Copy Number Variants and Segmental Duplications Show Different Formation Signatures

TL;DR

This study investigates the formation mechanisms of Copy Number Variants and Segmental Duplications, revealing distinct patterns and associations with genomic elements, and suggesting different underlying processes for their formation.

Contribution

It provides a comparative analysis of CNVs and SDs, highlighting their different formation signatures and associations with genomic repeats, which advances understanding of their evolutionary mechanisms.

Findings

SDs are significantly co-localized, following a power-law distribution.

Older SDs have a stronger association with Alu elements than younger SDs.

CNVs show no association with Alu elements, unlike SDs.

Abstract

In addition to variation in terms of single nucleotide polymorphisms (SNPs), whole regions ranging from several kilobases up to a megabase in length differ in copy number among individuals. These differences are referred to as Copy Number Variants (CNVs) and extensive mapping of these is underway. Recent studies have highlighted their great prevalence in the human genome. Segmental Duplications (SDs) are long (>1kb) stretches of duplicated DNA with high sequence identity. First, we analyzed the co-localization of SDs and find that SDs are significantly co-localized with each other, resulting in a power-law distribution, which suggests a preferential attachment mechanism, i.e. existing SDs are likely to be involved in creating new ones nearby. Second, we look at the relationship of CNVs/SDs with various types of repeats. We we find that the previously recognized association of SDs with Alu elements is significantly stronger for older SDs and is sharply decreasing for younger ones. While it might be expected that the patterns should be similar for SDs and CNVs, we find, surprisingly, no association of CNVs with Alu elements. This trend is consistent with the decreasing correlation between Alu elements and younger SDs, the activity of Alu elements has been decreasing and by now it they seem no longer active. Furthermore, we find a striking association of SDs with processed pseudogenes suggesting that they may also have mediated SD formation. Moreover, find strong association with microsatellites for both SDs and CNVs that suggests a role for satellites in the formation of both.