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Genome editing using programmable endonucleases
Hanečková, Radmila ; Sedláček, Radislav (advisor) ; Sýkora, Michal (referee)
Programmable endonucleases are engineered proteins that recognize specific nucleotide sequences and that are capable of introducing double-strand breaks within these sequences. Zinc-finger nucleases have been used extensively as a tool in genome editing, the practice of introducing changes into genomes of cell lines or whole organisms as a way to study gene function. Recently, new types of programmable endonucleases have emerged in the form of transcription activator like effector (TALE) nucleases and the CRISPR/Cas system. The types differ in respect to their mechanism of function, accessibility, selectivity, frequency of off-target cleavage and cytotoxic effects. Here, we compare zinc-finger nucleases, TALENs and the CRISPR/Cas system and explore their current and possible future applications in a broad spectrum of research ranging from developing genetically modified organisms to gene therapy. Powered by TCPDF (www.tcpdf.org)
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Generation and Characterization of Glutamate Carboxypeptidase II (GCPII)-Deficient Mice
Vorlová, Barbora ; Šácha, Pavel (advisor) ; Eckschlager, Tomáš (referee) ; Bařinka, Cyril (referee)
Glutamate carboxypeptidase II (GCPII) is a transmembrane glycoprotein, which consists of short intracellular and transmembrane domains, and a large extracellular domain possessing carboxypeptidase activity. In the human body, GCPII fulfils a neuromodulatory function in the brain and facilitates folate absorption in the small intestine. In addition to the brain and small intestine, high level of GCPII is also present in the prostate and kidney. However, GCPII function in these tissues has not been determined yet. To study the role of GCPII in detail, several research groups attempted to inactivate GCPII encoding gene Folh1 in mice. Surprisingly, the experiments led to rather conflicting results ranging from embryonic lethality to generation of viable GCPII-deficient mice without any obvious phenotype. This dissertation project aimed to dissect the discrepancy using alternative strategy for gene modification. For this purpose, we designed TALENs that specifically targeted exon 11 of Folh1 gene and manipulated mouse zygotes of C57BL/6NCrl genetic background. We analysed all genetically modified mice of F0 generation for presence of TALEN-mediated mutations and established 5 different GCPII-mutant mouse colonies from founder mice that altogether carried 2 frame-shift mutations and 3 small in-frame...
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Programmable nucleases in human therapy
Šlaufová, Marta ; Kašpárek, Petr (advisor) ; Černý, Jan (referee)
Most genome disorders cause severe symptoms and are usually incurable. Recent, rapid development of programmable nucleases (PNs) brought new possibilities for the treatment of many diseases, such as genetic disorders, infectious diseases or cancer. PNs are enzymes, which enable site specific DNA cleavage that can lead to targeted modification of desired genomic loci. They are composed of separable non-specific cleavage domain and DNA- binding domain. The DNA binding domain is in the form of modular DNA-binding proteins or complementarity-based pairing of the oligonucleotide. The non-specific cleavage domain mediates DSB stimulation, which is necessary for further genome editing. Development of zinc finger nucleases (ZFNs) followed by transcription activator-like effector nucleases (TALENs) enabled the first therapeutic approaches based on targeted manipulation of human genome. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas technology brought further simplification to the method and broadened the availability of PN-based toolkits. This thesis will provide a summary of the recent developments, application of PNs in the therapy of human patients and potential obstacles preventing their implementation in clinics.
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Generation and analysis of double deficient transgenic mice for kallikrein-related peptidase 5 and kallikrein-related peptidase 14
Hanečková, Radmila ; Sedláček, Radislav (advisor) ; Fulková, Helena (referee)
Kallikrein-related peptidases (KLKs) constitute a highly conserved serine protease family. Based on in vitro experiments, KLKs are predicted to play an important role in a number of physiolog- ical and pathophysiological processes. However, their role in vivo remains not fully understood, partially due to a lack of suitable animal models. In this work, we aim to prepare a KLK5 and KLK14 double-deficient mouse model. Both KLK5 and KLK14 were proposed to be involved in epidermal proteolytic networks critical for maintaining skin homeostasis. However, both KLK5 and KLK14 single-deficient mouse models show minimal or no phenotype, likely due to similar substrate specificity resulting in functional compensation. Double-deficient mice cannot be easily obtained by crossing due to localization of the Klk5 and Klk14 genes within the same locus on chromosome 7. We report that KLK5 and KLK14 double-deficient mice were success- fully generated, mediated by transcription activator-like effector nucleases (TALENs) targeting Klk14 by microinjection of TALEN mRNA into KLK5-deficient zygotes. Furthermore, we show that KLK5 and KLK14 double-deficient mice are viable and fertile. We believe that these novel mouse models may serve as a useful experimental tool to study KLK5 and KLK14 in vivo.
