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. Investigating the Role of Short Regulatory Elements in Plant Sexual Reproduction
Supervisor: Mgr. Petra Procházková Schrumpfová, Ph.D.
Annotation:
Plant sexual reproduction is a complex and coordinated developmental process, crucial especially for agricultural production. The PhD project will investigate the role of short cis-regulatory elements (CREs) within promoter regions, and their associated proteins, in the regulation of plant gametophyte development. Specifically, we will investigate the distribution and epigenetic changes of the motif telo-box, whose sequence is identical to the (TTTAGGG)n repeat previously identified in plant telomeres (physical ends of linear chromosomes). Telo-box belongs among CREs with a non-random distribution within the genome or even promoters. This research will shed light on the role of telo-boxes and other associated CREs in gene regulation during male gametophyte development and their involvement in epigenetic control in plants. Our research will provide insights into the evolution of these CREs not only in model plants, as in most primitive land plants (Bryophytes) and seed plants like Arabidopsis, but also in crop plants.
We are looking for highly motivated graduates to join the Laboratory of Functional Genomics and Proteomics (FGP). The laboratory is well-equipped with instrumentation for molecular biology and biochemistry. The research group will benefit from close collaboration with internal or international partnerships (EMBL Heidelberg, GE; ITQB, Lisabon, PT).
Recommended literature:
Lukáš Nevosád, Božena Klodová, David Honys, Radka Svobodová, Tomáš Raček, Petra Procházková Schrumpfová (2023) GOLEM: distribution of Gene regulatOry eLEMents within the plant promoters, arXiv Cornell university, doi: 2310.15206
Alžbeta Kusová, Lenka Steinbachová, Tereza Přerovská, Lenka Záveská Drábková, Jan Paleček, Ahamed Khan, Gabriela Rigóová, Zuzana Gadiou, Claire Jourdain, Tino Stricker, Daniel Schubert, David Honys, and Petra Procházková Schrumpfová (2023). Completing the TRB family: newly characterized members show ancient evolutionary origins and distinct localization, yet similar interactions. Plant Mol. Biol. 112, 61–83. doi: 10.1007/s11103-023-01348-2
Eva Dvořák Tomaštíková, Fen Yang, Kristína Mlynárová, Said Hafidh, Šárka Schořová, Alžbeta Kusová, Markéta Pernisová, Tereza Přerovská, Božena Klodová, David Honys, Jiří Fajkus, Ales Pecinka, Petra Procházková Schrumpfová (2023) RUVBL proteins are involved in plant gametophyte development. The Plant Journal. 144, 2. doi.org/10.1111/tpj.16136
Božena Klodová, David Potěšil, Lenka Steinbachová, Christos Michailidis, Ann-Cathrin Lindner, Dieter Hackenberg, Jörg D. Becker, Zbyněk Zdráhal, David Twell, and David Honys. (2023) Regulatory dynamics of gene expression in the developing male gametophyte of Arabidopsis. Plant reproduction. 36(3): 213–241. doi: 10.1007/s00497-022-00452-5
Keywords:
gene regulatory sequences, transcriptional regulation, gametophyte development, genomics, proteomics,
plants
