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Mammalian proteins carrying zinc finger arrays
Vobruba, Adam ; Svoboda, Petr (advisor) ; Mašek, Jan (referee)
A zinc finger is a small peptide motif stabilised by a single zinc ion, best known for its capability to specifically bind a 3-nucleotide sequence of DNA, depending on the exact amino acids present in the DNA-binding positions. Zinc fingers are unique in their ability to freely link together and form longer tandem arrays, which can bind DNA targets of any length and sequence determined by the combination of individual fingers. These arrays can easily mutate and be rebuilt to change binding specificity, allowing great flexibility and helping zinc fingers to their widespread presence in numerous endogenous proteins of various functions. This property of zinc finger arrays also made them a suitable tool for the creation of custom DNA- binding domains for genetic engineering. This thesis provides an overview of the discovery, structure and function of these domains and then reviews and discusses selected naturally occurring mammalian zinc finger proteins and their properties, showcasing diverse uses zinc finger arrays have been adapted for throughout evolution. The history and future of zinc fingers in artificial proteins created for gene therapy and research are discussed as well. Keywords: zinc finger, ZnF, KRAB, KZFP, CTCF, PRDM9, ZFN, mammals
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The effects of epigenetic factor PRDM9 on the fertility of rodent females
Gašić, Srdan ; Trachtulec, Zdeněk (advisor) ; Děd, Lukáš (referee) ; Fulková, Helena (referee)
The Prdm9 gene encodes a histone-3-lysine-4,36-trimethyltransferase that specifies meiotic recombination sites and guides programmed double-strand breaks (DSBs) in mice, rats, and humans. Some vertebrates lost Prdm9 but not fertility throughout evolution, while the removal of Prdm9 caused sterility in some mouse strains, such as C57BL/6 (B6). The reasons for such species-specific fertility differences are unknown. To resolve these different requirements for PRDM9 in fertility, we produced Prdm9 mutants in another mammalian species, Rattus norvegicus, strain SHR/OlaIpcv. The removal of Prdm9 function did not completely abolish fertility in rats (as in B6 mice). Here I demonstrate that the loss of rat PRDM9 delayed female meiosis and caused synapsis and DSB repair defects that lead to a significant oocyte loss. However, unlike Prdm9-deficient B6 mouse oocytes, about 10-15% of pachytene-like mutant rat oocytes synapsed their chromosomes and repaired DSBs to the levels similar to controls. Because of this, female rats lacking PRDM9 maintained some oocytes until adulthood and yielded offspring, while B6 mice lost oocytes around the time of birth. Nevertheless, the adult rat mutant oocytes were exhausted earlier than the control adult rat oocytes. Therefore, PRDM9-lacking female rats suffered from...
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Genes of early meiotic prophase I of spermatogenesis in house mouse
Škaloudová, Eliška ; Trachtulec, Zdeněk (advisor) ; Forman, Martin (referee)
Meiosis is an essential cellular process that is necessary for gamete formation in all sexually reproducing organisms. This work is focused on the description of the genes of early stages of meiotic division in males of a mammalian model, the house mouse. The first part summarizes meiosis focusing on prophase I, which is longer than prophase II. Prophase I is divided into five stages, namely leptotene, zygotene, pachytene, diplotene, and diakinesis. Mouse spermatogenesis and its differences from oogenesis are also briefly described. The second part provides a list of genes encoding proteins required for initiation of meiotic division, pairing and synapses of chromosomes, and initiation of the catalysis of double-strand breaks. Double-strand breaks are repaired by homologous recombination, which may result in so-called crossing-over, the major source of genetic variability. The work deals with the early stage of homologous recombination and components required for this process. Localization of meiotic double-strand breaks in the genome is not random and is under the control of the Prdm9 gene, which seems to take multiple roles, such as the formation of new subspecies of the house mouse. Knowledge of the genes controlling the early stages of meiotic division is a prerequisite to understanding some of...
