Microhomology-mediated circular DNA formation from oligonucleosomal fragments during spermatogenesis
Jun Hu,
Zhe Zhang,
Sai Xiao,
Yalei Cao,
Yinghong Chen,
Jiaming Weng,
Hui Jiang,
Wei Li,
Jia-Yu Chen,
Chao Liu
Affiliations
Jun Hu
State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Andrology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China
Zhe Zhang
Department of Urology, Department of Reproductive Medicine Center, Peking University Third Hospital, Beijing, China
Sai Xiao
Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
Yalei Cao
Department of Urology, Department of Reproductive Medicine Center, Peking University Third Hospital, Beijing, China
Yinghong Chen
Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
Jiaming Weng
Department of Urology, Department of Reproductive Medicine Center, Peking University Third Hospital, Beijing, China
Hui Jiang
Department of Urology, Department of Reproductive Medicine Center, Peking University Third Hospital, Beijing, China; Department of Urology, Peking University First Hospital Institute of Urology, Beijing, China
Wei Li
Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Science, Beijing, China
State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Andrology, Nanjing Drum Tower Hospital, Nanjing University, Nanjing, China; Nanchuang (Jiangsu) Institute of Chemistry and Health, Nanjing, China
Chao Liu
Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of Science, Beijing, China
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.
