Precise engineering of genomes holds great promise to advance our understanding of gene function and biotechnological applications. DNA double strand breaks are repaired via imprecise non-homologous end joining repair or via precise homology-directed repair processes. Therefore, we could harness the DSBs to engineer the genomes with a variety of genetic outcomes and with singlebase- level precision. The major barrier for genome engineering was the generation of site-specific DNA DSBs. Programmable DNA enzymes capable of making a complete and site-specific cut in the genome do not exist in nature. However, these enzymes can be made in in vitro as chimeric fusions of two modules, a DNA binding module and a DNA cleaving module. The DNA cleaving module can be programmed to bind to any user-defined sequence and the DNA cleaving module would generate DSBs in the target sequence. These enzymes called molecular scissors include zinc finger nucleases (ZFNs) and transcriptional activator like effector nucleases (TALENs). The programmability of these enzymes depends on protein engineering for DNA binding specificity which may be complicated, recourse intensive and suffer from reproducibility issues. Recently, clustered regularly interspaced palindromic repeats (CRISPR)/ CRISPR associated endonuclease 9 (Cas9) an adaptive immune system of bacterial and archaeal species has been developed for genome engineering applications. CRISPR/Cas9 is an RNA-guided DNA endonuclease and can be reprogrammed through the engineering of single guide RNA molecule (sgRNA). CRISPR/Cas9 activity has been shown across eukaryotic species including plants. Although the engineering of CRISPR/Cas9 is quite predictable and reproducible, there are many technological challenges and improvements that need to be made to achieve robust, specific, and efficient plant genome engineering. Here in this thesis, I developed a number of technologies to improve specificity, delivery and expression and heritability of CRISRP/Cas9-modification in planta. Moreover, I used these technologies to answer basic questions to understand the molecular underpinning of the interplay between splicing and abiotic stress. To improve Cas9 specificity, I designed and constructed a chimeric fusion between catalytically dead Cas9 (dCas9) and FOKI catalytic DNA cleaving domain (dCas9.FoKI). This synthetic chimeric fusion enzyme improved Cas9 specificity which enable precision genome engineering. Delivery of genome engineering reagents into plant cells is quite challenging, I developed a virus-based system to deliver sgRNAs into plants which facilitates plant genome engineering and could bypass the need for tissue culture in engineering plant genomes. To improve the expression of the CRISPR/Cas9 machinery in plant species, I developed a meiotically-driven expression of CRISPR/Cas9 which improved genome editing and heritability of editing in seed progeny, thereby facilitating robust genome engineering applications. To understand the molecular basis of the interplay between splicing stress and abiotic stress, I used the CRISPR/Cas9 machinery to engineer components of the U2snRNP complex coupled which chemical genomics to understand the splicing stress regulation in response to abiotic stress conditions. Finally, I harnessed the technological improvements and developments I have achieved with CRISPR/Cas9 system to develop a directed evolution platform for targeted trait engineering which expands and accelerates trait discovery and engineering of plant species resilient to climate change conditions.

Designer nucleases have greatly simplified small genome modifications in many genomes. They can precisely target a specific DNA sequence within a genome and make a double stranded break (DSB). DNA repair mechanisms of the DSB lead to gene mutations or gene modification by homologous directed repair (HDR) if a repair template is exogenously supplied. Thus, small, site directed mutations are easily and quickly achieved. However, strategies that utilize designer nucleases for more complex tasks are emerging and require optimization. To optimize CRISPR/Cas9 assisted targeting, an HPRT rescue assay was utilized to measure the relationship between targeting frequency and homology arm length in targeting constructs in mouse embryonic stem cells. The results show that different gene engineering exercises had different homology requirements.

Tuberous sclerosis complex (TSC) is a multisystem tumor-forming disorder caused by biallelic inactivation of TSC1 or TSC2. The primary cause of mortality arises from mesenchymal manifestations in the lung and kidney: pulmonary lymphangioleiomyomatosis (LAM) and renal angiomyolipomas (RAMLs). Despite a well-described monogenic etiology, there remains an incomplete understanding of disease pathogenesis. Consequentially, tractable models which fully recapitulate disease characteristics are lacking. Here, I develop and study novel tissue-engineered models of TSC lung and kidney disease. In my first chapter, I demonstrate that lung-mimetic hydrogel culture of pluripotent stem cell-derived diseased cells more faithfully recapitulates human LAM biology compared to conventional culture on two-dimensional plastic. Leveraging this culture system, I conducted a three-dimensional drug screen using a custom 800-compound library, tracking cytotoxicity and invasion modulation phenotypes at the single cell level. I identified histone deacetylase (HDAC) inhibitors as a group of anti-invasive agents that are also selectively cytotoxic towards TSC2-/- cells. HDAC inhibitor therapeutic effects remained consistent in vivo upon xenotransplantation of LAM cellular models into zebrafish. In my second chapter, I develop a genetically-engineered human renal organoid model which recapitulates pleiotropic features of RAMLs in vitro and upon orthotopic xenotransplantation. I find that loss of TSC1/2 affects multiple developmental processes in the renal epithelial, stromal, and glial compartments. First, loss of TSC1/2 leads to an expanded stroma by favouring stromal cell fate acquisition and alters terminal stromal cell identity. Second, epithelial cells in the TSC1/2-/- organoids exhibit a rapamycin-insensitive epithelial-to-mesenchymal transition. Third, a melanocytic population forms exclusively in TSC1/2-/- organoids, branching from MITF+ Schwann cell precursors of a bona fide neural crest-to-Schwann cell differentiation trajectory. Through these two thesis chapters, I realize the power of tissue-engineered models for the study of TSC. This work offers novel insights into the pathogenesis of RAMLs and identifies a new class of therapeutics suitable for trialing in patients with pulmonary LAM.

