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.
  • 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!
  • 2023-09-13: Last couple of days we met old friends and enjoyed new results at the plant Chromosome Biology meeting in Brno. Anna received the best poster prize for studzing Rabl organization in barley. Congratulations!
  • 2023-07-23: New collaborative paper shedding light on the functions of plant NSE6 led by Palecek lab (Full text).
  • 2023-08-21: Ramakrishna Yadala from Inna Lermontova lab (IPK) starts a short-term scientific mission funded by COST action Epi-Catch in our group. Good luck with the experiments.
  • 2023-08-21: Katarzyna Szewczyk from Poznań University of Life Sciences joins our group for her Erasmus internship. Welcome to Olomouc.
  • 2023-06-23: Katka's paper was selected for Research Highlight in the Plant Journal (Full text) and for the issue cover. Wow, congratulations!
  • 2023-06-16: Mitosis in barley visualized for the first time live in Katka's Plant Journal paper (Full text). 
  • 2023-05-04: Klara won a silver medal from the Dean of the Faculty of Natural Sciences of Palacky University. Congratulations.
  • 2023-04-19: Wonderful group field trip with a treasure hunt and pizza. It was fun for everyone.