The current lack of mechanistic understanding regarding how Polycomb targets are selected severely limits the potential for epigenetic manipulation in many eukaryotic systems. This proposal therefore addresses a key central question in chromatin biology: which factors specify a gene for Polycomb mediated silencing? It will make use of the recent identification of a single nucleotide polymorphism within the target gene that blocks cold induced silencing of the Polycomb switching system at FLOWERING LOCUS C (FLC) in Arabidopsis thaliana. At FLC, specific DNA binding proteins (VAL1, VAL2) and their partners interact in a not yet fully understood regulatory network with Polycomb proteins, which consequently convert environmental cues (prolonged cold) into stable epigenetic memory (silencing of the gene) to achieve flowering. I hypothesise that this regulation involves components of the Apoptosis and Splicing Associated Protein (ASAP) complex, the functions of which have been linked to RNA processing and RNA quality control. Thus, these protein interactions directly link DNA sequence specificity with co-transcriptional regulation through to Polycomb mediated epigenetic gene silencing. I aim to demonstrate that multiple cis and trans factors determine Polycomb target selection and that their combined actions synergize to nucleate Polycomb complexes at FLC, and thus switch the gene from an epigenetically active to a silent state. The proposed work will be achieved through interconnected molecular, biochemical and genetic avenues. It will yield novel and comprehensive mechanistic insights into the complexity and plasticity of epigenetic regulation of Polycomb target genes in plants, with broad impact on chromatin research in other organisms.

Polyploidization is one of the major driving forces of plant evolution and crop domestication and plays a key role in plant environmental adaptation. The function of multiple gene copies (homoeologous genes) from different subgenomes can vary from each other (sub/neofunctionalization), which is considered as the key to understanding polyploidy evolution and environmental adaptation. However, most sequence variations between homoeologous genes lie on the non-coding region or are synonymous mutations, which cannot lead to codon change. To data, very little is known about how the vast majority of sequence variations over the gene body regions drives subgenomes sub/neofunctionalization in polyploidy. Recently, Single Nucleotide Polymorphism (SNP) induced RNA structural alteration is demonstrated to play key roles in post-transcriptional regulations such as RNA decay and splicing. Further studies in human disease showed that SNP-induced RNA structural changes are associated with diverse human disease and phenotypes. And also, temperature can affect the RNA structures that more stably folded mRNAs tended to show lower decay rate. This brought attention to the existing function of synonymous mutations as well as non-coding SNPs. Thus, I hypothesize that SNP-induced RNA structural alteration might lead to the subgenomes sub/neofunctionalization and play an important role in temperature stress response. As tetraploid wheat is widely grown in the Europe and its yield is severely affected by heat stress, I will test my hypothesis in tetraploid wheat. Firstly, genome-wide RNA secondary structure profiling will be applied to compare SNP-induced RNA structure variations between subgenomes in tetraploid wheat. Secondly, I will investigate the roles of SNP-induced RNA structure variations in RNA stability and splicing pattern changes between subgenomes. Finally, I will assess the role of SNP-induced RNA structure variations in response to high temperature.