One of the major challenges facing medicine and drug discovery is the large number of genetic diseases caused by inherited mutations leading to a toxic gain-of-function, or loss-of-function of the disease protein. Microbiology offered a new glimpse of hope to address those disorders with the adaptation of the bacterial CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) defense system as a genome editing tool. Cas9 is a unique CRISPR-associated endonuclease protein that can be easily programmed with an RNA [a single-guide RNA (sgRNA)] that is complementary to nearly any DNA locus. Cas9 creates a double-stranded break (DSB) that can be exploited to knock out toxic genes or replenish therapeutic expression levels of essential proteins. In addition to a matching sgRNA sequence, Cas9 requires the presence of a short signature sequence [a protospacer adjacent motif (PAM)] flanking the target locus. Over the past few years, several Cas9-based therapeutic platforms have emerged to correct DNA mutations in a wide range of mammalian cell lines, ex vivo, and in vivo by adapting recombinant adeno-associated virus (rAAV). However, most of the applications of Cas9 in the field have been limited to Streptococcus pyogenes (SpyCas9), which, in its wild-type form, suffers from inaccurate editing at off-target sites. It is also difficult to deliver via an all-in-one (sgRNA+Cas9) rAAV approach due to its large size. In this thesis, I describe other Cas9 nucleases and their development as new AAV-based genome editing platforms for therapeutic editing in vivo in mouse disease models. In the first part of this thesis, I develop the all-in-one AAV strategy to deliver a Neisseria meningitidis Cas9 ortholog (Nme1Cas9) in mice to reduce the level of circulating cholesterol in blood. I also help characterize an enhanced Cas9 from another meningococcus strain (Nme2Cas9) and show that it is effective in performing editing not only in mammalian cell culture, but also in vivo by all-in-one AAV delivery. Additionally, I describe two AAV platforms that enable advanced editing modalities in vivo: 1) segmental DNA deletion by delivering two sgRNAs (along with Nme2Cas9) in one AAV, and 2) precise HDR-based repair by fitting Nme2Cas9, sgRNA and donor DNA within a single AAV capsid. Using these tools, we successfully treat two genetic disorders in mice, underscoring the importance of this powerful duo of AAV and Cas9 in gene therapy to advance novel treatment. Finally, I present preliminary data on how to use these AAV.Nme2Cas9 vectors to treat Alexander Disease, a rare progressive neurological disorder. These findings provide a platform for future application of gene editing in therapeutics.

La mutagenèse dirigée est un outil indispensable à toute étude microbiologique, car elle permet d’identifier le rôle de certains locus génétiques identifiés comme acteurs potentiels dans des contextes précis. Cependant, les protocoles de mutagenèse dirigée sont longs et laborieux, et leur mise en œuvre est l’un des points limitants en recherche. L’émergence de CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats) comme outil moléculaire a permis d’accélérer et de faciliter ces procédures de mutagenèse par contre-sélection. La limite de ces protocoles se situe dans la régénération de l’espaceur effectuant la contre-sélection. Notre plateforme CRISPR, dénommée Horus, offre une solution à cette limitation. Elle utilise du clonage in vivo afin de raccourcir autant la durée que la charge de travail du protocole, pour aboutir à l'obtention de mutants en une seule étape. Pour se faire nous avons conçu in silico un ARN guide synthétique capable d’agir comme un interrupteur génétique (porte logique ET) et de performer une contre sélection (discriminant les bactéries de types sauvages des mutants) via le système CRISPR-Cas9. / Site-directed mutagenesis is an essential tool for any microbiological study because it makes it possible to identify the role of certain loci identified as potential actors in specific contexts. However, site-directed mutagenesis protocols are long and laborious, and their implementation is one of the limiting points of research. The emergence of CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats) as a molecular tool has accelerated the facilitation of these counter-selection mutagenesis protocols. The limitation of these protocols lies in the regeneration of the protospacer mediating the counter selection. Our CRISPR platform, called Horus (HOmologuous Recombination Using SsDNA), offers a solution to this limitation. It uses in vivo cloning to shorten both the duration and the workload of the protocol, allowing to obtain mutants strains in just one step. To do so, we designed in silico a synthetic guide RNA capable of acting as a genetic switch (AND Gate) and performing counter-selection (discriminating WT bacteria from mutants) via the CRISPR-Cas9 system.

