Induction of epigenetic variation in tomato

The accessibility of a genetic region determines how efficiently it can be accessed by transcription complexes, regulatory enzymes, DNA damaging agents etc. The differential packaging of different genomic regions into condensed and open conformations balances the conflicting demands for transcriptional competence of genetic loci and the efficient storage and conservation of genetic information. Early models suggested a separation of the genome into highly condensed gene-poor heterochromatin and highly accessible gene-rich euchromatin. This strict separation is no longer maintainable, a we now know that even euchromatic regions frequently change their level of chromatin condensation, either as part of developmental programmes or in response to changing environmental conditions. Euchromatin also frequently contains mobile elements with a condensed chromatin structure, which can spread into adjacent DNA regions and reduce the local transcriptional competence. Moreover, many transgenes that integrate into euchromatin, can be packages into a heterochromatin-like conformation that renders them transcriptionally inactive. These epigenetic changes are reversible as they are controlled by reversible modifications of the DNA and the histone octamer around which the DNA is wound. Two key regulators of repressive epigenetic states are DNA methyltransferases (DNMTs) that control cytosine methylation, and histone methyltransferases (HMTs) that regulate methylation of lysine residue 9 at histone H3 (H3K9) and lysine residue 20 at histone H4 (H4K20met). HMTs compete with histone acetyl transferases (HATs), which convert repressive lysine methylation marks into open lysine acetylation marks. HATs again compete with histone deacetylases (HDACs), which remove lysine acetylation and generate substrates for HMTs. The objectives of this collaboration are to develop biochemical and transgenic strategies for the controlled destabilisation of repressive epigenetic states in tomato, to identify genomic regions that serve as markers for epigenetic change, and to examine the effects of epigenetic change on transcription and genome stability. This approach will be accompanied by proof-of-concept experiments in the epigenetic model system Arabidopsis thaliana, where many epigenetic regulators and genomic target loci have already been identified. Biochemical and phenotypic screens of tomato plants will search for transient and permanent effects of epigenetic disturbances to assess if this approach can be applied to enhance genetic variation.