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.
Originalsprog | Engelsk |
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Artikelnummer | 40 |
Tidsskrift | Epigenetics & Chromatin |
Vol/bind | 14 |
Antal sider | 11 |
ISSN | 1756-8935 |
DOI | |
Status | Udgivet - 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).
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