Tyrosine site-specific recombinases (Y-SSRs) are DNA editing enzymes that play a valuable role for the manipulation of genomes, due to their precision and versatility. They have been widely used in biotechnology and molecular biology for various applications, and are slowly finding their spot in gene therapy in recent years. However, the limited number of available Y-SSR systems and their often narrow target specificity have hindered the full potential of these enzymes for advanced genome engineering. In this PhD thesis, I conducted a comprehensive investigation of novel Y-SSRs and their potential for advancing genome engineering. This PhD thesis aims to address the current limitations in the genetic toolbox by identifying and characterizing novel Cre-type recombinases and demonstrating their impact on the directed evolution of designer recombinases for precise genome surgery. To achieve these aims, I developed in a collaboration a comprehensive prediction pipeline, combining a rational bioinformatical approach with knowledge of the biological functions of recombinases, to enable high success rate and high-throughput identification of novel tyrosine site-specific recombinase (Y-SSR) systems. Eight putative candidates were molecularly characterized in-depth to ensure their successful integration into future genome engineering applications. I assessed their activity in prokaryotes (E. coli) and eukaryotes (human cell lines), and determined their specificity in the sequence space of all known Cre- type target sites. The potential cytotoxicity associated with cryptic genomic recombination sites was also explored in the context of recombinase applicability. This approach allowed the identification of novel Y-SSRs with distinct target sites, enabling simultaneous use of multiple Y-SSR systems, and provided knowledge that will facilitate the assignment of novel and known recombinases to specific uses or organisms, ensuring their safe and effective implementation. The introduction of these novel Y-SSRs into the genome engineering toolbox opens up new possibilities for precise genome manipulation in various applications. The broader targetability offered by these enzymes could accelerate the development of novel gene therapies, as well as advance the understanding of gene function and regulation. Moreover, these recombinases could be used to design custom genetic circuits for synthetic biology, allowing researchers to create more complex and sophisticated cellular systems. Finally, I introduced the novel Y-SSRs into efforts aimed at developing designer recombinases for precise genome surgery, demonstrating their impact on accelerating the directed evolution process. Therapeutically relevant recombinases with altered DNA specificity have been developed for excision or inversion of specific DNA sequences. However, the potential for evolving recombinases capable of integrating large DNA cargos into naturally occurring lox-like sites in the human genome remained untapped so far. Thus, I embarked on evolving the Vika recombinase to mediate the integration of DNA cargo into a native human sequence. I discovered that Vika could integrate DNA into the voxH9 site in the human genome, and then, I enhanced the process through directed evolution. The evolved variants of Vika displayed a marked improvement in integration efficiency in bacterial systems. However, the translation of these results into mammalian systems has not yet been entirely successful. Despite this, the study laid the groundwork for future research to optimize the efficiency and applicability of Y-SSRs for genomic integration. In summary, this thesis made significant strides in the identification, characterization, and development of novel Y-SSRs for advanced genome engineering. The comprehensive prediction pipeline, combined with in-depth molecular characterization, has expanded the genetic toolbox to meet the growing demand for better genome editing tools. By exploring efficiency, cross-specificity, and potential cytotoxicity, this research lays the foundation for the safe and effective application of novel Y-SSRs in various therapeutic settings. Furthermore, by demonstrating the potential of these recombinases to improve efforts in creating designer recombinases through directed evolution, this research has opened new avenues for precise genome surgery. The successful development and implementation of these novel recombinases have the potential to revolutionize gene therapy, synthetic biology, and our understanding of gene function and regulation.

Approximately 10% of sequenced bacterial genomes are multipartite, consisting of two or more large chromosome-sized replicons. This genome organization can be found in many plant, animal, and human pathogens and symbionts. However, the advantage of harbouring multiple replicons remains unclear. One species with a multipartite genome is Sinorhizobium meliloti, a model rhizobium that enters into N2-fixing symbioses with various legume crops. In this work, S. meliloti derivatives lacking one or both of the secondary replicons (termed pSymA and pSymB) were constructed. Phenotypic characterization of these strains, including growth rate, metabolic capacity, and competitive fitness, provided some of the first experimental evidence that secondary replicons evolved to provide a niche specific advantage, improving fitness in a newly colonized environment. These results were further supported by characterizing the symbiotic phenotypes of 36 large-scale pSymA and pSymB deletion mutants. To further this analysis, an in silico S. meliloti genome-scale metabolic network reconstruction was developed and flux balance analysis used to examine the contribution of each replicon to fitness in three niches. These simulations were consistent with the hypothesis that metabolic pathways encoded by pSymB improve fitness specifically during growth in the plant-associated rhizosphere. Phylogenetic analysis of a pSymB region containing two essential genes provided a clean example of how a translocation from the primary chromosome to a secondary replicon can render the secondary replicon essential. Moreover, an experimental analysis of genetic redundancy indicated that 10-15% of chromosomal genes are functionally redundant with a pSymA or pSymB encoded gene, providing an alternative method for how secondary replicons can become essential and influence the evolution of the primary chromosome. Finally, the work presented here provides a novel framework for forward genetic analysis of N2-fixing symbiosis and the identification of the minimal N2-fixing symbiotic genome, which will help facilitate the development of synthetic symbioses. / Thesis / Doctor of Philosophy (PhD) / Many bacteria that enter into symbiotic or pathogenic relationships with plants, animals, and humans contain a genome that is divided into multiple chromosome-like molecules. One example is the N2-fixing legume symbiont Sinorhizobium meliloti, whose genome contains three chromosome-sized molecules. Here, the functions associated with each molecule in the S. meliloti genome were examined through a combination of experimental genetic analyses and computer based simulations. Results from these approaches suggested that adaptation to unique environments selected for the evolution of secondary chromosome-like molecules, with each predominately contributing to growth in a specific environment, including environments associated with an eukaryotic host. The genes on these replicons are therefore prime targets for manipulation of bacterium-host interactions, and represent reservoirs of valuable genes for use in synthetic biology applications. Additionally, the genome reduction approach employed in this study laid out a ground work for identification of the minimal N2-fixing symbiotic genome. This represents a crucial step towards successfully engineering improved nitrogen fixation, and the engineering of synthetic N2-fixing symbioses involving non-legumes and/or non-rhizobia.

