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.
  • 2024-06-03: We are happy to welcome our new Erasmus Plus student, Nikša Bekavac, from University of Zagreb, Croatia.
  • 2024-06-02: Eva's paper on another part of DNA-protein crosslink repair story is out in The Plant Journal. Congratulations! (Full text)
  • 2024-05-20: It is our great pleasure to welcome our new guest, Magdalena Wójcik-Jagła, from the group of Marcin Rapacz at the Agricultural University of Krakow. She will focus on the bioinformatic analysis of cold acclimation and deacclimation during her two-month stay.
  • 2024-05-15: The number of PhD students in our group has decreased to zero! Congratulations to Dr. Jovanka Vladejic and Dr. Martin Kovačik!
  • 2024-05-03: We enjoyed a wonderful team-building event full of beautiful nature, orchids, birds, beer, and amazing pizza. Thank you, Aleš!
  • 2024-05-02: Great success in the Student Scientific Competition for the Dean's Prize! Congratulations to Katka for her 3rd place and to Martin for his 1st place and being the absolute winner of the Bio & Eco category.
  • 2024-04-24: Young scientists from the entire institute enjoyed the very first IEB Young Researcher Retreat. The whole organizing team did a great job!
  • 2024-04-18: Martin's paper exploring the complexity of barley grain growth is now published in The Plant Cell. Congratulations! (Full text)
  • 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.