The interplay between chromatin labelling and transcription is crucial for precise regulation of gene expression. In our previous studies, we proved that tobacco BY-2 cell line, in spite of its artificial character, represent a suitable model to study de novo establishment of chromatin marks, namely DNA methylation. In plant cells, DNA methylation is triggered by small RNAs complementary to the target locus. These small RNAs can efficiently induce gene silencing at either transcriptional or posttranscriptional level. The tobacco BY-2 cell lines respond to the inducible production of small RNAs homogeneously and synchronously, which allows a detailed study of the dynamics of epigenetic processes, which is not possible at the whole plant level. The PhD project will be focused on the interplay between DNA methylation and histone marks, the stability/reversibility of the chromatin marks, the transition of posttranscriptional to transcriptional silencing and the role of selected factors in the dynamics of chromatin labelling (allowed by production of CRISPR/Cas9 mutated lines recently established in the laboratory). We offer an up-to-date topic that includes modern experimental approaches such as generation of genetically modified lines, chromatin-immunoprecipitation or sRNA transcriptome analyses. We expect applications from highly motivated students capable of independent work.

Five relevant publications of the research group: 

Čermák V, Tyč D, Přibylová A, Fischer L (2020) Unexpected variations in posttranscriptional silencing induced by differentially produced dsRNAs in tobacco cells. BBA – Gene Regulatory Mechanisms 1863(11):194647.

Přibylová A, Čermák V, Tyč D, Fischer L (2019) Detailed insight into the dynamics of the initial phases of de novo RNA-directed DNA methylation in plant cells. Epigenetics & Chromatin 12: 54

Čermák V; Fischer, L (2018) Pervasive read-through transcription of T-DNAs is frequent in tobacco BY-2 cells and can effectively induce silencing. BMC Plant biology 18: 252

Tyč D, Nocarová E, Sikorová L, Fischer L (2017) 5-Azacytidine mediated reactivation of silenced transgenes in potato (Solanum tuberosum) at the whole plant level. Plant Cell Reports 36: 1311-1322

Nocarová E, Fischer L (2009) Cloning of transgenic tobacco BY-2 cells; an efficient method to analyze and reduce high natural heterogeneity of transgene expression. BMC Plant Biology 9:44.

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