Tesis por compendio / [ES] La mejora genética vegetal tiene como objetivo la obtención de plantas con rasgos mejorados o características novedosas que podrían ayudar a superar los objetivos de sostenibilidad. Para este fin, la biotecnología vegetal necesita incorporar nuevas herramientas de ingeniería genética que combinen una mayor precisión con una mayor capacidad de mejora. Las herramientas de edición genética recientemente descubiertas basadas en la tecnología CRISPR/Cas9 han abierto el camino para modificar los genomas de las plantas con una precisión sin precedentes. Por otro lado, los nuevos enfoques de biología sintética basados en la modularidad y la estandarización de los elementos genéticos han permitido la construcción de dispositivos genéticos cada vez más complejos y refinados aplicados a la mejora genética vegetal. Con el objetivo final de expandir la caja de herramientas biotecnológicas para la mejora vegetal, esta tesis describe el desarrollo y la adaptación de dos nuevas herramientas: una nueva endonucleasa específica de sitio (SSN) y un interruptor genético modular para la regulación de la expresión transgénica. En una primera parte, esta tesis describe la adaptación de CRISPR/Cas12a para la expresión en plantas y compara la eficiencia de las variantes de Acidaminococcus (As) y Lachnospiraceae (Lb) Cas12a con Streptococcus pyogens Cas9 (SpCas9) descritos anteriormente en ocho loci de Nicotiana benthamiana usando expresión transitoria. LbCas12a mostró la actividad de mutagénesis promedio más alta en los loci analizados. Esta actividad también se confirmó en experimentos de transformación estable realizados en tres plantas modelo diferentes, a saber, N. benthamiana, Solanum lycopersicum y Arabidopsis thaliana. Para este último, los efectos mutagénicos colaterales fueron analizados en líneas segregantes sin la endonucleasa Cas12a, mediante secuenciación del genoma descartándose efectos indiscriminados. En conjunto, los resultados muestran que LbCas12a es una alternativa viable a SpCas9 para la edición genética en plantas. En una segunda parte, este trabajo describe un interruptor genético reversible destinado a controlar la expresión génica en plantas con mayor precisión que los sistemas inducibles tradicionales. Este interruptor, basado en el sistema de recombinación del fago PhiC31, fue construido como un dispositivo modular hecho de partes de ADN estándar y diseñado para controlar el estado transcripcional (encendido o apagado) de dos genes de interés mediante la inversión alternativa de un elemento regulador central de ADN. El estado del interruptor puede ser operado externa y reversiblemente por la acción de los actuadores de recombinación y su cinética, memoria y reversibilidad fueron ampliamente caracterizados en experimentos de transformación transitoria y estable en N. benthamiana. En conjunto, esta tesis muestra el diseño y la caracterización funcional de herramientas para la ingeniería del genómica y biología sintética de plantas que ahora ha sido completada con el sistema de edición genética CRISPR/Cas12a y un interruptor genético reversible y biestable basado en el sistema de recombinación del fago PhiC31. / [CA] La millora genètica vegetal té com a objectiu l'obtenció de plantes amb trets millorats o característiques noves que podrien ajudar a superar els objectius de sostenibilitat. Amb aquesta finalitat, la biotecnologia vegetal necessita incorporar noves eines d'enginyeria genètica que combinen una major precisió amb una major capacitat de millora. Les eines d'edició genètica recentment descobertes basades en la tecnologia CRISPR/Cas9 han obert el camí per modificar els genomes de les plantes amb una precisió sense precedents. D'altra banda, els nous enfocaments de biologia sintètica basats en la modularitat i l'estandardització dels elements genètics han permès la construcció de dispositius genètics cada vegada més complexos i sofisticats aplicats a la millora genètica vegetal. Amb l'objectiu final d'expandir la caixa d'eines biotecnològiques per a la millora vegetal, aquesta tesi descriu el desenvolupament i l'adaptació de dues noves eines: una nova endonucleasa específica de lloc (SSN) i un interruptor genètic modular per a la regulació de l'expressió transgènica . En una primera part, aquesta tesi descriu l'adaptació de CRISPR/Cas12a per a l'expressió en plantes i compara l'eficiència de les variants de Acidaminococcus (As) i Lachnospiraceae (Lb) Cas12a amb la ben establida Streptococcus pyogens Cas9 (SpCas9), en vuit loci de Nicotiana benthamiana usant expressió transitòria. LbCas12a va mostrar l'activitat de mutagènesi mitjana més alta en els loci analitzats. Aquesta activitat també es va confirmar en experiments de transformació estable realitzats en tres plantes model diferents, a saber, N. benthamiana, Solanum lycopersicum i Arabidopsis thaliana. Per a aquest últim, els efectes mutagènics col·laterals van ser analitzats en línies segregants sense l'endonucleasa