Pecinka Lab:Research

Centre of Plant Structural and Functional Genomics Institute of Experimental Botany of the Czech Academy of Sciences, v. v. i. Šlechtitelů 31 Olomouc, CZ-783 71 Czech Republic Contact

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Genome and epigenome maintenance Deoxyribonucleic acid (DNA) is the main genetic information storage molecule of all organisms and therefore it needs to be protected from sequence changes. This is ensured by genome maintenance mechanisms - proofreading activity of DNA polymerases, DNA repair and control of repetitive DNA sequences by epigenetic means. Defective or incomplete function of these mechanisms may result in rapid accumulation of mutations, chromosomal breakage or rearrangements, reduced fitness and development of diseases. Figure 1 xxxxxxx Prior Work xxxxxx Figure 2 xxxxxxx Figure 3 Figure 4 xxxxxxxx Current Projects Natural variation in the DNA repair mechanisms We are interested to identify genes or natural alleles that confer an altered DNA repair capacity and are involved in fine-tuning of the DNA repair machinery under natural conditions. Currently, two QTL mapping projects are running in the lab focusing on responses on A. thaliana to UV-B light and DNA replication blocking agent hydroxyurea. An effective source of DNA damage in nature is UV light. To reduce other than DNA damage effects, we use UV-C radiation that is the most potent inducer of pyrimidine dimers - a specific type of crosslinks between two pyrimidine bases (C and T). Pyrimidine dimers cause a physical barrier for transcription and replication and therefore need to be repaired. This is facilitated by Arabidopsis photolyases UVR2 (PHR1) and UVR3. However, it is not clear how the whole machinery is regulated under natural latitudinal and altitudinal light intensity (including UV) gradients. To address this, we use different Arabidopsis natural accessions and screen for their relative survival after high dose of UV-C (Figure 1A). Analysis of approximately 100 accessions revealed great differences ranging from full resistance to full sensitivity (Figure 1B). Figure 5 xxxxxx Expression Profiling and eQTL mapping xxxxx QTL cloning xxxxxxx Functional molecular evolution xxxxxxxx Bibliography Atwell, s., Huang, Y.S., Vilhjalmsson, B.J., Willems, G. et al. (2010): Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465:627-631. Kakutani, T., Jedelloh, J.A., Flower, S.K., Munakata, K. and Richards, E.J. (1996): Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proceedings of the National Academy of Sciences USA 93:12406-12411. Mandakova, T., Joly, S., Krzywinski, M., Mummenhoff, K. and Lysak, M.A. (2010): Fast Diploidization in Close Mesopolyploid Relatives of Arabidopsis. Plant Cell 22:2277-2290. Mathieu, O., Reinders, J., Čaikovski, M., Smathajitt, C. and Paszkowski, J. (2007): Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation. Cell 130:851-862. Steimer, A., Amedeo, P., Afsar, K., Fransz, P., Mittelsten Scheid, O. and Paszkowski, J. (2000): Endogenous Targets of Transcriptional Gene Silencing in Arabidopsis. Plant Cell 12:1165–1178. The Arabidopsis Genome Initiative (2000): Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815.