Reconstruction of segmental duplication rates and associated genomic features by network analysis

Abstract

AO_SCPLOWBSTRACTC_SCPLOWSegmental duplications (SDs) are long genomic duplications fixed in a genome. SDs play an important evolutionary role: entire genes together with regulatory sequences can be duplicated. Ancestral segmental duplications gave rise to genes involved in human brain development, as well as provided sites for further genomic rearrangements. Some duplicated loci were extensively studied, however, universal principles or biological factors of SDs propagation are not fully described yet. Segmental duplications can be arranged into a network where edges correspond to real duplication events, while nodes to affected genomic sites. This gave us an opportunity to estimate how many duplications happened in each locus. We studied genomic features associated with increased duplication rates with especial interest in high-copy repeats distribution relative to duplicated regions breakpoints. Our comprehensive study of genomic features associated with duplications and those associated with increased duplication rates allowed us to identify several biological factors affecting a segmental duplication process. We found genomic features associated with increased duplication rates, three signatures of duplication process and associations of SDs with different classes of high-copy repeats.