Cas12a, mitjançant seqüenciació completa del genoma i descartant efectes indiscriminats. En conjunt, els resultats mostren que LbCas12a és una alternativa viable a SpCas9 per a l'edició genètica en plantes. En una segona part, aquest treball descriu un interruptor genètic reversible destinat a controlar l'expressió gènica en plantes amb major precisió que els sistemes induïbles tradicionals. Aquest interruptor, basat en el sistema de recombinació del bacteriòfag PhiC31, va ser construït com un dispositiu modular fet de parts d'ADN estàndard i dissenyat per controlar l'estat transcripcional (encès o apagat) de dos gens d'interès mitjançant la inversió alternativa d'un element regulador central d'ADN. L'estat de l'interruptor pot ser operat externa i reversiblement per acció dels actuadors de recombinació i la seva cinètica, memòria i reversibilitat van ser àmpliament caracteritzats en experiments de transformació transitòria i estable en N. benthamiana. En conjunt, aquesta tesi mostra el disseny i la caracterització funcional d'eines per a l'enginyeria del genòmica i biologia sintètica de plantes que ara ha sigut completat amb el sistema d'edició genètica CRISPR/Cas12a i un interruptor genètic biestable i reversible basat en el sistema de recombinació del bacteriòfag PhiC31. / [EN] Plant breeding aims to provide plants with improved traits or novel features that could help to overcome sustainability goals. To this end, plant biotechnology needs to incorporate new genetic engineering tools that combine increased precision with higher breeding power. The recently discovered genome editing tools based on CRISPR/Cas9 technology have opened the way to modify plant¿s genomes with unprecedented precision. On the other hand, new synthetic biology approaches based on modularity and standardization of genetic elements have enabled the construction of increasingly complex and refined genetic devices applied to plant breeding. With the ultimate goal of expanding the toolbox of plant breeding techniques, this thesis describes the development and adaptation to plant systems of two new breeding tools: a site-specific nuclease (SSNs), and a modular gene switch for the regulation of transgene expression. In a first part, this thesis describes the adoption of the SSN CRISPR/Cas12a for plant expression and compares the efficiency of Acidaminococcus (As) and Lachnospiraceae (Lb) Cas12a variants with the previously described Streptococcus pyogens Cas9 (SpCas9) in eight Nicotiana benthamiana loci using transient expression experiments. LbCas12a showed highest average mutagenesis activity in the loci assayed. This activity was also confirmed in stable genome editing experiments performed in three different model plants, namely N. benthamiana, Solanum lycopersicum and Arabidopsis thaliana. For the latter, off-target effects in Cas12a-free segregating lines were discarded at genomic level by deep sequencing. Collectively, the results show that LbCas12a is a viable alternative to SpCas9 for plant genome engineering. In a second part, this work describes the engineering of a new reversible genetic switch aimed at controlling gene expression in plants with higher precision than traditional inducible systems. This switch, based on the bacteriophage PhiC31 recombination system, was built as a modular device made of standard DNA parts and designed to control the transcriptional state (on or off) of two genes of interest by alternative inversion of a central DNA regulatory element. The state of the switch can be externally and reversibly operated by the action of the recombination actuators and its kinetics, memory, and reversibility were extensively characterized in N. benthamiana using both transient expression and stable transgenics. Altogether, this thesis shows the design and functional characterization of refined tools for genome engineering and synthetic biology in plants that now has been expanded with the CRISPR/Cas12a gene editing system and the phage PhiC31-based toggle switch. / Bernabé Orts, JM. (2019). Development and characterization of two new tools for plant genetic engineering: A CRISPR/Cas12a-based mutagenesis system and a PhiC31-based gene switch [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/133055 / Compendio

This masters thesis has a few objectives. One of them is to acquaint with the problems of genome engineering, especially with fragmentation of DNA, the macromolecule DNA, the methods for purification and separation of the nucleic acids, the enzymes used for modification of these acids, amplification and get to know with cluster and gradient analysis as well. The next aim is to peruse the existed application and compare it to the layout of the proposed application, that is the third aim. The last one from the objectives is the implementation and the report how was the application tested by the real data. The results will be discussed as well as the possibilities of the further extension.

