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The normal regulation of the Hedgehog (Hh) pathway is essential for embryonic development, stem cell maintenance, and gametogenesis for both vertebrates and invertebrates, whereas the aberrant pathway regulation can cause various developmental defects and cancers. Hence, it is important to understand the precise mechanism of how the Hh pathway is regulated. Much of our understanding of the Hh pathway comes from studies in Drosophila but applies also to vertebrates. In Drosophila, Hh signal transduction terminates with regulation of the transcriptional activator, Cubitus interruptus (Ci). In the absence of Hh signaling, Ci is 1) processed to a repressor form via the Costal2 (Cos2) complex and suppresses the transcription of Hh target genes or 2) inhibited by binding to Cos2 and Suppressor of Fused (Su(fu)). Once the cells receive Hh ligand, however, 1) Ci processing is inhibited and 2) inhibition by Su(fu), and possibly Cos2, is countered by Fused (Fu) kinase, which ultimately transforms Ci into an activator form that goes into the nucleus and induces the transcription of Hh target genes. How Fu alleviates Su(fu) inhibition and facilitates the activation of Ci is not well understood, and it was only discovered recently that Ci is the direct target of Fu phosphorylation. Many studies of Hh signaling have been conducted under artificial conditions, where proteins are often overexpressed, leading to findings that sometimes do not reflect in vivo events, where relative protein stoichiometry is important. For this dissertation, I investigated how Ci activation is regulated by Su(fu) and Fu using CRISPR/Cas to generate different Ci variants expressed at physiological levels in fly wing discs. I looked at how different regions of Ci, including known phosphorylation sites, contribute to the regulation of Ci activity. From this study, I propose that different sets of Ci phosphorylation events mediated by Fu are responsible for changes in Ci-Su(fu) interactions, by altering Ci-Su(fu) interfaces, but also by changing intramolecular Ci-Ci interactions and thereby transforming Ci to an active conformation, leading to target gene activation in response to Hh.

<p>Recent advances in gene targeting technology have significantly shaped modern-day mouse genetics, as they allow for the accurate analysis of gene function <em>in vivo</em>. By capitalizing on conventional methodologies that are based on homologous recombination, the advent of artificially engineered nucleases, like transcription activator-like effector nucleases (TALENs), enables precise genome editing without the need for conventional targeting vectors, which typically possess long “arms” of homology that are difficult to work with, even with recombineering strategies employing bacterial artificial chromosomes. Unlike traditional techniques, these novel nucleases can be engineered in less than a week and together with compact targeting vectors, can be used to easily manipulate almost any locus in the mouse genome.</p> <p>The current selection of commercially available antibodies makes it difficult to assess the specific roles of protein isoforms during early development. The Tcf/Lef family of transcription factors comprise of key downstream effector proteins of the canonical Wnt/β-catenin signal transduction cascade. This pathway is implicated in the regulation of self-renewal and is dysregulated in a number of human diseases including cancers. Among the Tcf/Lef factors, Tcf3 has been heavily studied in mouse embryonic stem cells, due at least in part to the observation that its transcript levels are expressed at the highest levels compared to the others. Recently, it was proposed that a switch takes place between a repressive state mediated by Tcf3 to an activating β-catenin-Tcf1 complex in response to Wnt signals. Here, we use TALEN technology to introduce an epitope tag at the endogenous locus of <em>mTcf7</em>, the gene encoding the Tcf1 protein. By tagging the N-terminus of full-length and N-terminally truncated dominant-negative variants of Tcf1, we establish a tool to better study a previously unappreciated role for Tcf1 in regulating embryonic stem cell self-renewal and differentiation. Furthermore, we also show that the tagged variants generated exhibit similar protein expression levels to those of wild-type controls, and display nuclear localization as expected.</p> / Master of Science (MSc)

