Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure.
Ontology highlight
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.
SUBMITTER: Chen W
PROVIDER: S-EPMC8383416 | biostudies-literature |
REPOSITORIES: biostudies-literature
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