Knowledge on the human genome and specific sequences associated with human diseases is continuously growing. The ability to connect human genetics to cellular mechanisms and physiology raises the need for medicine to get to gene specific therapeutics. In order to achieve gene-specific modification, tools are required to enable sequence-specific DNA cleavage. Not long ago, the RNA-guided endonuclease Cas9 was shown to effectively facilitate gene editing in humans. Cas9 endonuclease, which is naturally part of an adaptable bacterial immune system, can be easily adjusted to recognize and cleave specific DNA sequences in a 20 nt RNA-DNA complementary manner. The easy adjustability and high efficiency of Cas9 gave rise to hopes that this genome engineering tool could pave the way to ‘gene surgery’ in humans. However, to achieve DNA cleavage, the endonuclease and its guiding RNA need to be sufficiently accessible in the nucleus of target cells. Viruses, which evolution has made well adapted to transfer their own genetic information into cells can be exploited for transfer of foreign genetic material. Replication deficient retroviruses therefore represent interesting vehicles for gene delivery. Retroviruses preferentially incorporate their own genetic information in the form of RNA into viral particles. Typically, viral RNA of retroviruses is reverse transcribed into DNA during viral infection and integrated into host cell chromosomes. In this respect, integration-competent or integration-deficient lentiviral (HIV-derived) vectors (ICLV/IDLV) were reported to be efficient ‘gene shuttles’ for Cas9 delivery. In contrast, up to now Foamy viruses (FV), which represent a distinct subfamily in the family of retroviruses have not previously been tested for their efficiency to transduce CRISPR/Cas9 components. FV show several unique characteristics some of which make them interesting candidates for gene therapy, such as high transduction efficiency on a wide variety of human cell lines or a special capability to efficiently transfer and provide non-viral RNA in target cells. In this thesis the unique characteristic of FVs, which allow for the efficient transduction of non-viral RNAs, was exploited for transient FV mediated (TraFo) Cas9 expression. It is shown in this thesis that gene knock-out (KO) achieved with TraFo Cas9 particles appears to have several advantages over ICLV or IDLV mediated Cas9 transduction. In this work, it could be demonstrated that a single application of TraFo Cas9 supernatant results in high efficiency of GFP KO in osteosarcoma cells (U2OS). The efficiency of gene KO with TraFo Cas9 particles exceeded gene KO frequencies achieved with similar volumes of ICLV or IDLV supernatant for Cas9 transduction. In addition, transient Cas9 delivery achieved with TraFo particle supernatant resulted in remarkably reduced Cas9 off-target cleavage compared to corresponding infections with ICLV or IDLV particles. The results show, that TraFo Cas9 represents an interesting addition to the currently utilized methods for transient Cas9 delivery. One particular feature of TraFo particle transduction is especially noteworthy – TraFo mediated transduction does not depend on any particular adjustment on the encapsidated non-viral RNA sequence (such RNA only needs to be present in sufficient amounts during virus assembly) nor does it depend on any modification of viral proteins. The easy adaptability of TraFo mediated non-viral RNA transfer is an especially remarkable feature, since science continues to both developing new variants of Cas9 and continues to find new and interesting members of the pool of CRISPR enzymes. In this regard TraFo particles represent interesting vehicles to transiently provide mRNA transcripts of such new protein candidates in cells. The ability of TraFo particles to provide the RNA sequence needed to guide Cas9 (termed sgRNA) to its target DNA sequence in cells was additionally investigated. It was assumed that typically engaged RNA polymerase (RNAP) III transcription of sgRNAs hampers transduction with TraFo particles, since RNAP III-derived transcripts are not actively exported into the cytoplasm and show low stability. An additional CRISPR enzyme Csy4 was used, which is able to specifically cleave RNA. This enabled TraFo mediated transfer of RNAP II transcripts (with active nuclear export and higher stability than RNAP III transcripts) with embedded sgRNA sequences. It was demonstrated that a simultaneous infection of cells with TraFo particles providing bicistronic transcripts of Cas9 and Csy4 on the one side and RNAP II-derived transcripts with embedded sgRNA sequences on the other, enabled reasonable GFP gene inactivation in U2OS cells. Gene KO with RNAP II transcripts as a result significantly exceeds TraFo transduction of RNAP III-derived sgRNA. Interestingly, with regard to gene KO, it was found that de novo transcription of sgRNAs from viral DNA (by integration-competent or integration-deficient