Chromatin organization and function

Pecinka 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.
  • 2024-04-01: After a succesfull defense, Serhii Mykhailyk became a member of our group. Congratulations, Serhii.
  • 2024-03-18: We are happy to welcome our new Erasmus student, Metka Rus, from Slovenia. Good luck in your work, Metka.
  • 2024-02-14: We celebrated Katka's success with a group trip to the Earth caves of Sloup-Sosůvka.
  • 2024-02-13: Welcome our new doctor! Katka just got her PhD. Congratulations!
  • 2024-02-07: Jovanka's paper has been published! Check out the DNA damage response in barley here! (Full text)
  • 2024-01-16: The team-building activity in the laser game arena was really nice. There were good shots during the game, followed by one shot after the game and a good burger in the pub. It was a great evening!
  • 2024-01-08: We welcome Serhii Mykhailyk, who came to us for an internship as part of the COST action EPICATCH.
  • 2023-12-14: We really enjoyed a nicely prepared Christmas party full of games and fun. Thanks to the organizers!
  • 2023-12-14: Katka's paper about holder for live-cell confocal microscopy is now published. Congratulations! (Full text)
  • 2023-11-28: We participated in the selling of mulled vine at the Christmas market in Olomouc. Raised money will go to support kids with special needs.
  • 2023-10-12: We spent a nice time with other coleagues from our institute on a beautiful trip full of puzzles and games. Thanks to all organizers!
  • 2023-09-27: Eva presented our work about the importance of SUMOylation in the repair of DNA-protein crosslinks in Arabidopsis on EMBO Workshop in Portugal. Good job!