Short single-stranded DNAs with putative non-canonical structures comprise a new class of plasma cell-free DNA

研究成果: ジャーナルへの寄稿学術誌査読

3 被引用数 (Scopus)

抄録

Background: Cell-free DNA (cfDNA), which is extracellular DNA present in the circulating plasma and other body fluids, is currently investigated as a minimally invasive, highly informative biomarker. While nucleosome-sized cfDNA fragments have been investigated intensively, shorter DNA fragments in the plasma have not been studied due to several technical limitations. Results: We aimed to investigate the existence of shorter cfDNA fragments in the blood. Using an improved cfDNA purification protocol and a 3′-end-labeling method, we found DNA fragments of approximately 50 nucleotides in length in the human plasma, present at a molar concentration comparable to that of nucleosome-sized fragments. Unfortunately, these short fragments cannot be recovered by widely used cfDNA isolation methods. In addition, they are composed of single-stranded DNA (ssDNA), thus escaping detection in previous studies. Therefore, we established a library-preparation protocol based on our unique ssDNA ligation technique and applied it to the isolated cfDNA. Deep sequencing of these libraries revealed that the short fragments are derived from hundreds of thousands of genomic sites in open chromatin regions and enriched with transcription factor-binding sites. Remarkably, antisense strands of putative G-quadruplex motifs occupy as much as one-third of the peaks by these short fragments. Conclusions: We propose a new class of plasma cfDNA composed of short single-stranded fragments that potentially form non-canonical DNA structures.

本文言語英語
論文番号225
ジャーナルBMC biology
19
1
DOI
出版ステータス出版済み - 12月 2021

!!!All Science Journal Classification (ASJC) codes

  • バイオテクノロジー
  • 構造生物学
  • 生態、進化、行動および分類学
  • 生理学
  • 生化学、遺伝学、分子生物学(全般)
  • 農業および生物科学(全般)
  • 植物科学
  • 発生生物学
  • 細胞生物学

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