| Abstract [eng] |
SUMMARY Computational Mapping Of Nucleosomes In Human Genome: Occupancy At The Elements Of A Regulatory Build Gabriele Stockunaite Master Thesis Systems biology master program Vilnius university This work investigates patterns of nucleosome occupancy by measuring the base pair distances between nucleosomes and regulatory elements and TSS in the human genome. The goal of this work is to identify nucleosome occupancy patterns in regulatory regions in relation to the activity of the genes that are regulated. It was done by collecting coordinates of regulatory elements, TSS and nucleosome positions for human organism from selected existing data on academic databases. Then, creating a table of distances between them. Then, performing analysis of distance distributions between nucleosomes, closest TSS and closest regulatory element coordinates (or positions) to confirm hypothesis that patterns exist by using unsupervised learning algorithms – PCA, UMAP and t-SNE. Finally, perform gene overexpression analysis on the classified gene groups to identify any common biological process themes. The conclusions were made that most likely distance for promoters, which in relation to nucleosome, tend to be downstream such that distance N – Reg is positive and between 1000 to 3000 bps. Second tendency is that largest concentration of Transcription factor binding site regulatory elements is seen in +1000/-1000 region around the nucleosome. However, contrary to what was expected the results show that various types of regulatory elements can have different types of distance distributions independently from their type. Finally, 5 profiles of Reg-N-TSS distance distributions were found and for each gene group an overexpression analysis was done finding dominant topics for identified profiles such as participation in metal ions metabolism processes or immune system related biological processes and gene product pathways. |