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Function and regulation of ETV4 and MSX1 transcription factors in colon cancer progression
Hrčkulák, Dušan ; Kříž, Vítězslav (advisor) ; Libusová, Lenka (referee)
Colon cancer causes approximately seven percent of all cancer-related deaths in the world and presumably due to modern lifestyle, it is also one of the most frequently diagnosed cancers. The inefficiency of standard treatment indicates the need for intensive research of molecular mechanisms of cancer development. The canonical Wnt signaling pathway is essential for maintenance of the progenitor phenotype of stem cells in crypts of the intestine and controls repopulation of the epithelia, in physiological conditions. However, aberrant activation leads to tumor formation. Although Wnt signaling in cancer has been subjected to thorough investigation, there is still a lot of questions concerning further branching of the pathway. As a model of Wnt/β-catenin triggered colorectal cancer, we use mice with mutated APC, which is the tumor suppressor involved in this pathway. Previous expression profiling of the intestinal tumors from relevant mice revealed two transcription factors: ETV4 and MSX1 which are significantly overexpressed in cancer cells. In this project we elucidate whether the overexpression is really tumor restricted and Wnt dependent or there is a crosstalk with another signal transduction pathway. We investigate the function and regulation of these transcription factors by synthetic reporter assays,...
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Genome editing using programmable endonucleases
Hanečková, Radmila ; Sedláček, Radislav (advisor) ; Sýkora, Michal (referee)
Programmable endonucleases are engineered proteins that recognize specific nucleotide sequences and that are capable of introducing double-strand breaks within these sequences. Zinc-finger nucleases have been used extensively as a tool in genome editing, the practice of introducing changes into genomes of cell lines or whole organisms as a way to study gene function. Recently, new types of programmable endonucleases have emerged in the form of transcription activator like effector (TALE) nucleases and the CRISPR/Cas system. The types differ in respect to their mechanism of function, accessibility, selectivity, frequency of off-target cleavage and cytotoxic effects. Here, we compare zinc-finger nucleases, TALENs and the CRISPR/Cas system and explore their current and possible future applications in a broad spectrum of research ranging from developing genetically modified organisms to gene therapy. Powered by TCPDF (www.tcpdf.org)
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TAL Effectors: Tools for DNA Targeting
Jankele, Radek ; Svoboda, Petr (advisor) ; Černý, Jan (referee)
Two decades of research on interactions between Xanthomonas phytopathogenic bacteria and their hosts resulted in discovery of a novel Transcription Activator-Like Effector (TALE) protein family, which confers bacterial virulence in plants. TALEs bind selectively to plant promoters and activate expression of cognate genes enabling bacterial reproduction and dissemination. TALEs mediate recognition of specific promoter boxes in a simple and predictable manner. The TALE central repeat domain contains tandem repeats, which specifically contact single consecutive nucleotides in the target sequence via polymorphic amino acid residues. Repeats stack together in an unique right-handed superhelical assembly, which wraps around the DNA duplex. Validated TALE-DNA binding code shows, that two polymorphic amino acids NI, HD, NH, NG and NN in each repeat mediate recognition of A, C, G, T and A/G, respectively. The order of repeats determines recognized sequence in DNA sense strand. Custom TALE DNA-binding domains with desired specificities can be created within one week at low cost. Such designed domains fused to nuclease or activation domains are useful in research, biotechnology and gene-therapy for targeted gene editing and gene regulation. Notably, gene editing with custom-designed TALE nucleases (TALENs) allows for...
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Targeted mutagenesis of the endogenous gene in \kur{D. melanogaster} genome by engineered nucleases
RENNER, Marek
Several techniques have recently been described for precise mutagenesis of selected target sites in the genome. This thesis establishes the method of gene targeting by CRISPR/Cas system in D. melanogaster and compares it with gene targeting using TALENs. To test the mutagenesis systems, we choose an endogenous gene encoding concentrative nucleoside transporter gene (CNT1). We have received two mutants containing large deletions affecting the N-terminal part of the CNT1 gene. We show that CRISPR/Cas is useful tool for targeted gene disruption in D. melanogaster.
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