Dataset Information
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 | 2021 Aug
REPOSITORIES: biostudies-literature
Publications
Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure.
Epigenetics & chromatin 20210823 1
<h4>Background</h4>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.<h4>Methods</h4>Here, we developed a method of sequencing enzyme-accessible chromatin in circular DNA (CCDA-seq) based on the use of m ...[more]