SHORT TANDEM REPEAT ANALYSIS IN RECOMBINATION HOTSPOTS ACROSS THE HUMAN GENOME.

Mehdin MASINOVIC

Bachelor's thesis

Short tandem repeat analysis of recombination hotspots

Abstract:

Short tandem repeats are one of the most abundant tandem repeat types and are an important source of genetic variation. Comparative studies have analyzed their abundance in promoters, genes, and other relevant regions in the human genome, but short tandem repeats in recombination hotspots have yet to be fully characterized. Using the R package entitled STRAH, we analyzed the frequency of 310 distinct short tandem repeats in 37527 recombination hotspots across the human reference genome. We generated pattern-specific comparisons for all repeat types among recombination hotspots, regions directly surrounding them, and the remaining genomic region of the human genome. We detected that C/G-rich repeats tend to be enriched in recombination hotspots, observed that A/T-rich repeats are more enriched in regions unrelated to recombination, and found that repeats are present in very low numbers if they do not contain consecutively repeated DNA bases. Collectively, our results provide a standardized, genome-wide characterization of short tandem repeats in recombination hotspots and their surrounding regions, highlight pattern-specific differences that depend on repeat length and repeat type, and give insight into short tandem repeat enrichment in relation to recombination hotspots across the human genome.

Language used: English

Date on which the thesis was submitted / produced: 2. 11. 2020

Thesis defence

• Date of defence: 27. 11. 2020
• Supervisor: doc. Dr. Irene Tiemann-Boege

UNIVERSITY OF SOUTH BOHEMIA IN ČESKÉ BUDĚJOVICE

Faculty of Science

Bachelor programme / field:
Applied Informatics / Bioinformatics