Pečinka Group

A longstanding aim of our group is to understand genome organization and functions in plants. We study how DNA is assembled into chromatin and chromosomes and how do the chromatin factors control plant development, stress resistance and genome stability.
Genetic information is stored in cell nucleus on chromosomes. Eukaryotic chromosomes accommodate genes and large amounts of repetitive sequences, some of which are required for telomere, centromere and nucleolar organizer functions. Number of repeats varies greatly among plant species and , in combination with common polyploidization, is responsible for enormous nuclear genome size variation in plants. Furthermore, ratio of genes and repeats often determines overall 3D organization of chromosomes during interphase. Large genomes, such as our model species barley (Hordeum vulgare, 2n=2x=14, ca. 5 Gbp/1C) shows Rabl organization with polar localization of centromeres and telomeres. In contrast, smaller genomes, including our other main model Arabidopsis thaliana (2n=2x=10, ca. 150 Mbp/1C), do not maintain strict clustering of centromeres and have variable positioning of telomeres. In Arabidopsis, centromeres are attached to the nuclear periphery, while telomeres associate with nucleolus. Although described about century ago, molecular mechanisms determining such organizations and their consequences for e.g. nuclear division, DNA damage repair or homolog search remain unknown. We try understanding large scale plant genome organization during normal and DNA damage situations by focusing on the functions of Structural maintenance of chromosomes 5/6 (SMC5/6) complex. SMC5/6 works as intermolecular DNA linker, which ensures plant genome stability by so far unknown mechanism(s). Arabidopsis SMC5/6 mutants are not only DNA damage hypersensitive, but have many other not well understood phenotypes including sensitivity to DNA methylation inhibitors, defects during reproductive development and hyper-immune responses. Roles of SMC5/6 complex in maintaining genome functions in plants with large and Rabl-organized genomes are unknown.

Chromatin properties are determined epigenetically, i.e. by the DNA-interacting proteins and their modifications as well as the regulatory RNAs. Major chromatin states include heterochromatic, which is condensed, repeat-rich and transcriptionally repressed, while euchromatin is open and contains transcriptionally permissive modifications. Chromatin controls transcription in response to developmental and environmental signals and affect plant stress resistance and yield. Our group studies establishment, maintenance and functions of eu-and heterochromatin in plants during cell division and reproduction. This is of important because many plant products (proteins, sugars, oils, fibers) are obtained from plant reproductive tissues.
  • 2022-04-20: Read our new review on the functions of SMC5/6 complex during plant reproductive development (Full text).
  • 2022-04-05: Fen successfully finished her Ph.D. Big congratulations Dr. Fen Yang!
  • 2022-04-01: Klára starts her 3 month internship at the lab of Stefanie Rosa at the SLU Uppsala. Exciting!
  • 2022-01-11: Cytidine analog zebularine induces DNA-protein crosslinks in Arabidopsis. Read our story how the DNA methylation inhibitor became a DNA damaging agent (Full text). 
  • 2021-12-01: Martin is back from the internship to the lab of Rudiger Simon at CEPLAS/HHU in Dusseldorf (DE) with a great RNA in situ training experience!
  • 2021-10-05: Again Arabidopsis SMC5/6 complex - now unraveling its role in the maintenance of meiosis and gamete formation in tetraploid Arabidopsis (Full text). 
  • 2021-09-25: Arabidopsis SMC5/6 complex mutants produce a large number of unreduced pollen and triploid offspring (Full text). 
  • 2021-09-01: Jovanka returning from her 3-month internship in the groups of Aline Probst and Samuel le Goff at Clérmont-Ferrand University (FR). Welcome home Jovanka!
  • 2021-09-01: Martin leaving for 3-months internship to the lab of Rudiger Simon at CEPLAS/HHU in Dusseldorf (DE). Good luck with the experiments!
  • 2021-08-23: The first plant (barley) chromosome proteome published in collaboration with Šebela lab. Our work points to a perichromosomal protein coat in plants. (Full text)
  • ​2021-08-19: Presentation of our work about chromatin organization in barley endosperm nuclei on INDEPTH Main meeting in Thessaloniki (GR).