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

Publikation: Bidrag til tidsskriftTidsskriftartikelfagfællebedømt

  • 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

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.

OriginalsprogEngelsk
Artikelnummer40
TidsskriftEpigenetics & Chromatin
Vol/bind14
Antal sider11
ISSN1756-8935
DOI
StatusUdgivet - 2021

Bibliografisk note

Funding Information:
This research was supported by the Science, Technology, and Innovation Commission of Shenzhen Municipality (Grant Number JSGG20170824152728492). The supporter had no role in designing the study, data collection, analysis, and interpretation, or in writing the manuscript.

Publisher Copyright:
© 2021, The Author(s).

Antal downloads er baseret på statistik fra Google Scholar og www.ku.dk


Ingen data tilgængelig

ID: 279119757