Under most conditions, meiotic recombination is essential for ensuring that organisms adapt to ever changing biotic and abiotic conditions and, as such, it shapes evolutionary change within and between species. The interplay between selection and recombination plays a role shaping levels diversity within populations. Remarkably, recombination is itself an evolving trait that varies at many levels: between distant species of eukaryotes, between closely related species and among populations (and individuals) of the same species. Recombination rates also vary across genomes. Most of the causes and mechanisms of this plasticity in recombination rates and distribution are not clearly understood. Also, our understanding of how this variability in recombination rates influences levels of diversity within populations and across genomes is incomplete. Here, I present a study combining molecular genetics with bioinformatic techniques to characterize recombination landscapes in Drosophila melanogaster. I present a model that accounts for a significant fraction of the variation in crossover rates across the genome of Drosophila melanogaster. Our predictive model suggests that crossover distribution is influenced by both meiosis-specific chromatin dynamics and very local constitutively open chromatin associated with DNA motifs that prevent nucleosome stabilization. I also present a novel method for genomic scans to identify recent events of adaptation in using nucleotide diversity data. In addition, I characterized variability in recombination rates in different populations of D. melanogaster and detected that the highest degree of variability in recombination rates across the genome is associated with intermediate genomic scales, and that this intermediate scale also plays a major role in explaining differences in recombination among populations. Our report is the first linking variation in recombination rates across genomes (genomic) and among populations (evolutionary), possibly suggesting a common mechanistic/genomic cause. Finally, I present preliminary data of the first large-scale project to study the effects of multiple environmental conditions in recombination rates at genome-wide level. In conclusion, these studies provide a new framework to investigate variation in recombination rates and to understand the genomic causes and evolutionary consequences.

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<p>Chromatin structure plays an important role in gene regulation, especially in differentiating the diverse cell types in humans. In this dissertation, we analyze the nucleosome positioning and open chromatin profiles genome-wide and investigate the relationship with transcription initiation, the activity of regulatory elements, and expression levels. We mainly focus on the results of DNase-seq experiments, but also employ annotations from MNase-seq, FAIRE-seq, ChIP-seq, CAGE, and RNA microarrays. Our methods are based on computational approaches including managing large data sets, statistical analysis, and machine learning. We find that different transcription initiation patterns lead to distinct chromatin structures, suggesting diverse regulatory strategies. Moreover, we present a tool for comparing genome-wide annotation tracks and evaluate DNase-seq against a unique assay for detecting open chromatin. We also demonstrate how DNase-seq can be used to successfully predict rotationally stable nucleosomes that are conserved across cell types. We conclude that DNase-seq can be used to study genome-wide chromatin structure in an effort to better understand how it regulates gene expression.</p> / Dissertation

Cis-regulatorische Elemente wie Promotoren und Enhancer, die die Regulation der Transkription von Genen steuern, befinden sich in Regionen des dekondensierten Chromatins. DNase-seq und ATAC-seq sind weit verbreitete Verfahren, um solche offenen Chromatinregionen genomweit zu untersuchen. Die einzel-Nukleotid-Auflösung von DNase-seq wurde des Weiteren genutzt, um Transkriptionsfaktor-Bindungsstellen (TFBS) in regulatorischen Regionen durch TF-Footprinting zu bestimmen. Kürzlich durchgeführte Studien haben jedoch gezeigt, dass DNase I einen Sequenzbias aufweist, welcher nachteilige Auswirkungen auf die Footprinting-Effizienz hat. Auch wurden das Footprinting und die Auswirkungen des Sequenzbias auf ATAC-seq noch nicht umfassend untersucht. In dieser Arbeit nehme ich einen systematischen Vergleich der beiden Methoden vor und zeige, dass die beiden Methoden unterschiedliche Sequenzbiases haben und korrigiere diese protokollspezifischen Biases beim Footprinting. Der Einfluss von Bias-Korrekturen der Footprinting Ergebnisse ist für DNase-seq größer als für ATAC-seq, und Footprinting mit DNase-seq führt zu besseren Ergebnissen in unserer Datensätze. Trotz dieser Unterschiede zeige ich, dass die Integration replizierter Experimente die Ableitung von qualitativ hochwertigen Footprints ermöglicht, wobei die beiden Techniken weitgehend übereinstimmen. Diese Techniken werden ferner eingesetzt, um die cis-regulatorischen Elemente zu charakterisieren, die die Embryogenese der Fruchtfliege Drosophila melanogaster bestimmen. Durch die Verwendung von Embryonen die sich im richtigen Entwicklungsstadium befinden, sowie gewebespezifischer Kernsortierung mit offenem Chromatin-Profiling können zeitlich und gewebespezifisch aufgelöste vermeintliche cis-regulatorische Elemente definiert werden. Zusammengenommen demonstrieren diese Analysen die Fähigkeit der offenen Chromatin-Profilierung und der Computeranalyse zur Aufklärung der Mechanismen der Genregulation. / Cis-regulatory elements such as promoters and enhancers, that govern transcriptional gene regulation, reside in regions of open chromatin. DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBS) in regulatory regions through TF footprinting. However, recent studies have demonstrated the sequence bias of DNase I and its adverse effects on footprinting efficiency. Furthermore, footprinting and the impact of sequence bias have not been extensively studied for ATAC-seq. In this thesis, I undertake a systematic comparison of the two methods and demonstrate that the two methods have distinct sequence biases and correct for these protocol-specific biases when performing footprinting. The impact of bias correction on footprinting performance is greater for DNase-seq than for ATAC-seq, and footprinting with DNase-seq leads to better performance in our datasets. Despite these differences, I show that integrating replicate experiments allows the inference of high-quality footprints, with substantial agreement between the two techniques. These techniques are further employed to characterize the cis-regulatory elements governing the embryogenesis of a complex organism, the fruit fly Drosophila melanogaster. Combining tight staging of embryos and tissue-specific nuclear sorting with open chromatin profiling, enables the definition of temporally and tissue-specifically resolved putative cis-regulatory elements. Taken together, these analyses demonstrate the power of open chromatin profiling and computational analysis in elucidating the mechanisms of transcriptional gene regulation.

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