Epigenetic control of repetitive DNA in the genome of Arabidopsis lyrata
Project code: PE 1853/2-2
A large part of eukaryotic genome consists of repetitive DNA. Although repeats are primarily considered as genomic parasites or 'junk' DNA, in specific cases they regulate protein coding genes and constitute centromeres, telomeres and rDNAs. In addition, they contribute to genome rearrangements due to recombination and transposition activity. To preserve the genome, repeats are maintained inactive by transcriptional gene silencing (TGS), an epigenetic control mechanism that brings DNA into transcriptionally inactive and inaccessible heterochromatic state.
The model plant Arabidopsis thaliana and its close relative A. lyrata differ by repetitive DNA element copy numbers (26,990 versus 80,225, respectively) and their genome occupancy (24% versus 30%, respectively; Hu et al., 2011). Recent studies revealed an incomplete silencing of several repeats in A. lyrata, however, the genetic and molecular basis of this remains unknown and makes A. lyrata an attractive model for studies of genome maintenance and epigenetic control (reviewed in de Meaux and Pecinka, 2012). We develop experiments that will help understand the molecular basis of this difference. Via in silico comparative studies of genes involved in TGS we identify potential candidates responsible for the reduced epigenetic control of repetitive DNA in A. lyrata and test these candidates by molecular means. In a complementary approach, we generate genome-wide profiles of specific chromatin modifications which will indicate species specific differences. The control of transposable elements can be attenuated by abiotic stress (Pecinka et al., 2010; Ito et al., 2011). We test whether this factor contributed to the larger number of repetitive elements in the A. lyrata genome.
Publications related to the project
- Pietzenuk B, Markus C, Gaubert H, Bagwan N, Merotto A, Bucher E, Pecinka A. Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements. Genome Biol. 2016 Oct 11;17(1):209.
- Rawat V, Abdelsamad A, Pietzenuk B, Seymour DK, Koenig D, Weigel D, Pecinka A, Schneeberger K. Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data. PLoS One 2015 Sep 18;10(9).
- de Meaux, J. and Pecinka, A. The Arabidopsis genus: An emerging model to elucidate the molecular basis of interspecific differences in transposable element activity. Mobile Genetic Elements 2:142-144 (2012).
- Hu, T.T., Pattyn, P., Bakker, E.G., Cao, J., Cheng, J.F., Clark, R.M. et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics 43:476–481 (2011).
- Ito, H., Gaubert, H., Bucher, E., Mirouze, M., Vaillant, I. and Paszkowski, J. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 472: 115-119 (2011).
- Pecinka, A., Dinh, H.Q., Baubec, T., Rosa, M., Lettner, N. and Scheid, O.M. Epigenetic Regulation of Repetitive Elements Is Attenuated by Prolonged Heat Stress in Arabidopsis. Plant Cell 22: 3118-3129 (2010).
