RNA-based Epigenetic Control of Transposons

Transposons are potentially mobile genetic elements residing in their host genomes. For a long time after their discovery, these elements were considered to be exclusively parasitic, as they need the host cell machinery for their amplification within the genome. In contrast, research over the past decades revealed that transposon can be advantageous for their hosts by contributing to genome evolution and increasing genetic variability. However, transposon activity needs to be tightly regulated to avoid detrimental consequences to the host organism such as loss of genome integrity, cancer and sterility. The most prominent control mechanisms of transposon activity are destruction of transposon RNA (post-transcriptional gene silencing) and repression of transposon expression (transcriptional gene silencing). On both levels of transposon control, non-coding RNAs are core components conferring flexibility and at the same time specificity of the defense response. Small interfering RNAs are important for guiding effector proteins to transposons for destruction of their mRNAs or deposition of silencing marks such as DNA methylation and histone modifications. In contrast, the contribution of long non-coding RNAs to transposon control is less understood as long non-coding RNAs are produced by essential RNA polymerases in most organisms. However, Arabidopsis thaliana encodes specific RNA polymerase complexes dedicated to the production of non-coding RNAs and plants harboring mutant subunits of these RNA polymerase complexes are viable thereby facilitating the analysis of long non-coding RNA. Moreover, transposons still transpose and even vary in their activity in the different Arabidopsis thaliana ecotypes thereby allowing the analysis of natural variation of transposon control. My proposed research will focus on the roles of long non-coding RNA in silencing. Firstly, I will investigate if long non-coding RNAs transcribed by RNA polymerase V (POL V) in Arabidopsis thaliana guide the small interfering RNA-effector complex to transposon targets of silencing. Alternatively, I will address a hypothetical direct recruitment of the complex by the DNA sequence at target loci. Secondly, I will discover if long non-coding RNAs produced by POL V are targeting the de novo DNA methyltransferase DRM2 (DOMAINS REARRANGED METHYLTRANSFERASE 2) to transposon loci. Alternatively, I will elucidate if IDN2 (INVOLVED IN DE NOVO 2) is involved in this process, as it was suggested to bridge small interfering RNA-long non-coding RNA hybrids. Thirdly, I will discover what destines a specific transposon to be a target for silencing mediated by long non-coding RNAs with the aim to reveal locus specific variability in transposon silencing. I will compare transcriptional activity, chromatin status and relative age of the transposon insertions of silenced transposons and related elements that are not targets of long non-coding RNA mediated silencing. This way, my work will gain novel fundamental insights into the contribution of long non-coding RNAs to transposon control and explore locus specificity of silencing.