Šimková Group

     The major aim of our group is to dissect complex genomes of small grain cereals at both structural and functional level. Our approaches frequently exploit our lab’s unique pipeline for chromosome and nuclei flow sorting and a well-established technique of optical mapping. Capitalising on these technologies, we aided in generating reference genomes of several crop species, contributed to cloning a Russian wheat aphid resistance gene and revealed the fine structure and dynamic transcription of ribosomal DNA loci in bread wheat and barley. Besides, we adopted the chromatin-conformation-capture technique Hi-C to study chromatin packaging during the cell cycle and, complemented by a variety of epigenetic techniques, to map cis-regulatory elements controlling transcription during barley development.


Ph.D. position

Cis-regulatory elements controlling transcription during barley development

Gene transcription is controlled by an interplay of transcription factors and non-coding genomic regions located in the vicinity of genes - promoters, enhancers and silencers - collectively termed cis-regulatory elements (CREs). The emergence of these regulators dates to the origins of multicellularity. They have been mapped and characterized in many animal genomes but their knowledge in plants is rather limited. Association mapping in several crops indicated the connection of putative CREs with important agronomical traits, thus localization of these elements and linking them to their target genes appears as a vital background for crop breeding and bioengineering.
In our new GAČR-funded project, we aim to identify and characterize promoter and putative enhancer regions in barley by combining data obtained by transcriptomic, epigenomic and chromatin-conformation-capture-based techniques. The predicted CREs and generated chromatin state and interactome maps of several barley tissues improve functional annotation of the barley genome and shed light on processes controlling embryo development and tissue differentiation in cereals. The major role of the PhD student will lie in the data processing part of the project, including bioinformatic evaluation and integration of generated datasets and graphical visualization of the results. Therefore, background in bioinformatics and/or (bio)statistics is highly beneficial for this position.

For more information, contact Hana Šimková at simkovah%at%ueb.cas.cz.