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Chromatin Molecular Complexes

Prof. RNDr. Jiří Fajkus, CSc.
Research Group Leader

THEMATIC RESEARCH FOCUS

RESEARCH AREAS

Structure, evolution and maintenance of telomeres and their role in chromosome stability and plant speciation; this includes characterisation of nucleoprotein composition of telomeres and telomerases, biophysical analysis of interactions between telomere components by quantitative methods, analysis of structure-function relationships of telomerase subdomains and analysis of alternative (telomeraseindependent) strategies of telomere maintenance
Epigenetic mechanisms in the regulation of gene expression, chromosome stability and telomere maintenance
Structure, evolution and function of SMC complexes; characterisation of SMC5-6 complex subunits and MAGE proteins in vitro and in vivo; their role in DNA repair and chromosome dynamics

MAIN OBJECTIVES

Structure, evolution and maintenance of telomeres and their role in chromosome stability and plant speciation. Epigenetic regulations.

CONTENT OF RESEARCH

Chromatin is the supramolecular complex of DNA, proteins and other associated molecules (e.g. RNA species). It is the building material of chromosomes, which can be observed during cell division in their most condensed state. Chromatin was first discovered in plant cells – as were cells themselves, or genes.

While the nucleotide sequence of the DNA component of chromatin constitutes the genetic material of the cell, the other chromatin components (and also modifications of bases in DNA itself) participate in so-called epigenetic functions. These include spatiotemporal regulation of gene activity and DNA replication, correct and precise segregation of genetic material to daughter cells, maintenance of chromosome stability, protection of genetic material from damage. Last but not least, chromatin structure compacts several metres of genomic DNA to fit the single cell nucleus of only several microns in diameter, while remaining functional despite the high degree (105-106) of compaction.

Our research group addresses the following topics in current chromatin and epigenetic research:

The structure, evolution and maintenance of telomeres (terminal parts of linear chromosomes) and their role in chromosome stability and plant speciation. This includes characterisation of nucleoprotein composition of telomeres and telomerases (ribonucleoprotein enzymes performing telomere elongation), biophysical analysis of interactions between telomere components in vivo and in vitro, including quantitative methods, analysis of structure-function relationships of telomerase subdomains and analysis of alternative (telomerase-independent) strategies of telomere maintenance. We are also interested in the roles of telomeres and their components in DNA damage signalling and DNA repair.
Epigenetic mechanisms involved in the regulation of gene expression, chromosome stability and telomere main tenance. This includes analysis of epigenetic marks (e.g. DNA methylation, covalent modifications of histones, variant histones, nucleosome positioning and dynamics). Experimental analysis of nucleosome positioning is supported by computer predictions based on DNA deformability sequence pattern recently derived by the group of E. N. Trifonov. This pattern represents the cracking of the so-called chromatin code, which has been searched for since 1980.
Structure, evolution and function of SMC 5-6 and SMC-like complexes (Structure Maintenance of Chromatin). Characterisation of SMC5-6 complex subunits, and MAGE (melanoma antigen) proteins in vitro and in vivo. Association of SMC complex subunits and MAGE proteins with specific chromatin domains (e.g. telomeres, centromeres, rDNA loci). Roles of SMC and MAGE proteins in DNA repair, transcription and chromosome dynamics.

KEY RESEARCH EQUIPMENT

PLANNED RESEARCH INFRASTRUCTURE

Technology Units

Molecular biology, genomics and proteomics of plants
Plant Cytogenomics

CURRENT RESEARCH INFRASTRUCTURE

The current research infrastructure includes fluorescence microscopy, centrifugation and ultracentrifugation, preparative and analytical chromatography, electrophoresis, in situ and Southern hybridisation, phosphofluoroimaging, real-time PCR and a documentation system for chemiluminiscence and fluorescence.

MAIN PROJECTS

Characterisation of MAGE proteins: cofactors of E3-ubiquitin ligases? (IAA501630902), Academy of Sciences of the Czech Republic, 2009-2011, J. Paleček, Masaryk University.
Telomeres and telomerase: transition from molecular to structural biology approach (IAA500040801), Academy of Sciences of the Czech Republic, 2008-2012, E. Sýkorová, Institute of Biophysics AS CR, J. Fajkus, Masaryk University.
Epigenetic mechanisms of plant telomeres regulation (GAP501/11/0569), Czech Science Foundation, 2011-2014, M. Fojtová, Masaryk University.
Loss of specific DNA repeats in response to dysfunction of CAF1 in plants (GAP501/11/0289), Czech Science Foundation, 2011-2015, J. Fajkus, Masaryk University.
Molecular basis of cell and tissue regulations (MSM0021622415), Ministry of Education, Youth and Sports, 2005-2011, J. Fajkus, Masaryk University.

SELECTED PUBLICATIONS

MOZGOVA, I., MOKROS, P., FAJKUS, J. Dysfunction of Chromatin Assembly Factor 1 Induces Shortening of Telomeres and Loss of 45S rDNA in Arabidopsis thaliana. Plant Cell. 2010, 22(8), p. 2768-2780.
FOJTOVA, M., et al. Telomere maintenance in liquid crystalline chromosomes of dinoflagellates. Chromosoma. 2010, 119(5), p. 485- 493.
DVORACKOVA, M., et al. AtTRB1, a telomeric DNA-binding protein from Arabidopsis, is concentrated in the nucleolus and show highly dynamic association with chromatin. Plant Journal. 2010, 61(4), p. 637-649.
HOFR, C., et al. Single-Myb-histone proteins from Arabidopsis thaliana: a quantitative study of telomere-binding specifi city and kinetics. Biochemical Journal. 2009, 419, p. 221-228.
RUCKOVA, E., et al. Role of alternative telomere lengthening unmasked in telomerase knock-out mutant plants. Plant Molecular Biology. 2008, 66(6), p. 637-646.

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