retroviral vector [ICRV/IDRV] transduction) when combined with TraFo Cas9 transduction was superior to a TraFo transduction of sgRNA transcripts. IDRV mediated transduction was optimized in order to minimize the risk of unfavorable genome modification of cells by viral DNA integration. By adding the coding sequence of a fluorescent marker to the viral vector, it was demonstrated that a smaller number of viral particles helps to significantly lower the frequency of viral DNA integration. In addition, the expression of a fluorescent marker opened up the opportunity to further reduce the cell fraction with continuous marker gene expression by flow cytometric cell sorting. The IDRV/ICRV sgRNA and TraFo Cas9 delivery system was then challenged for use on immortalized and primary T cells. Primary T cells represent interesting targets for genetic engineering since modified T cells can be utilized as ‘living drugs’ (by expression of chimeric antigen receptors – CARs) against cancer cells. Efficient gene inactivation was observed on the immortalized T cell line – Jurkat. Transduction of primary T cells pointed to certain restrictions of the split two-virus delivery system for sgRNA and Cas9 transduction. However, despite certain limitations, it was possible to demonstrate that this FV-derived Cas9 delivery system is also feasible on primary tissue, and further optimization could make it an interesting alternative delivery method for CAR therapy. The ability of IDRV vector genomes to provide repair template donor DNA to induce homologous recombination (HR) was additionally investigated. DNA double-strand breaks in eukaryotic cells are typically repaired by the error prone non-homologous end joining pathway (often leading to frame-shift mutations by small insertions or deletions) or HR. Delivery of a homologous DNA sequence during DNA cleavage enables site-specific integration of exogenous DNA sequences. The work of this thesis showed that IDRV vector genomes providing repair template donor DNA allow for HR in a homology length dependent manner. Besides the length of homology, it was also observed, that the length of sequence which should be integrated (KI) remarkably influences the frequency of HR. HR is therefore engaged significantly more frequently if single nucleotides, rather than a whole gene, are provided as sequences within a repair template. In addition, viral vectors were augmented with additional fluorescent marker sequences. It could subsequently be demonstrated that the majority of cells showed accurate sequence-specific DNA integration. Furthermore, several indications were found, which lead to the assumption that the ratio of KI to homologous sequence markedly influences the accuracy of HR. Using the previously obtained knowledge it was further possible to tag an essential human protein by FV vector mediated transient Cas9 and repair template transduction. It was found that the large packaging capacity of FV vectors can be exploited to enable selection and flow cytometric sorting of cells with correct site-specific DNA integration. In summary, the results of this thesis demonstrate for the first time that FV mediated non-viral mRNA Cas9 transduction in combination with retroviral delivery of sgRNA (and repair template sequence) are a promising basis for several different interesting applications with relevance for not only basic research, but also for gene therapy.:1. Introduction 1 1.1 Gene therapy 1 1.2 Viral vectors for gene therapy 2 1.3 History of retroviral research 2 1.4 Taxonomy of Retroviruses 3 1.5 Foamy Viruses 4 1.5.1 Morphology of Foamy Virus 6 1.5.2 Foamy Virus replication 7 1.5.3 Foamy virus proteins, as part of a viral vector system 10 1.6 Genetic engineering 14 1.6.1 ‘DNA scissors’ – Zinc-finger and Transcription-activator like effector nucleases 15 1.6.2 History of CRISPR/Cas9 as a tool for genetic engineering 16 1.7 CRISPR/Cas immunity in prokaryotes 18 1.8 CRISPR/Cas9 functioning 21 1.9 Double-strand break repair in eukaryotic cells 21 1.9.1 Classical NHEJ 23 1.9.2 Homologous recombination 24 1.9.3 DSB repair in vertebrates 26 1.10 DSBs in context of CRISPR/Cas9 cleavage 27 1.11 Thesis Aim: CRISPR/Cas9 transduction with FV particles 28 2. Materials and Methods 30 2.1 Materials 30 2.1.1 Chemicals 30 2.1.2 Buffers and Solutions 30 2.1.3 Bacterial Growth Media 33 2.1.4 Cell Culture Media 34 2.1.5 Antibodies 34 2.1.6 Enzymes 35 2.1.7 Commercial Kits and additional reagents 36 2.1.8 Size Markers 36 2.1.9 Antibiotics 36 2.1.10 Bacterial strains 37 2.1.11 Cell lines 37 2.1.12 Devices and Software 37 2.1.13 Oligonucleotides 38 2.1.14 Plasmids 46 2.1.15 sgRNA sequences 56 2.1.16 Consumable material 57 2.2 Molecular Biology Methods 58 2.2.1 Restriction of DNA 58 2.2.2 Polymerase chain reaction 59 2.2.3 Gibson assembly 60 2.2.4 Agarose gel electrophoresis 60 2.2.5 Ligation 61 2.2.6 Cultivation of bacteria 62 2.2.7 Transformation 62 2.2.8 Plasmid Preparation 63 2.2.9 Sequencing 65 2.3 Cell culture