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Search for Patterns of DNA Secondary Structures and Histone Modifications

Student: Arina Nostaeva

Supervisor: Maria Poptsova

Faculty: Faculty of Computer Science

Educational Programme: Data Analysis for Biology and Medicine (Master)

Final Grade: 8

Year of Graduation: 2020

Thesis on the topic: "Search for patterns of DNA secondary structures and histone modifications." In the work - 55 pages containing 24 figures, 11 tables, 52 bibliographic sources, 1 appendix. Abstract: Advances in experimental technology for the detection of G-quadruplex have made it possible to detect G4 at the genome level. It has been shows that G4 play an important role in many genomic processes. Nevertheless, the relationship of G4 with the epigenetic code is poorly understood. In this work, we searched for the associations of G-quadruplexes with three histone labels - H3K4me3, H3K9ac and H3K27ac, and tested hypotheses such as the presence of differences in the motifs of G-quadruplexes enriched in common and tissue-specific histone labels, and the presence of differences in the distribution of G-quadruplex sequences between these sets. Keywords: G-quadruplexes, histone marks, epigenetics, machine learning. Object of study: G-quadruplexes, histone marks H3K4me3, H3K9ac and H3K27ac. Subject of study: association of G-quadruplexes and histone marks. The work contains the introduction, 7 chapters, conclusion, bibliography and appendix. The introduction includes the introduction to G-quadruplexes, their role in the genome, and problem statement. The first chapter is devoted to review of detection methods for G-quadruplexes and the study of data on them. The second chapter contains information on histone label data and methods for working with them. The third chapter describes the machine learning methods in this study and the results on them. The fourth chapter contains the description and analysis of the associations between G-quadruplexes and histone labels. The fifth chapter is devoted to finding the connection between G-quadruplexes and histone marks inside promoters. The sixth chapter describes the validation of the results obtained in the previous chapter. The seventh chapter contains information on the analysis of transcription factor enrichment in sets of G-quadruplex sequences. In conclusion, the main conclusions are presented: the brief description of the conclusions of the chapters, the summary of the results in the form of the need for further research, and the description of the plans. The appendix contains graphs not included in the text of the fifth chapter.

Full text (added May 22, 2020)

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