Predicting Recombination Hotspots in Yeast Based on DNA Sequence and Chromatin Structure

Meiotic recombination does not occur evenly across the genome, but instead occurs at relatively high frequencies in some genomic regions (hotspots) and relatively low frequencies in others (coldspots). Recombination depends not only on sequence features, but also on chromatin structure. Identification and characterization of hotspots and coldspots are considerably significant as the information about hot/cold spots would shed light on the mechanism of recombination and genome evolution. In this study, we analyzed the correlation between recombination and nucleosome occupancy, and presented a model for predicting recombination hotspots based on the sequence and nucleosome occupancy in yeast. Our results show that the regions with high nucleosome occupancy have high recombination rate in the yeast genome and an improved prediction accuracy of 81.6% is achieved when nucleosome occupancy is used as an additional feature. Keywords: Increment of diversity, nucleosome occupancy, quadratic discriminant analysis, recombination hotspots, tetranucleotide frequencies.