Epigenetics & Chromatin (Aug 2021)

Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure

  • Weitian Chen,
  • Zhe Weng,
  • Zhe Xie,
  • Yeming Xie,
  • Chen Zhang,
  • Zhichao Chen,
  • Fengying Ruan,
  • Juan Wang,
  • Yuxin Sun,
  • Yitong Fang,
  • Mei Guo,
  • Yiqin Tong,
  • Yaning Li,
  • Chong Tang

DOI
https://doi.org/10.1186/s13072-021-00416-5
Journal volume & issue
Vol. 14, no. 1
pp. 1 – 11

Abstract

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Abstract Background Although extrachromosomal DNA (ecDNA) has been intensively studied for several decades, the mechanisms underlying its tumorigenic effects have been revealed only recently. In most conventional sequencing studies, the high-throughput short-read sequencing largely ignores the epigenetic status of most ecDNA regions except for the junctional areas. Methods Here, we developed a method of sequencing enzyme-accessible chromatin in circular DNA (CCDA-seq) based on the use of methylase to label open chromatin without fragmentation and exonuclease to enrich ecDNA sequencing depth, followed by long-read nanopore sequencing. Results Using CCDA-seq, we observed significantly different patterns in nucleosome/regulator binding to ecDNA at a single-molecule resolution. Conclusions These results deepen the understanding of ecDNA regulatory mechanisms.

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