Chromatin Molecular Complexes - Jiří Fajkus

PhD Topics

1. Complexes Maintaining Chromatin Structure

Supervisor: assoc. prof. Jan Paleček

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. However, there is not much information about its looping activity and molecular insights into these functions. In our lab, we study assembly and functions of the SMC5/6 complexes (http://www.ncbr.muni.cz/SPEC/). New student will use combination of genetic (fission yeast model), biochemical, proteomic and bioinformatic approaches to see how the enigmatic SMC5/6 complexes work.

Recommended literature:

Palecek, J.J. and Gruber S.: Kite Proteins: a Superfamily of SMC/Kleisin Partners Conserved Across Bacteria, Archaea, and Eukaryotes, Structure 23(12): 2183-90, doi: 10.1016/j.str.2015.10.004, 2015

Zabrady et al: Chromatin association of the SMC5/6 complex is dependent on binding of its NSE3 subunit to DNA. Nucleic Acids Research, 44(3), 1064-79, doi:10.1093/nar/gkv1021, 2016

Palecek, J.J. : SMC5/6: Multifunctional Player in Replication, Genes, 10(1): 14, pii: E7. doi: 10.3390/genes10010007, 2019

Adamus et al,: Molecular insights into the architecture of the human SMC5/6 complex. Journal of Molecular Biology, 432 (13): 3820-3837, doi: 10.1016/j.jmb.2020.04.024, 2020

Keywords: Chromatin structure, genome stability, SMC complexes

 

2. Plant telomeres and telomerases

Supervisor: prof. Jiří Fajkus

Annotation:

The origin of linear chromosomes associated with divergence of eukaryotes led to the evolution of mechanisms counteracting the incomplete replication of chromosome ends––the telomeres. The most common mechanism to overcome the end-replication problem involves a ribonucleoprotein complex enzyme––telomerase. Telomerase elongates the 3_-end of telomeric DNA using the catalytic activity of its core protein subunit––telomerase reverse transcriptase (TERT) - which can repeatedly add a short DNA stretch to telomeric DNA. The sequence added by telomerase is directed by a template region in telomerase RNA (TR), the other core telomerase subunit. In addition to these two core subunits, the complex of telomerase involves several other associated proteins which affect various steps of telomerase function in vivo, as, e.g. telomerase assembly, trafficking, localisation, processivity, or its recruitment to telomeres. Importantly, TR functions not only as the telomerase templating subunit but also as a scaffold to assemble the entire functional telomerase complex. Recently we identified genuine TRs across land plants (Fajkus et al., 2019). This opened a possibility to investigate plant telomere and telomerase structure, function and evolution and elucidate the principle of its reversible regulation in plants, contrary to its permanent developmental silencing is humans. 

Recommended literature:

Fajkus P., Peška V. et al.: Telomerase RNAs in land plants. Nucleic Acids Res. 47:18, 9842–9856 (2019).

Procházková Schrumpfová, P.; Fojtová, M.; Fajkus, J. Telomeres in Plants and Humans: Not So Different, Not So Similar. Cells 2019, 8, 58.

Keywords: Telomeres, telomerase, RNA-protein interactions, bioinformatics, evolution

 

3. Proteins involved in the regulation of telomeric repeats

Supervisor: Petra Prochazkova Schrumpfova, Ph.D.

Annotation:

Telomeres are the physical ends of linear chromosomes that protect these ends against erroneous recognition as unrepaired chromosomal breaks and regulate the access to telomerase, a reverse transcriptase that solves the problem terminal DNA loss in each cell cycle. Telomeric structures are known to be composed of short repetitive DNA sequences (telomeric repeats), histone octamers, and number of proteins that bind telomeric DNA, either directly or indirectly, and together, form the protein telomere cap.

Interestingly, telomeric repeats are not exclusively located at the chromosome ends, but they belong among cis-regulatory elements present in promoters of several genes. The distribution of short telomeric repeats (telo-boxes) within the genome is not random, and proteins associated with these telomeric motifs may serve as the epigenetic regulatory mechanisms facilitating metastable changes in gene activity.

The telomeric cap proteins of diverse organisms are less conserved than one might expect. In plants, knowledge of telomere-associated proteins associated with telomeres and regulation of access to telomerase complex is incomplete. The research aims to elucidate the roles of candidate proteins involved in telomerase biogenesis in plants. The outcomes contribute to the characterization of new telomere- or telomerase-associated proteins, complete our knowledge of telomerase assembly or telomere maintenance in plants. In addition, we would like to examine the regulatory factors associated with the telo-boxes present in promoters of the genes active during plant development.

Recommended literature:

Petra Procházková Schrumpfová and Jirí Fajkus Composition and Function of Telomerase—A Polymerase Associated with the Origin of Eukaryotes. Biomolecules 2020, 10, 1425; doi:10.3390/biom10101425

Fajkus, P.; Peška, V.; Závodník, M.; Fojtová, M.; Fulnečková, J.; Dobias, Š.; Kilar, A.; Dvořáčková, M.; Zachová, D.; Nečasová, I.;  Sims, J.; Sýkorová E. and Fajkus J. Telomerase RNAs in land plants. Nucleic Acids Res. 2019, 47, 9842–9856, doi:10.1093/nar/gkz695.

Schořová, Š.; Fajkus, J.; Záveská Drábková, L.; Honys, D.; Procházková Schrumpfová, P. The plant Pontin and Reptin homologues, RuvBL1 and RuvBL2a, colocalize with TERT and TRB proteins in vivo, and participate in telomerase biogenesis. Plant J. 2019, 98, 195–212, doi:10.1111/tpj.14306.

Procházková Schrumpfová, P.; Fojtová, M.; Fajkus, J. Telomeres in Plants and Humans: Not So Different, Not So Similar. Cells 2019, 8, 58, doi:10.3390/cells8010058.

Procházková Schrumpfová, P.; Schořová, Š.; Fajkus, J. Telomere- and Telomerase-Associated Proteins and Their Functions in the Plant Cell. Front. Plant Sci. 2016, 7, doi:10.3389/fpls.2016.00851.

Keywords: telomerase; telomeres; proteins; telo-box; regulatory elements; telomerase assembly; plant development