CDCA-seq resolve the different chromatin structure on integral circular DNAs

Chen, W.; Weng, Z.; Xie, Z.; Xie, Y.; Zhang, C.; Chen, Z.; Ruan, F.; Wang, J.; Sun, Y.; Guo, M.; Fang, Y.; Tong, Y.; Li, Y.; Tang, C.

doi:10.1101/2021.03.31.437970

bioRxiv · 10.1101/2021.03.31.437970

CDCA-seq resolve the different chromatin structure on integral circular DNAs

Chen, W.·Weng, Z.·Xie, Z.·Xie, Y.·Zhang, C.·Chen, Z.·Ruan, F.·Wang, J.·Sun, Y.·Guo, M.·Fang, Y.·Tong, Y.·Li, Y.·Tang, C.

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Abstract

Although extrachromosomal DNA (ecDNA) has been intensively studied for several decades, the mechanisms underlying its tumorigenic effects have been revealed only recently. In the majority of conventional sequencing studies, the high-throughput short-read sequencing largely ignores the epigenetic status of most ecDNA regions except for the junctional areas. Here, we developed the sequencing of enzyme-accessible chromatin in circular DNA (CCDA-seq) method, which uses methylase to label open chromatin without fragmentation and exonuclease to enrich the ecDNA sequencing depth, followed by long-read nanopore sequencing. Using CCDA-seq, we observed significantly different patterns in nucleosome/regulator binding in ecDNA at a single-molecule resolution. These results deepen the understanding of ecDNA regulatory mechanisms.

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Chen, W., Weng, Z., Xie, Z., Xie, Y., Zhang, C., Chen, Z., Ruan, F., Wang, J., Sun, Y., Guo, M., Fang, Y., Tong, Y., Li, Y., Tang, C.. 2021-04-02. CDCA-seq resolve the different chromatin structure on integral circular DNAs. https://doi.org/10.1101/2021.03.31.437970

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