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Genetic interactions of the Prdm9 gene
Šebestová, Lenka ; Trachtulec, Zdeněk (advisor) ; Král, Jiří (referee)
The Prdm9 gene (PR domain containing 9, Meisetz, Hybrid sterility 1) encodes enzyme that trimethylates histone 3 on lysines 4 and 36. These methylation marks determine the positions of DNA double-strand breaks that are repaired by meiotic homologous recombination. In this study, we assayed genetic interactions of Prdm9 with two genes important for spermatogenesis - Mili (Piwil2) involved in piRNA biogenesis and Mybl1 encoding transcription factor that regulates many genes important for prophase I, including piRNA precursors. We crossed laboratory mice carrying mutation in Prdm9 with heterozygotes for mutation in Mybl1 or Mili, and created compound heterozygotes and, in case of Mybl1, also double homozygotes. We assessed body weight and male fertility parameters (weight of testes, sperm count, malformed sperm, percentage of tubules containing spermatocytes and of abnormal nuclei of pachytene spermatocytes) of these mice and compared them to controls. We also investigated the effect of Mybl1 and Mili mutations on fecundity of F1 intersubspecific hybrids. Our results revealed possible interactions of Prdm9 and Mybl1 in the laboratory mouse. Decreased gene dosage of Mybl1 reduced fertility of intersubspecific F1 hybrids. Interaction between Prdm9 and Mili in both laboratory mouse and F1 hybrids remain...
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Genomic architecture and molecular mechanisms of hybrid sterility in mice.
Vališková, Barbora ; Forejt, Jiří (advisor) ; Janko, Karel (referee) ; Macholán, Miloš (referee)
Hybrid sterility is one of the reproductive isolation mechanisms restricting gene flow between the related species and leading to speciation. PR domain containing 9 (Prdm9), the only known vertebrate hybrid sterility gene, determines the sites of programmed DNA double-strand breaks (DSBs) and thus specifies hotspots of meiotic recombination but in hybrids between two mouse subspecies causes failure of meiotic chromosome synapsis and hybrid male sterility. In the present study on sterile hybrids, the five smallest autosomes were more prone to asynapsis. To manipulate with the synapsis rate, random stretches of consubspecific homology were inserted into several autosomal pairs. Twenty seven or more megabases of consubspecific sequence fully restore synapsis in a given autosome. Further, at least two symetric DN double-strand breaks per chromosome were necessary for successful synapsis. Moreover, F1 hybrids had sperm when synapsis was rescued in at least three of four segregating chromosomes. To verify the assumption of a lack of symmetric DSBs in meiotic chromosomes of sterile males the chemotherapeutic drug cisplatin was used to induce exogenous DNA DSBs. Cells treated with 5 mg/kg and 10 mg/kg of cisplatin showed increased number of DSBs monitored by immunostaining of RPA and DMC1 sites and...
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The role of histone modifications and gene expression in mouse spermatogenesis
Křivánková, Klára ; Mihola, Ondřej (advisor) ; Jansa, Petr (referee)
The production of haploid sperm is a precondition for sexual reproduction of males. PRDM9 protein is a histone methyltransferase which localizes sites of meiotic recombination in many mammals. Mouse males of the C57BL/6J (B6) strain deficient for Prdm9 (Prdm9-/- ) are sterile, while Prdm9-/- males of PWD/Ph (PWD) strain have reduced sperm count. The comparison of the distribution of trimethylation of histone 3 on lysine 36 (H3K36me3) in genome of Prdm9-/- males of these two strains will help to determine the role of this epigenetic modification on meiotic recombination and fertility of Prdm9-/- males. The second part of this thesis is focused on transgenic males. Male offspring from the first generation of B6 female and PWD male crosses (B6PF1) have reduced fertility parameters due to incompatibility of Prdm9 alleles. The fertility parameters of B6PF1 hybrids carrying CHORI-34-289M8 or RP24-346I22 transgene are even lower. The candidate gene, which participates in the reduction of fertility of the transgenic B6PF1 hybrids, was determined as the proteasome subunit encoding gene Psmb1, because its relative transcription level best correlates with sperm count. The reason of lowered fertility thus might be a defect in proteasome assembly. The investigation of the fitness of transgenic animals is...
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Genetic interactions of the Prdm9 gene
Šebestová, Lenka ; Trachtulec, Zdeněk (advisor) ; Král, Jiří (referee)
The Prdm9 gene (PR domain containing 9, Meisetz, Hybrid sterility 1) encodes enzyme that trimethylates histone 3 on lysines 4 and 36. These methylation marks determine the positions of DNA double-strand breaks that are repaired by meiotic homologous recombination. In this study, we assayed genetic interactions of Prdm9 with two genes important for spermatogenesis - Mili (Piwil2) involved in piRNA biogenesis and Mybl1 encoding transcription factor that regulates many genes important for prophase I, including piRNA precursors. We crossed laboratory mice carrying mutation in Prdm9 with heterozygotes for mutation in Mybl1 or Mili, and created compound heterozygotes and, in case of Mybl1, also double homozygotes. We assessed body weight and male fertility parameters (weight of testes, sperm count, malformed sperm, percentage of tubules containing spermatocytes and of abnormal nuclei of pachytene spermatocytes) of these mice and compared them to controls. We also investigated the effect of Mybl1 and Mili mutations on fecundity of F1 intersubspecific hybrids. Our results revealed possible interactions of Prdm9 and Mybl1 in the laboratory mouse. Decreased gene dosage of Mybl1 reduced fertility of intersubspecific F1 hybrids. Interaction between Prdm9 and Mili in both laboratory mouse and F1 hybrids remain...
