, they also rely on epigenetic and post-transcriptional modifications. To engineer new, high yield, crop varieties despite global climate change, we need to expand our basic knowledge of the mechanisms involved in the adaptation to stress such non-genetically based alterations. The HEAT-EpiRNA project aims in this context, at fostering knowledge on the emerging role of the epitranscriptome in plants response to heat stress.
RNA polymerase II transcribed RNAs undergo modifications, which landscape was pinned as the epitranscriptome of a cell. The most abundant of these marks are the internal N6-methyl adenosines (m6A). m6A features, methylation and demethylation machineries, are conserved in higher plants together with their capital role in reproduction and development. Animal studies showed that m6As attract readers that in turn drive interpreters to the transcript. They act in the basal control of gene expression, regulating splicing, translation, mRNA stability and chromatin structure. Identifying the mechanisms underlying the stress-induced modifications of gene expression is still under investigation. m6A and its readers are however recently emerging as crucial actors. In animals, the redistribution of a cytoplasmic m6A reader to the nucleus is determinant for the selective synthesis of heat stress proteins, in the context of a massive downregulation of translation, and therefore central for cell survival. This provides a first proof that m6A and its readers are involved in the stress induced reprogramming of gene expression. We posit that a mean to achieve such alterations relies on a change of readers attracted to the transcripts and/or on their stress-induced regulation. However, the landcape of readers, how they are functionally regulated, what are their molecular and physiogical roles for organism survival to stress are unknown. Our initial work supports that the stress-induced regulation of readers is a widespread phenomenon. We also identified the first Arabidopsis plant readers and found that at least one of them is likely regulated by heat specific phosphorylations. While another one is seemingly involved in the heat-induced decay of house-keeping mRNAs. The HEAT-EpiRNA project aims at understanding the role and regulatory mode of m6A readers in the cellular acclimation process to heat and decipher their importance in the plant thermotolerance program. Three work packages will permit, through an untargeted approach, to identify Arabidopsis heat-specific readers (WP1), assess their role in heat stress response at the post-transcriptional level in the cytoplasm (WP2) and decipher their functions in the nucleus (WP3). In addition, they will uncover how heat-induced post-translational modifications of readers regulate their activity (WP2-3). Our project gathers two French and two UK labs, with shared interest in m6A based regulations, bringing their technical skills and knowledge of plant m6A (P3), heat stress and cytoplasmic mRNA regulations (P1), chromatin based regulations (P2) and nuclear maturation of mRNAs (P4). This consortium has already produced a large amount of preliminary data and biological materials, strongly supporting the global strategy and work program of our project. HEAT-EpiRNA is therefore a pioneer program (as DNA epigenetic programs were a few years ago) that will gather fundamental knowledge on the dynamic of epitranscriptomic regulations and will pave the way for development of plants species that are better adapted to global climate change.