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Regulation of alternative splicing via chromatin modifications
Hozeifi, Samira ; Staněk, David (advisor) ; Krásný, Libor (referee) ; Lanctôt, Christian (referee)
Alternative splicing (AS) is involved in expansion of transcriptome and proteome during cell growth, cell death, pluripotency, cell differentiation and development. There is increasing evidence to suggest that splicing decisions are made when the nascent RNA is still associated with chromatin. Here, I studied regulation of AS via chromatin modification with main focus on histone acetylation. First, we demonstrate that activity of histone deacetylases (HDACs) influences splice site selection in 700 genes. We provided evidence that HDAC inhibition induces histone H4 acetylation and increases RNA Polymerase II (RNA Pol II) processivity along an alternatively spliced element. In addition, HDAC inhibition reduces co-transcriptional association of the splicing regulator SRp40 with the target fibronectin exon. Further we showed that histone acetylation reader, Brd2 protein, affect transcription of 1450 genes. Besides, almost 290 genes change their AS pattern upon Brd2 depletion. We study distribution of Brd2 along the target and control genes and find that Brd2 is specifically localized at promoters of target genes only. Surprisingly, Brd2 interaction with chromatin cannot be explained solely by histone acetylation, which suggests that other protein-domains (in addition to bromodomains) are important for...
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Differentiation within yeast populations of Saccharomyces cerevisiae: influence of cultivation conditions
Šimek, Jan ; Palková, Zdena (advisor) ; Dostál, Jiří (referee)
Long-time research of chronologically aging yeast populations of Saccharomyces cerevisiae laboratory strains revealed that yeasts are able to differentiate into specialized cell types. Differentiation of liquid cultures growing in glucose rich medium and differentiation of colonies growing on solid glycerol medium has been previously studied. These populations create two fractions of cells with diverse morphology which adapt their metabolism and physiology to enable a long-term survival of the yeast population in environment with limited nutritional potential. In this study, yeast subpopulations isolated from colonies growing on solid glucose medium and liquid cultures cultivated in glycerol medium were characterized. Newly isolated cell types were compared with already known cell types isolated from colonies and liquid cultures. Selected metabolic processes and stress resistance were analysed in studied populations. Based on previous studies of yeast differentiation, a spectrum of GFP-labelled marker proteins was choosen and production and localization of these marker proteins was monitored within yeast populations. Results of the analyses showed that type of medium and cultivation influence development and metabolism of each yeast cell type. Key words: Saccharomyces cerevisiae, BY4742, cell...
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