methods 66 2.3.1 Passaging of cells 66 2.3.2 Cell counting 66 2.3.3 Freezing and thawing of cells 66 2.3.4 Seeding and fixation of cells for microscopy 67 2.4 Virological Methods 67 2.4.1 Polyethyleneimine transfection 67 2.4.2 Integration-competent, integration-deficient and ‘transient’ retroviral vectors 68 2.4.3 Infection of adherent cells 70 2.4.4 Infection of suspension cells 71 2.4.5 Flow cytometry 72 2.4.6 Multiplicity of infection (MOI) 72 2.4.7 Particle preparation 73 2.5 Nucleic acid composition in viral particles and culture cells 73 2.5.1 Isolation of total RNA from viral particles 73 2.5.2 RNA isolation from culture cells 73 2.5.3 Reverse transcription of viral or cellular RNA 73 2.5.4 DNA isolation from culture cells 74 2.5.5 Quantitative PCR (qPCR) analysis 74 2.5.6 T7 endonuclease assay 75 2.6 Protein biochemistry methods 76 2.6.1 Cell lysates 76 2.6.2 Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) 76 2.6.3 Semi-dry Western Blot 77 2.6.4 Immunodetection 78 2.6.5 Stripping of Western blot membranes 78 2.6.6 Immunostaining of cells for FACS analysis 78 2.7 Microscopy methods 79 2.7.1 Fluorescence microscopy 79 2.7.2 Confocal Laser scanning Microscopy (CLSM) 79 2.7.3 Live-cell imaging 79 3. Results 80 3.1 Transient foamy virus transduction of non-viral mRNA transcripts 80 3.2 Transient foamy virus transduction of Cas9-encoding mRNA transcripts 81 3.3 Cas9-encoding nucleic acids and their ‘effects’ in cells after retroviral transduction 84 3.4 Off-target analysis after TraFo Cas9 delivery 87 3.5 Transient fomy virus transduction of Cas9 and sgRNAs 89 3.6 Retroviral vectors providing sgRNAs and a fluorescent protein 92 3.6.1 Gene knock-out with retroviral vectors under saturated conditions 92 3.6.2 MOI adjusted ID sgRNA vector supernatants for comparison of residual vector integration 94 3.6.3 Gene knock-out in murine embryonic fibroblasts 95 3.7 Influence of Cas9 expression on IDRV vector genome integration 96 3.8 TraFo Cas9 mediated T cell receptor knock-out in immortalized and primary human T cells 97 3.9 Homology-directed repair after FV CRISPR/Cas9 mediated double-strand breaks 99 3.9.1 Length of homologous donor DNA and its influence on HDR 100 3.9.2 Effect of freezing viral supernatants on the frequency of HDR 102 3.9.3 Effect of donor DNA mismatches on the frequency of HDR 104 3.10 Investigation on donor DNA integration with additional fluorescent markers 105 3.11 Lentiviral and foamyviral transduction of HDR donor DNA 107 3.12 HDR mediated single nucleotide substitutions after TraFo CRISPR/Cas9 delivery 109 3.13 Tagging of an endogenous protein after TraFo CRISPR/Cas9 delivery 111 3.13.1 Specific CRISPR/Cas9 mediated cleavage of endogenous hPLK1 gene 111 3.13.2 Homology-directed repair of the hPLK1 gene for endogenous gene tagging 113 3.13.3 Confocal fluorescence microscopy analysis of GFP-Plk1 HeLa cell populations 118 4. Discussion 120 4.1 Genetic engineering – potential and risks 120 Chapter I Transient FV vectors – mRNA delivery vehicles for CRISPR/Cas9 mediated gene editing 122 4.2 Non-viral Cas9-encoding mRNA transfer in foamy virus particles 122 4.2.1 Fate of Cas9-encoding nucleic acids in cells after TraFo Cas9 transduction 124 4.2.2 Potential adjustments to further improve TraFo Cas9 transduction 125 4.2.3 Lentiviral in contrast to TraFo transduction of Cas9-encoding nucleic acids 126 4.3 Efficiency of Cas9-mediated gene knock-out with different retroviral vectors 127 4.4 Type of retroviral Cas transduction and its influence on the specificity of Cas9 cleavage 127 4.5 Alternative approaches to deliver Cas9-encoding mRNA in human cells 129 4.6 Transient sgRNA transduction with TraFo particles 131 Chapter II Delivery of foreign DNA with FV-derived vectors – enabling gene knock-out and homology-directed repair 133 4.7 Gene inactivation by TraFo Cas9 transduction and sgRNA expression from retroviral vector genomes 133 4.7.1 Gene editing in immortalized and primary T cells 135 4.8 Homology-directed repair with IDRV genomes 137 4.8.1 The influence of the length of sequence homology on HR 138 4.8.2 The influence of freezing viral supernatants on HR 139 4.8.3 Widening the applicability of TraFo vector particles for improved HR 140 4.8.4 The influence of mismatching nucleotides on HR 140 4.8.5 Visualization of inaccurate HR or additional dsDNA integration 141 4.8.6 The influence of the ratio of knock-in and homologous sequence on the accuracy of HR 142 4.8.7 Alternatives to double-stranded donor DNA 143 4.9 Endogenous gene tagging with IDPV donor DNA transduction 145 4.9.1 Alternative approaches for endogenous protein tagging 146 5. Conclusion 148 6. Summary 150 6.1 Summary 150 6.2 Zusammenfassung 153 7. Supplementary 157 8. References 159 9. Appendices 182 9.1 Indices 182 9.1.1 Abbreviations 182 9.1.2 Index of Figures 185 9.1.3 Index of Tables 187 9.2 Curriculum Vitae 188 9.3 Publication Record 189 9.4 Congress Contributions 189 9.5 Patent Applications 189 10. Statement of Authorship 190