Quantitative assessment reveals the dominance of duplicated sequences in germline-derived extrachromosomal circular DNA

Abstract

Extrachromosomal circular DNA (eccDNA) originates from linear chromosomal DNA in various human tissues under physiological and disease conditions. The genomic origins of eccDNA have largely been investigated using in vitro–amplified DNA. However, in vitro amplification obscures quantitative information by skewing the total population stoichiometry. In addition, the analyses have focused on eccDNA stemming from single-copy genomic regions, leaving eccDNA from multicopy regions unexamined. To address these issues, we isolated eccDNA without in vitro amplification (naïve small circular DNA, nscDNA) and assessed the populations quantitatively by integrated genomic, molecular, and cytogenetic approaches. nscDNA of up to tens of kilobases were successfully enriched by our approach and were predominantly derived from multicopy genomic regions including segmental duplications (SDs). SDs, which account for 5% of the human genome and are hotspots for copy number variations, were significantly overrepresented in sperm nscDNA, with three times more sequencing reads derived from SDs than from the entire single-copy regions. SDs were also overrepresented in mouse sperm nscDNA, which we estimated to comprise 0.2% of nuclear DNA. Considering that eccDNA can be integrated into chromosomes, germline-derived nscDNA may be a mediator of genome diversity.

Evolutionary Honing in and Mutational Replacement: How Long-Term Directed Mutational Responses to Specific Environmental Pressures Are Possible

“…Evidence exists consistent with the operation of the focal mechanism in sperm (Vinckenbosch et al, 2006;Park et al, 2012;Mouakkad-Montoya et al, 2021). Also as in the case of gene fusion, this mechanism may facilitate long-term evolution: where high quantities of the gene product are needed, it could alleviate the pressure on gene expression, and where usage of a gene by multiple processes leads to its high expression, duplication and specialization of it into two or more paralogs could facilitate evolution by resolving pleiotropy (Livnat, 2017).…”

SVA Retrotransposons and a Low Copy Repeat in Humans and Great Apes: A Mobile Connection

“…Starting from a few anecdotal observations ( Fujimura et al 2011 ; Durkin et al 2012 ) integration of extrachromosomal circular DNA (eccDNA) has only been recognized as a mechanism of SD formation in the last years. Recently, SDs were found to be significantly overrepresented in sperm eccDNA ( Mouakkad-Montoya et al 2021 ). To date, only a relatively small number of duplication events generated by this mechanism has been characterized ( Chicote et al 2020 ; Takahashi and Innan 2020 ).…”

Accurate Identification of Extrachromosomal Circular DNA from Long-read Sequences

“…To aid the user to investigate the eccDNA architecture, CReSIL provides a function to generate the config file, populate the chromosomal origin information and genomic annotations, and plot it in Circos for visualization. Detection of eccDNA from WGLS challenging 43 ; however, it can be possible to uncover the higher copy eccDNA over the genomic background (Fig. 5).…”

“…Detection of eccDNA from WGLS challenging 43 ; however, it can be possible to uncover the higher copy eccDNA over the genomic background (Fig. 5).…”