We explored the presence of extrachromosomal circular DNA (eccDNA) in the plasma of pregnant women. Through sequencing following either restriction enzyme or Tn5 transposase treatment, we identified eccDNA molecules in the plasma of pregnant women. These eccDNA molecules showed bimodal size distributions peaking at ∼202 and ∼338 bp with distinct 10-bp periodicity observed throughout the size ranges within both peaks, suggestive of their nucleosomal origin. Also, the predominance of the 338-bp peak of eccDNA indicated that eccDNA had a larger size distribution than linear DNA in human plasma. Moreover, eccDNA of fetal origin were shorter than the maternal eccDNA. Genomic annotation of the overall population of eccDNA molecules revealed a preference of these molecules to be generated from 5'-untranslated regions (5'-UTRs), exonic regions, and CpG island regions. Two sets of trinucleotide repeat motifs flanking the junctional sites of eccDNA supported multiple possible models for eccDNA generation. This work highlights the topologic analysis of plasma DNA, which is an emerging direction for circulating nucleic acid research and applications.

中文翻译：

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母体血浆中染色体外环状DNA的鉴定和表征。

我们探讨了孕妇血浆中染色体外环状DNA（eccDNA）的存在。通过限制性酶或Tn5转座酶处理后的测序，我们在孕妇血浆中鉴定了eccDNA分子。这些eccDNA分子显示出双峰大小分布，峰值分布在〜202和〜338 bp，在两个峰的整个大小范围内观察到明显的10 bp周期性，表明它们的核小体起源。另外，eccDNA的338bp峰占优势，表明eccDNA在人血浆中的分布比线性DNA大。此外，胎儿来源的eccDNA比母亲的eccDNA短。eccDNA分子总体种群的基因组注释显示，这些分子优先从5'非翻译区（5'-UTR），外显子区，和CpG岛地区。eccDNA的连接位点两侧的两组三核苷酸重复基序支持eccDNA生成的多种可能模型。这项工作强调了血浆DNA的拓扑分析，这是循环核酸研究和应用的新兴方向。