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.
News
  • 2021-01-15: Did you know about the healing potential of carnivorous plants. Collaboration with the colleagues from Krakow and Gdańsk (Full text)
  • 2020-12-10: Anna receives a prize from the director of CRH for excellent publication in the Plant Journal about the effects of cytidine analogs (Full text)
  • 2020-12-02: We were awarded the standard grant from the Czech Science Foundation to study gene imprinting and hybridization barriers in barley. Thank you GAČR!
  • 2020-10-26: Martin’s fine protocol on the preparation of minute tissues from barley seeds is published. Big congratulations! (Full text)
  • 2020-10-14: Collaborative publication on the identification of genes encoding PCR1 and PRC complexes in hexaploid bread wheat. Nice work. (Full text)
  • 2020-10-01: Amazing work of Anna on the „Dynamics of endoreduplication in developing barley seeds“ including new parameter „Super-cycle value“ for quantification of endoreduplication is now online (Full text).
  • 2020-08-17: The review paper „Chromatin dynamics during interphase and cell division: similarities and differences between model and crop plants“ is published in the Journal of Experimental Botany (Full text). A great collaborative effort of COST Action INDEPTH.
  • 2020-04-20: Double life of cytidine analogs – from DNA demethylating to DNA damage agents. See more in our recent paper (Full text)
  • 2020-03-23: Congratulations to Eva for her new paper on TPX-LIKE functions in Arabidopsis (Full text)
  • 2020-03-17: Klára agreed to share some institute/group impressions from her private analog photo diary. Enjoy! (link)

Projects

Publications