Final Report Summary - REVOLUTION (RNA silencing in regulation and evolution)
The REVOLUTION project addressed the role of small RNA molecules in genetic and epigenetic regulatory networks of plants. Before the project started it was understood that there are several different types of these small RNAs and the aim was to use Arabidopsis as a model to investigate their role in growth development and evolution. We showed first that they are derived from approximately 20000 loci in the Arabidopsis genome – similar to the number of protein-coding genes – and that they are associated with both posttranscriptional and transcriptional/epigenetic mechanisms with the latter class being the most prevalent. This information has then allowed us to make other findings that have taken our research in three inter-related directions. First we found that the epigenetic siRNAs are very abundant in the developing seed and when they are expressed specifically from the maternal genome. This finding then prompted us to ask about the role of RNA silencing in hybrid plants and led to our discovery that the parental genomes can interact through the involvement of small RNA; these RNAs from one genome can find targets in the second genome where they trigger heritable epigenetic change. This finding indicates that the formation of hybrids is important not only because it creates new combinations of genes but also because, via RNA mediated mechanisms it triggers new and heritable epigenetic marks that have the potential to influence the phenotype of the hybrid organism. The project is leading to new understanding of both natural and artificial evolution (plant breeding) and it is a central component of a follow up ERC funded project (TRIBE).
A second major finding concerned positive feedback mechanisms in RNA silencing at the posttranscriptional level. We established that small RNA can trigger new production of secondary siRNA provided that it is specifically 22nt long. We knew previously that secondary siRNA production triggered cascades of RNA silencing but we did not understand why these cascades are constrained. The requirement for small RNA of a specific length provides a partial explanation because most of the small RNA is either 21nt or 24nt long and produced through pathways that compete with the 22nt RNA pathway. This finding will help understand genetic regulatory cascades and networks in plants. New findings that emerged towards the end of this project will be important in the understanding of regulatory networks. These data that are being written up after the project finished have shown that there is an additional unsuspected initiation stage of RNA-mediated epigenetic change. We knew previously about establishment and maintenance phases but now we understand that there is this earlier initiation process about which there are few details at present. We will investigate the mechanism and its application in follow up work.
The third major line of research in REVOLUTION related to mobile small RNA. Until recently RNA was considered as a molecule that is a coding sequence or regulator operating within a cell. Viruses were known as mobile RNA but cellular RNAs were thought to remain inside a cell. We designed an approach based on grafting different genotypes of plant and thereby confirmed that small silencing RNA can indeed move and that it mediates epigenetic silencing in the recipient cell. The biological implications of this finding remain to be discovered and at present we can only say that the epigenetic sRNAs are likely to be implicated in many of the epigenetic marks in plant genomes. In future work we intend to find out to whether we can harness mobile small RNA to target the introduction of heritable epigenetic effects on plant genotypes. We will be aiming to generate epigenetically modified crop plants.
A second major finding concerned positive feedback mechanisms in RNA silencing at the posttranscriptional level. We established that small RNA can trigger new production of secondary siRNA provided that it is specifically 22nt long. We knew previously that secondary siRNA production triggered cascades of RNA silencing but we did not understand why these cascades are constrained. The requirement for small RNA of a specific length provides a partial explanation because most of the small RNA is either 21nt or 24nt long and produced through pathways that compete with the 22nt RNA pathway. This finding will help understand genetic regulatory cascades and networks in plants. New findings that emerged towards the end of this project will be important in the understanding of regulatory networks. These data that are being written up after the project finished have shown that there is an additional unsuspected initiation stage of RNA-mediated epigenetic change. We knew previously about establishment and maintenance phases but now we understand that there is this earlier initiation process about which there are few details at present. We will investigate the mechanism and its application in follow up work.
The third major line of research in REVOLUTION related to mobile small RNA. Until recently RNA was considered as a molecule that is a coding sequence or regulator operating within a cell. Viruses were known as mobile RNA but cellular RNAs were thought to remain inside a cell. We designed an approach based on grafting different genotypes of plant and thereby confirmed that small silencing RNA can indeed move and that it mediates epigenetic silencing in the recipient cell. The biological implications of this finding remain to be discovered and at present we can only say that the epigenetic sRNAs are likely to be implicated in many of the epigenetic marks in plant genomes. In future work we intend to find out to whether we can harness mobile small RNA to target the introduction of heritable epigenetic effects on plant genotypes. We will be aiming to generate epigenetically modified crop plants.