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RNA silencing in epigenetics

In plants, fungi and perhaps in animals, a consequence of RNA silencing is epigenetic modification of DNA and chromatin and, consequently, modification of chromosome structure and function. These epigenetic modifications are often associated with changes in gene expression - normally silencing but also with gene activation. We are interested in the mechanism of this epigenetic silencing and its effects on chromosome structure and aspects of growth development and evolution of plants. An intriguing possibility, suggested by our work on RNA-mediated epigenetic silencing, is that heritable epigenetic changes could be mediated by siRNAs that are induced in response to disease, stress or other external stimuli.

rna progenitor
Heritable silencing: these plants are viewed under UV light. The progenitor plants have a transgene that causes them to fluoresce green. We silenced this gene in these progenitor plants and then observed that the silencing persisted in several generations of progeny plants. In the absence of green fluorescence these plants fluoresced red due to their chlorophyll.

One set of projects involves RNA polymerase IV. This protein is similar to the well characterised Polymerases I-III. However, Pol IV is distinct in that it is specifically required for biogenesis of RNA in RNA silencing pathways including those involved in epigenetic processes. We are currently testing the biochemical activity and nature of proteins associated with PolIV and characterising the genetic loci that are affected by PolIV mediated silencing.

rna nucleus
An Arabidopsis nucleus reacted with PolIV antibodies (green) or a stain for DNA (DAPI- blue). The images show PolIV is present in localised regions of the chromatin and in a structure in the nucleolus (the region that does not stain for DNA).