Microhomology-mediated circular DNA formation from oligonucleosomal fragments during spermatogenesis

Abstract

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. 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 break-point 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 lights on eccDNA biogenesis mechanism in mammalian germline cells and provide a potential new way for quality assessment of sperms.

Dynamics of extrachromosomal circular DNA in rice

“…In fact, our study also found that eccDNA is significantly abundant in the TE region, especially in the LTR region. Aligning with the findings reported by Hu et al 32 , our research also uncovered a significant correlation between eccDNAs and DNA Repeats within TEs. This observation suggests the possibility that DNA transposons may undergo circularization, either as an alternative to or concurrently with reintegration into the genome, a hypothesis that warrants further exploration.…”

eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data

“…By driving oncogene overexpression and fostering genetic diversity, eccDNA plays a crucial role in tumor evolution and resistance to therapies [ 6–9 ]. Additionally, eccDNA can influence spermatogenesis and act as innate immunostimulants in normal tissue [ 10 , 11 ]. Due to its structural diversity, functional versatility and variable abundance, investigations into eccDNA shed light on the molecular mechanisms underlying DNA repair pathways, genomic instability and gene expression regulation.…”