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The role of H3K36 methylation in DNA repair of germinal and somatic cells
Křivánková, Klára ; Mihola, Ondřej (advisor) ; Schierová, Michaela (referee)
Histone modifications affect many cellular processes including DNA damage repair. This thesis focusses on the methylation of lysine 36 of histone 3 (H3K36). The role of this modification in the localization of DNA double-stranded breaks in germinal cells is described in the first part of this thesis. Double-stranded breaks initiate meiotic recombination, which is essential for successful meiosis. This thesis also describes three histone methyltransferases. The first is PRDM9, an enzyme expressed only in oocytes and spermatocytes during meiotic prophase and responsible for the localization of recombination hotspots in most mammals. The second part of this thesis deals with the role of H3K36 methylation in DNA damage repair in somatic cells using homologous recombination (HR) and nonhomologous DNA ending joining (NHEJ). The proteins SETD2 and SETMAR are described in the second part. SETD2 trimethylates H3K36, and H3K36me3 is recognized by the LEDGF protein. Through LEDGF, other components necessary for HR are recruited to DNA. SETMAR dimethylates H3K36 and together with this histone modification promote DNA break repair with NHEJ. The research of H3K36 methylation is important for a better understanding of each DNA repair mechanisms. The correct repair of DNA breaks is necessary for maintaining...
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Maping of genes modifying the subspecies-specific roles of the meiotic gene Prdm9
Škaloudová, Eliška ; Trachtulec, Zdeněk (advisor) ; Schierová, Michaela (referee)
The PRDM9 (PR domain containing 9) protein is an epigenetic factor that trimethylates lysine 4 of histone H3 and thereby determines the future meiotic double-strand breaks - sites important for proper segregation of homologous chromosomes. Males of the Mus musculus domesticus (Mmd) origin with homozygous deletion in Prdm9 (Prdm9-/- ) are sterile with a complete arrest in meiotic prophase I, in contrast to the same mutant males of the M. m. musculus (Mmm) subspecies. The aim of this diploma thesis was to identify the genomic loci responsible for the phenotypic difference of these Prdm9-/- males. The major research tool was a population of 182 Mmm x Mmd Prdm9-/- males. The mapping method of quantitative trait loci (QTLs) was based on relating the genotypes of single-nucleotide and microsatellite polymorphisms to the observed phenotypes. At least two QTLs on Chr X were identified. The Mmm alleles of these QTLs reduced fertility of Prdm9-/- males. Both QTLs were confirmed and narrowed down using two types of subconsomic strains. It was not possible to confirm other QTLs, particularly on autosomes. This QTL mapping is the first step towards the identification of genes that modify the resulting phenotype of Prdm9-/- animals. This identification should help designing studies of human infertility that...
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Genes of early meiotic prophase I of spermatogenesis in house mouse
Škaloudová, Eliška ; Trachtulec, Zdeněk (advisor) ; Forman, Martin (referee)
Meiosis is an essential cellular process that is necessary for gamete formation in all sexually reproducing organisms. This work is focused on the description of the genes of early stages of meiotic division in males of a mammalian model, the house mouse. The first part summarizes meiosis focusing on prophase I, which is longer than prophase II. Prophase I is divided into five stages, namely leptotene, zygotene, pachytene, diplotene, and diakinesis. Mouse spermatogenesis and its differences from oogenesis are also briefly described. The second part provides a list of genes encoding proteins required for initiation of meiotic division, pairing and synapses of chromosomes, and initiation of the catalysis of double-strand breaks. Double-strand breaks are repaired by homologous recombination, which may result in so-called crossing-over, the major source of genetic variability. The work deals with the early stage of homologous recombination and components required for this process. Localization of meiotic double-strand breaks in the genome is not random and is under the control of the Prdm9 gene, which seems to take multiple roles, such as the formation of new subspecies of the house mouse. Knowledge of the genes controlling the early stages of meiotic division is a prerequisite to understanding some of...
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