An Investigation of Segmental Duplications across Topologically Associating Domains

Abstract

High-throughput chromosome conformation capture (Hi-C) reveals organization within genomes. Topologically associating domains (TADs) make up one level of organization and are identified by applying algorithms to Hi-C data. TADs have boundaries disrupted by structural variants (SVs), hypothesized to form due to recombination that occurs between segmental duplications (SDs). Little research is available about the effects of SDs at TAD boundaries. This project aimed to understand the distribution of SDs near TADs and determine any overlap between the two features. We analyzed public data and found SDs to have low breakpoint frequency and coverage at TAD boundaries. We then processed a new set of Hi-C data and found most SDs had a minimal distance of 200 kb or closer to TADs with a modest bimodal distribution. Of the total SDs analyzed, fewer than half had at least one overlap within a TAD. Further statistical analysis must be done as we only conducted a preliminary investigation.