Chromatin Molecular Complexes - Jiří Fajkus

PhD Topics

1. SMC complexes dynamics

Supervisor: doc. Mgr. Jan Paleček, Dr. rer. nat.

Annotation

The SMC (Structure Maintenance of Chromosome) complexes are the key components of higher-order chromatin fibers and play important roles in genome stability. Three SMC complexes are present in most eukaryotic cells: cohesin (SMC1/3), condensin (SMC2/4) and SMC5/6 complex. Cohesin can make internal loops or embrace two sister chromatids (feature essential for proper chromosome segregation); condensin interconnects loops to condense chromatin during mitosis. The SMC5/6 complex is involved in the homologous recombination-based DNA repair, in replication fork stability and processing, and in cohesin regulation. In our lab, we study assembly and functions of SMC5/6 complexes (http://www.ncbr.muni.cz/SPEC/). New student will use combination of genetic (fission yeast model), biochemical (mostly yeast two-hybrid system and other binding assays) and bioinformatics methods to get deep insights into SMC5/6 features.

Keywords: Structure Maintenance of Chromosome, SMC complexes, SMC5/6; genome stability, chromatin fibers

2. Structure, function and evolution of plant telomere components

Supervisor: prof. RNDr. Jiří Fajkus, CSc.

Annotation

Telomeres are terminal, but nevertheless integral parts of chromosomes, and as such they are also formed and function as supramolecular nucleoprotein (chromatin) structures. Their DNA component is usually formed by repetitive DNA whose incomplete end-replication by the conventional replication machinery can be compensated by elongation via a specific ribonucleoprotein complex with RNA-dependent DNA polymerase activity – the telomerase. Besides preventing the replicative shortening, telomeres also protect chromosome ends from being mistaken for unrepaired chromosome breaks. For the latter function, protein components of telomeres are responsible. Our group has described evolutionary changes in plant telomere DNA repeats and some protein components of plant telomeres in typical telomeres in the model system of Arabidopsis thaliana. It will be important to follow-up these studies with description of further protein components of telomeres together with testing their functional importance for telomere maintenance and chromosome stability. In addition, the impact of the evolutionary change in telomere DNA sequence on its protein interactors will be examined. Background in molecular biology, biochemistry and bioinformatics will be an asset for selection of a suitable candidate. Literature: Fajkus, P., Peska, V., Sitova, Z., Fulneckova, J., Dvorackova, M., Gogela, R., Sykorova, E., Hapala, J. and Fajkus, J. (2016) Allium telomeres unmasked: the unusual telomeric sequence (CTCGGTTATGGG)n is synthesized by telomerase. Plant J, 85, 337-347. Prochazkova Schrumpfova, P., Schorova, S. and Fajkus, J. (2016) Telomere- and Telomerase-Associated Proteins and Their Functions in the Plant Cell. Front Plant Sci, 7, 851. Schrumpfova, P.P., Vychodilova, I., Dvorackova, M., Majerska, J., Dokladal, L., Schorova, S. and Fajkus, J. (2014) Telomere repeat binding proteins are functional components of Arabidopsis telomeres and interact with telomerase. Plant J, 77, 770-781.

Keywords: plant telomere DNA repeats, telomere maintenance, telomerase

3. The role of cytokinins in determination of organ identity.

Supervisor: Mgr. Markéta Pernisová, Ph.D.
Consultants: prof. RNDr. Jiří Fajkus, CSc., Helene Robert Boisivon, Ph.D.

Annotation

Plants, in comparison to animals, are unique in a developmental plasticity that allows their adaptation to changing environmental conditions. Plants undergo postembryonic de novo organogenesis and can continually regenerate organs. This ability is a critically important developmental adaptation in plants. The phytohormones auxin and cytokinin are thought to be major regulators of plant organogenesis. Auxin is necessary to induce de novo organ development, while cytokinins modulate the organogenic response resulting in root or shoot formation. Although the function of several members of cytokinin signalling pathway has already been described, their role in the determination of organ identity is still elusive. The goal of the project will be i) to analyse cytokinin effect in de novo organogenesis and ii) to identify and analyse regulatory factors important for that process. We expect: creativity, self-reliance, willingness to learn new approaches. We offer: experimental work on the project, excellent lab equipment, high-end confocal microscopes, help with both intellectual and practical issues, friendly lab staff, attractive environment of university campus, competitive salary corresponding to the work efficiency.

Keywords: cytokinin signalling, plant organogenesis, organ identity