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Šimková Group

     Our research focuses on the study of the complex genomes of cereal crops, particularly barley, with the main aim of elucidating the relationship between chromatin organization and gene expression.  Through our expertise in optical mapping, we have contributed to generating quality reference genomes for several cereal species, which has laid the foundation for advanced genomic, transcriptomic and epigenomic studies. Currently, we are mainly interested in cis elements controlling gene transcription – promoters, enhancers and silencers – and in their interplay with transcription factors. We identify and study these elements by combining epigenome and transcriptome profiling with analysis of evolutionary sequence conservation. Furthermore, we have applied the chromatin-conformation-capture technique Hi-C to study functional chromatin interactions and to address the dynamics of chromatin packaging during the cell cycle in barley. We have created an interactive database and browser, BarleyEpiBase, to make the generated datasets accessible to the research community. Now we proceed to validate the predicted cis-regulatory elements using a luciferase reporter assay and CRISPR-based editing. Confirmed elements that affect agronomically important traits can serve as favourable targets for molecular breeding of cereal crops.
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Vacancies

Functional analyses of transcription regulators in barley genome
Intended for master's students starting their studies in 2025 (click for more information)

Group members

Leader
Hana Šimková Ph.D.
Postdoc
Helena Toegelová Ph.D.
Postdoc
Zuzana Tulpová Ph.D.
Ph.D. student
Šimon Pavlů Msc.
Ph.D. student
Ondřej Kopecký Msc.

Former members

Pavla Navrátilová Ph.D.
Veronika Kapustová Msc.
Tomáš Beseda Msc.

Projects

Genome-wide mapping of cis-regulatory elements controlling transcription . . .
Leader
Hana Šimková Ph.D.
Gene transcription is controlled by interplay of transcription factors and non-coding cis-regulatory elements (CREs) - promoters, enhancers and silencers. Since association mapping in maize indicated connection of putative CREs with expression QTLs for important traits, localization of these elements and linking them to their target genes become a vital background for crop breeding and bioengineering. In the project, we aim to precisely delimit and . . .
Dynamics and evolution of multigene ribosomal RNA loci in Triticeae
Leader
Hana Šimková Ph.D
Ribosomal RNA gene loci (rDNA) have been among extensively studied components of eukaryotic genomes. They were shown to be associated with nucleolus, the largest functional domain of the nucleus and the site of ribosomal biogenesis.  Despite the biological importance, detailed information on molecular organization of rDNA regions is missing, especially in plants. This is mainly due to structure of rDNA loci, which are organized as long arrays of . . .
MITOCHROM: Three-dimensional organization of nuclear chromatin in plants . . .
Leader
Prof. Jaroslav Doležel
Recent methodological advances provided novel insights into the spatial genome organization in mammalian cell nuclei and its functional role. This progress contrasts with the limited knowledge on higher order chromatin folding in mitotic chromosomes. Our preliminary data on chromatin contact frequency at megabase resolution obtained in barley mitotic chromosomes suggest remarkable differences in mitotic chromosome organization between . . .

Publications