Microhomology-mediated circular DNA formation from oligonucleosomal fragments during spermatogenesis

• Published in: eLife Vol. 12
• Main Authors: Hu, Jun, Zhang, Zhe, Xiao, Sai, Cao, Yalei, Chen, Yinghong, Weng, Jiaming, Jiang, Hui, Li, Wei, Chen, Jia-Yu, Liu, Chao
• Format: Journal Article
• Language: English
• Published: Cambridge eLife Sciences Publications Ltd 17.10.2023; eLife Sciences Publications, Ltd
• Subjects: Bioinformatics; Biosynthesis; Cell death; Circular DNA; Developmental Biology; DNA fragmentation; Euchromatin; extrachromosomal circular DNA; Genetics and Genomics; Genomes; Heterochromatin; Meiosis; microhomology; Mitochondrial DNA; Morphology; Quality control; Recombination hot spots; Sperm; Spermatogenesis
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/eLife.87115

The landscape of extrachromosomal circular DNA (eccDNA) during mammalian spermatogenesis, as well as the biogenesis mechanism, remains to be explored. Here, we revealed widespread eccDNA formation in human sperms and mouse spermatogenesis. We noted that germline eccDNAs are derived from oligonucleosomal DNA fragmentation in cells likely undergoing cell death, providing a potential new way for quality assessment of human sperms. Interestingly, small-sized eccDNAs are associated with euchromatin, while large-sized ones are preferentially generated from heterochromatin. By comparing sperm eccDNAs with meiotic recombination hotspots and structural variations, we found that they are barely associated with de novo germline deletions. We further developed a bioinformatics pipeline to achieve nucleotide-resolution eccDNA detection even with the presence of microhomologous sequences that interfere with precise breakpoint identification. Empowered by our method, we provided strong evidence to show that microhomology-mediated end joining is the major eccDNA biogenesis mechanism. Together, our results shed light on eccDNA biogenesis mechanism in mammalian germline cells.