The CRISPR/Cas9 system has become the predominant tool for genome editing. Targeted modifications can be introduced while repairing double strand breaks (DSBs), induced by the CRISPR/Cas9 system. The DSB is repaired by either non-homologous end joining (NHEJ) or homologous recombination (HR), and the repair is commonly processed through NHEJ because it is the dominant repair pathway in most cell types. The goal of this study is to modulate DNA repair system of somatic cells to increase the frequency of homology-directed repair (HDR) through HR by chemical treatment and the frequency of NHEJ by serum starvation. CRISPR/Cas9 systems targeting RAG2 gene and donor DNA to replace endogenous RAG2 were transfected into porcine fetal fibroblast (PFF) cells and the cells were treated with various chemicals that were known to inhibit NHEJ or stimulate HR. Among the chemical treated groups, cells treated with thymidine showed an average of 5.85-fold increase in HDR compared to the control group; the difference ranged from 1.37 to 9.59. There was no positive effect on the frequency of HDR after treating transfected cells with other chemicals. Placing PFFs under low amount of serum (serum deprivation) could enrich the cells in G0/G1 phase, but there was little difference in the frequency of NHEJ. Our results indicate that modulating DNA repair pathways during CRISPR/Cas9-mediated gene targeting could change the outcome of the targeted events. / Master of Science / The CRISPR/Cas9 system is the newest generation of genetic engineering tool for genome editing. Genetic modifications can be introduced while repairing double strand breaks (DSBs) on DNA, induced by the CRISPR/Cas9 system. The DSB is repaired by either non-homologous end joining (NHEJ) or homologous recombination (HR), and the repair is commonly processed through NHEJ because it is the dominant repair pathway in most cell types. The goal of this study is to modulate DNA repair system of somatic cells to increase the frequency of homology-directed repair (HDR) through HR by chemical treatment and the frequency of NHEJ by serum starvation. Among the chemical treated groups, cells treated with thymidine showed an average of 5.85-fold increase in HDR compared to the control group; the difference ranged from 1.37 to 9.59. There was no positive effect on the frequency of HDR after treating transfected cells with other chemicals. Placing pig fibroblast under low amount of nutrient could enrich the cells in G0/G1 phase of cell cycle, but there was little difference in the frequency of NHEJ. Our results indicate that modulating DNA repair pathways during CRISPR/Cas9-mediated gene targeting could change the outcome of the targeted events.

The tumor suppressor gene HIC1 encodes a BTB/POZ transcription repressor. Its promotor is frequently hypermetylated in large numbers of tumors. HIC1 also functions as a negative modulator of the Wnt signalling pathway, which fundamentally participates in regulation of stem cell renewal of the intestinal epithelium. Thanks to its structural features the intestinal epithelium represents a convenient model tissue to study stem cells and their pathology. To overcome the embryonic lethality of the complete Hic1 "knock-out" the conditional deletion of the gene in adult mouse tissue was chosen to evaluate the Hic1 biological aktivity. By the chip expression analysis of mouse embryonic fibroblasts we discovered a number of new target genes of Hic1, the most interesting of them - in respect to cancer - we considered the Toll-like receptor 2 gene. The expression of Hic1 target genes is likely to be co-regulated by p53 although the direct regulation wasn't proved. Hic1 affects the proportion of the differentiated intestinal epithelial cells types possibly via regulation of Atoh1. After conditional deletion of Hic1 in the intestinal epithelium we observed and quantitatively confirmed a significant increase of the amounts of goblet cells. We concluded that Hic1 affects differentiation pathways in intestinal...

Il gene-targeting in colture cellulari associato alla tecnica del trasferimento nucleare oggi rappresenta il sistema d'elezione nella creazione di animali transgenici. Purtroppo la ricombinazione omologa (HR) è poco efficiente soprattutto in cellule somatiche. La positive-negative selection (PNS) è la tecnica di arricchimento usata per geni non attivamente trascritti nel tipo cellulare utilizzato. In questo lavoro abbiamo scelto come locus bersaglio la b-lattoglobulina bovina e testato tre nuove cassette di selezione negativa, che non codificando per antibiotico-resistenze, determinano condizioni di coltura meno tossiche. / Gene-targeting of cultured cells combined with nuclear transfer currently is the most effective procedure to produce transgenic livestock. Nevertheless homologous recombination (HR) is a low frequency event in mammalian cells, above all in somatic cells. Positive-negative selection (PNS) is the enrichment strategy to target genes that are not actively transcribed in the cell type of choice. In this work we chose to target the bovine b-lactoglobulin gene and we tested three new negative selection cassettes in bovine fibroblasts. Such new targeting vectors allow a single selective drug employ and produce less toxic culture conditions.

