Understanding the mechanism of recombination has important implications for genome evolution and genomic variability. The work presented in this thesis studies the properties of recombination by investigating the effects it has on genome evolution in humans and dogs. Using alignments of human genes with chimpanzee and macaque orthologues we studied substitution patterns along the human lineage and scanned for evidence of positive selection. The properties mirror the situation in human non-coding sequences with the fixation bias ‘GC-biased gene conversion’ (gBGC) as a driving force in the most rapidly evolving regions. By assigning candidate genes to distinct classes of evolutionary forces we quantified the extent of those genes affected by gBGC to 20%. This suggests that human-specific characters can be prompted by the fixation bias of gBGC, which can be mistaken for selection. The gene PRDM9 controls recombination in most mammals, but is lacking in dogs. Using whole-genome alignments of dog with related species we examined the effects of PRDM9 inactivation. Additionally, we analyzed genomic variation in the genomes of several dog breeds. We identified that non-allelic homologous recombination (NAHR) via sequence identity, often GC-rich, creates structural variants of genomic regions. We show that these regions, which are also found in dog recombination hotspots, are a subset of unmethylated CpG-islands (CGIs). We inferred that CGIs have experienced a drastic increase in biased substitution rates, concurrent with a shift of recombination to target these regions. This enables recurrent episodes of gBGC to shape their distribution. The work presented in this thesis demonstrates the importance of meiotic recombination on patterns of molecular evolution and genomic variability in humans and dogs. Bioinformatic analyses identified mechanisms that regulate genome composition. gBGC is presented as an alternative to positive selection and is revealed as a major factor affecting allele configuration and the emergence of accelerated evolution on the human lineage. Characterization of recombination-induced sequence patterns highlights the potential of non-methylation and establishes unmethylated CGIs as targets of meiotic recombination in dogs. These observations describe recombination as an interesting process in genome evolution and provide further insights into the mechanisms of genomic variability.

The advances of high-throughput technologies, such as next-generation sequencing and microarrays, have rapidly improved the accessibility of molecular profiles in tumor samples. However, due to the immaturity of relevant theories, analyzing these data and systematically understanding the underlying mechanisms causing diseases, which are essential in the development of therapeutic applications, remain challenging. This dissertation attempts to clarify the effects of DNA copy number alterations (CNAs), which are known to be common mutations in genetic diseases, on steady- state gene expression values, time-course expression activities, and the effectiveness of targeted therapy. Assuming DNA copies operate as independent subsystems producing gene transcripts, queueing theory is applied to model the stochastic processes representing the arrival of transcription factors (TFs) and the departure of mRNA. The copy-number-gene-expression relationships are shown to be generally nonlinear. Based on the mRNA production rates of two transcription models, one corresponding to an unlimited state with prolific production and one corresponding to a restrictive state with limited production, the dynamic effects of CNAs on gene expression are analyzed. Simulations reveal that CNAs can alter the amplitudes of transcriptional bursting and transcriptional oscillation, suggesting the capability of CNAs to interfere with the regulatory signaling mechanism. With this finding, a string-structured Bayesian network that models a signaling pathway and incorporates the interference due to CNAs is proposed. Using mathematical induction, the upstream and downstream CNAs are found to have equal influence on drug effectiveness. Scoring functions for the detection of unfavorable CNAs in targeted therapy are consequently proposed. Rigorous experiments are keys to unraveling the etiology of genetic diseases such as cancer, and the proposed models can be applied to provide theory-supporting hypotheses for experimental design.

Developmental disorders including: autism, intellectual disability, and congenital abnormalities are present in 3-8% of live births and display a huge amount of phenotypic and genetic heterogeneity. Traditionally, geneticists have identified individual monogenic diseases among these patients but a majority of patients fail to receive a clinical diagnosis. However, the genomes of these patients frequently harbour large copynumber variants (CNVs) but their interpretation remains challenging. Using pathway analysis I found significant functional associations for 329 individual phenotypes and show that 39% of these could explain the patients’ multiple co-morbid phenotypes; and multiple associated genes clustered within individual CNVs. I showed there was significantly more such clustering than expected by chance. In addition, the presence of a multiple functionally-related genes is a significant predictor of CNV pathogenicity beyond the presence of known disease genes and size of the CNV. This clustering of functionally-related genes was part of a broader pattern of functional clusters across the human genome. These genome-wide functional clusters showed tissuespecific expression and some evidence of chromatin-domain level regulation. Furthermore, many genome-wide functional clusters were enriched in segmental duplications making them prone to CNV-causing mutations and were frequently seen disrupted in healthy individuals. However, the majority of the time a pathogenic CNV affected the entire functional cluster, where as benign CNVs tended to affect only one or two genes. I also showed that patients with CNVs affecting the same functional cluster are significantly more phenotypically similar to each other than expected even if their CNVs do not affect any of the same genes. Lastly, I considered one of the major limitations in pathway analysis, namely ascertainment biases in functional information due to the prioritization of genes linked to human disease, and show how the modular nature of gene-networks can be used to identify and prioritize understudied genes.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第21990号 / 医博第4504号 / 新制||医||1037(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 武藤 学, 教授 松田 文彦, 教授 小川 誠司 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

This master thesis deals with analysis of structural variation of genome and with methods of its sequencing across all generations. Subsequently it contains a description of copy number variation and methods of its detection. The experimental part focuses on algorithm proposal for CNV detection according analysis and testing of uneven coverage in genome, variable representation of GC content and distance of sequence reads. Finally, the algorithm for detecting copy number variation is tested on genomic data of bacteria Klebsiella pneumoniae.

