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Peak identification from ChIP-nexus data.
Drahoňovská, Lucie ; Převorovský, Martin (advisor) ; Gahurová, Lenka (referee)
Proteins play a very important role in live organisms. Their roles are for example structural, transport, regulatory or catalytic. What genes will be expressed, what proteins will be made and at what rate can have a strong impact on the function or even health of the organism. Gene expression is significantly regulated by transcription factors, whose activity may cause multiple diseases or disorders (Latchman 1997). Studying those factors and their function is therefore very important. Several methods were developed to this cause, ChIP-chip, ChIP-seq, ChIP-exo and ChIP-nexus. They enable us to study the binding sites of transcription factors and other DNA-binding proteins with various degrees of resolution. In this thesis I am going to describe the above mentioned methods and peak callers, softwares used for analysis of data obtained by those methods. I will also attempt to do peak calling of ChIP-nexus data of Cbf11 protein and compare the outcomes.
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Identification of key regulators of gene expression in mammalian oocyte and embryo
Jansová, Denisa ; Šušor, Andrej (advisor) ; Gahurová, Lenka (referee) ; Lin, Chih-Jen Lance (referee)
Mammalian oocyte is a highly differentiated cell which gives rise to an embryo after fertilization. Importantly, fully-grown oocytes become transcriptionally inactive at the end of the growth phase. During following stages of development, i. e. meiotic maturation of the oocyte and early embryonic development, only transcripts previously synthesized and stored are used. The tight correlation between mRNA distribution and subsequent protein localization and function provides a mechanism of spatial and temporal regulation of gene expression used by various cell types. However, not much is known about mRNA localization and translation in the mammalian oocyte and early embryo. The aim of my thesis was to determine the localization of transcripts and components of translational machinery in the mammalian oocyte and embryo and to uncover the mechanisms of spatiotemporal regulation of translation as a prerequisite for correct oocyte and embryo development. We have shown that nuclei of both mouse and human oocytes contain RNA molecules and RNA binding proteins. Following the nuclear envelope breakdown (NEBD), translational hot-spots occur in the area surrounding the nuclear region. We suppose that mRNAs previously retained in the nucleus are released to the cytoplasm during NEBD and their subsequent...
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