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(農学) / 甲第19047号 / 農博第2125号 / 新制||農||1032 / 31998 / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 小川 順, 教授 喜多 恵子, 教授 栗原 達夫 / 学位規則第4条第1項該当

Here we developed multiple genetic systems through which genetic modifications driven by DNA breaks caused by the I-SceI nuclease can be assayed in the yeast Saccharomyces cerevisiae and in human cells. Using the delitto perfetto approach for site-directed mutagenesis in yeast, we generated isogenic strains in which we could directly compare the recombination potential of different I-SceI variants. By genetic engineering procedures, we generated constructs in human cells for testing the recombination activity of the same I-SceI variants. Both in yeast and human cells we performed gene correction experiments using oligonucleotides (oligos) following modification and/or optimization of existing gene targeting protocols and development of new ones. We demonstrated that an I-SceI nicking enzyme can stimulate recombination on the chromosome in S. cerevisiae at multiple genomic loci. We also demonstrated in yeast that an I-SceI-driven nick can activate recombination 10 kb distant from the initial site of the chromosomal lesion. Moreover we demonstrated that an I-SceI nick can stimulate recombination at the site of the nick at episomal and chromosomal loci in human cells. We showed that an I-SceI double-strand break (DSB) could trigger recombination up to 2 kb distant from the break at an episomal target locus in human cells, though the same was not observed for the nick. Overall, we demonstrated the capacity for I-SceI nick-induced recombination in yeast and human cells. Importantly, our findings reveal that the nick stimulates gene correction by oligos differently from a DSB lesion, as determined by genetic and molecular analyses in yeast and human cells. This research illustrates the promise of targeted gene correction following generation of a nick.

The protozoan parasite Leishmania (Viannia) braziliensis (L. braziliensis) is the main cause of human tegumentary leishmaniasis in the New World, a disease affecting the skin and/or mucosal tissues. Despite its importance, the study of the unique biology of L. braziliensis through reverse genetics analyses has so far lagged behind in comparison with Old World Leishmania spp. In this study, we successfully applied a cloning-free, PCR-based CRISPR–Cas9 technology in L. braziliensis that was previously developed for Old World Leishmania major and New World L. mexicana species. As proof of principle, we demonstrate the targeted replacement of a transgene (eGFP) and two L. braziliensis single-copy genes (HSP23 and HSP100). We obtained homozygous Cas9-free HSP23-and HSP100-null mutants in L. braziliensis that matched the phenotypes reported previously for the respective L. donovani null mutants. The function of HSP23 is indeed conserved throughout the Trypanosomatida as L. major HSP23 null mutants could be complemented phenotypically with transgenes from a range of trypanosomatids. In summary, the feasibility of genetic manipulation of L. braziliensis by CRISPR–Cas9-mediated gene editing sets the stage for testing the role of specific genes in that parasite’s biology, including functional studies of virulence factors in relevant animal models to reveal novel therapeutic targets to combat American tegumentary leishmaniasis. / Alexander von Humboldt-Stiftung / Revisión por pares

The utility of a model organism for studying biological processes is closely tied to its amenability to genome manipulation. Although tools for targeted genome engineering in mice have been available since 1987, most organisms including zebrafish have lacked efficient reverse genetic tools, which has stymied their broad implementation as a model system to study biological processes. The development of zinc finger nucleases (ZFNs) that can create double-strand breaks at desired sites in a genome has provided a universal platform for targeted genome modification. ZFNs are artificial restriction endonucleases that comprise of an array of 3- to 6-C2H2-zinc finger DNA-binding domains fused with the dimeric cleavage domain of the type IIs endonuclease FokI. C2H2-zinc fingers are the most common, naturally occurring DNA-binding domain, and their specificity can be engineered to recognize a variety of DNA sequences providing a strategy for targeting the appended nuclease domain to desired sites in a genome. The utility of ZFNs for gene editing relies on their activity and precision in vivo both of which depend on the generation of ZFPs that bind desired target sites high specificity and affinity. Although various methods are available that allow construction of ZFPs with novel specificities, ZFNs assembled using existing approaches often display negligible in vivo activity, presumably resulting from ZFPs with either low affinity or suboptimal specificity. A root cause of this deficiency is the presence of interfering interactions at the finger-finger interface upon assembly of multiple fingers. In this study we have employed bacterial-one-hybrid (B1H)-based selections to identify two-finger zinc finger units (2F-modules) containing optimized interface residues that can be combined with published finger archives to rapidly yield ZFNs that can target more than 95% of the zebrafish and human protein-coding genes while maintaining a success rate higher than that of ZFNs constructed using available methods. In addition to genome engineering in model organisms, this advancement in ZFN design will aid in the development of ZFN-based therapeutics. In the process of creating this archive, we have undertaken a broader study of zinc finger specificity to better understand fundamental aspects of DNA recognition. In the process we have created the largest protein-DNA interaction dataset for zinc fingers to be described that will facilitate the development of better predictive models of recognition. Ultimately, these predictive models would enable the rational design of synthetic zinc finger proteins for targeted gene regulation or genomic modification, and the prediction of genomic binding sites for naturally occurring zinc finger proteins for the construction of more accurate gene regulatory networks.