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Indiana University-Purdue University Indianapolis (IUPUI) / Because colorectal cancer (CRC) is the fourth most common cancer and the second leading cause of cancer death in the US, identifying biomarkers that might inform disease prevention and early diagnosis is of great public health importance. Mitochondria are key cytoplasmic organelles containing an independent genome, i.e., mitochondrial DNA (mtDNA). It has been increasingly recognized that mtDNA copy number (mtDNAcn) is a biomarker for mitochondrial function and cellular oxidative stress. To date, the few studies that have assessed associations between mtDNAcn and CRC outcomes have yielded inconsistent findings. Further, no epidemiologic study has examined the relationship between insulinemic potential of lifestyle and mtDNAcn. Therefore, in this dissertation, three studies were conducted using data from the Nurses’ Health Study and the Health Professionals Follow-Up Study. First, the association between pre-diagnostic leukocyte mtDNAcn and CRC risk was studied in a nested casecontrol study (324 cases/658 controls). Lower mtDNAcn was significantly associated with increased risk of CRC and proximal colon cancer. That inverse association remained significant among individuals with ≥ 8 years’ follow-up since blood collection, suggesting that mtDNAcn might serve as a long-term predictor of CRC risk. Second, possible associations of pre-diagnostic mtDNAcn with overall and CRC-specific survival were examined among 587 CRC patients. MtDNAcn was not significantly associated with survival overall or in subgroups by cancer location, grade, or stage. Among current smokers, there was an inverse association between one standard deviation (SD) decrease in mtDNAcn and increased overall death risk. Among patients diagnosed at or before 70.5 years of age and those with anti-inflammatory diets, reduced mtDNAcn was associated with lower CRC-specific death risk. Lastly, the cross-sectional association between empirical lifestyle index for hyperinsulinemia (ELIH) and mtDNAcn was investigated among 2,835 subjects without major chronic diseases (cancers, diabetes, and cardiovascular diseases). A significant inverse association was found: least-squares means ± SD of mtDNAcn z-score decreased dramatically across ELIH quintiles. Overall, the findings from this dissertation will contribute to the evaluation of mtDNAcn as a potential biomarker for CRC risk and prognosis, and inform future interventions designed to reduce the insulinemic potential of lifestyle factors to preserve mitochondrial function. / 2022-04-06

The introduction of new genetic information into microbial production organisms is one of the keystones of modern biotechnology, this can be achieved i.a. by the introduction of plasmids. Extrachromosomal plasmids replicate autonomously and show a plasmid-specific plasmid copy number (PCN) per cell. In growing cells, a fine-tuned copy number regulation is achieved by a tightly controlled balance of the initiator of replication and the repressor. In theory, the plasmid copy number can be influenced at will by a targeted manipulation of this balance. In order to allow transient PCN changes in growing cells, an inducible, precisely adjustable strategy is needed. In this thesis, cop, the repressor of plasmid replication of pE194, was over-expressed independently from the native regulatory system. The developed overexpression system was used to force a severe imbalance in favor of the repressor, therefore intentionally driving the loss of replicating plasmid from the population. As a consequence, cells that previously incorporated the plasmid into their genome gain a selective advantage as they stably inherit an antibiotic resistance encoded on the now non-replicative plasmid. In established genomic modification strategies, a forced imbalance is dependent on elevated temperatures. However, the established protocols for genomic modifications are time-consuming and require extensive screening for clones with the desired genotype. The aim of this thesis was to conceive and establish a novel vector for a reliable, faster and more efficient protocol with a minimal screening requirement. The promotor controlling the repF-cop operon was characterized by supplying the repressor Cop in trans, revealing a complete repression at high Cop concentrations. Furthermore, the gradual dose-dependency of this repression could be shown. Over several intermediate steps, the novel All-in-one vector pBAio was designed. With this vector, the PCN in growing cells can be controlled and even fine-tuned. Forcing a complete stop of plasmid replication, resulted in a 100% plasmid integration rate that eliminated the need for integrand screening and increased the efficiency (i.e. mutant to wild type ratio). The new, pBAio-based protocol allows for fast and efficient markerless genomic modification in different, industrially relevant Bacillus sp..

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第21300号 / 医博第4389号 / 新制||医||1030(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 戸井 雅和, 教授 小川 修, 教授 武田 俊一 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM