Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure
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- Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure
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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.
Original language | English |
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Article number | 40 |
Journal | Epigenetics & Chromatin |
Volume | 14 |
Number of pages | 11 |
ISSN | 1756-8935 |
DOIs | |
Publication status | Published - 2021 |
Bibliographical note
Publisher Copyright:
© 2021, The Author(s).
- Chromatin accessibility, ecDNA, mA, Methylation, Methyltransferase
Research areas
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