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. / Chen, Weitian; Weng, Zhe; Xie, Zhe; Xie, Yeming; Zhang, Chen; Chen, Zhichao; Ruan, Fengying; Wang, Juan; Sun, Yuxin; Fang, Yitong; Guo, Mei; Tong, Yiqin; Li, Yaning; Tang, Chong.

I: Epigenetics & Chromatin, Bind 14, 40, 2021.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Chen, W, Weng, Z, Xie, Z, Xie, Y, Zhang, C, Chen, Z, Ruan, F, Wang, J, Sun, Y, Fang, Y, Guo, M, Tong, Y, Li, Y & Tang, C 2021, 'Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure', Epigenetics & Chromatin, bind 14, 40. https://doi.org/10.1186/s13072-021-00416-5

APA

Chen, W., Weng, Z., Xie, Z., Xie, Y., Zhang, C., Chen, Z., Ruan, F., Wang, J., Sun, Y., Fang, Y., Guo, M., Tong, Y., Li, Y., & Tang, C. (2021). Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure. Epigenetics & Chromatin, 14, [40]. https://doi.org/10.1186/s13072-021-00416-5

Vancouver

Chen W, Weng Z, Xie Z, Xie Y, Zhang C, Chen Z o.a. Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure. Epigenetics & Chromatin. 2021;14. 40. https://doi.org/10.1186/s13072-021-00416-5

Author

Chen, Weitian ; Weng, Zhe ; Xie, Zhe ; Xie, Yeming ; Zhang, Chen ; Chen, Zhichao ; Ruan, Fengying ; Wang, Juan ; Sun, Yuxin ; Fang, Yitong ; Guo, Mei ; Tong, Yiqin ; Li, Yaning ; Tang, Chong. / Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure. I: Epigenetics & Chromatin. 2021 ; Bind 14.

Bibtex

@article{6519e97c4cff44a6bf7a23db99c3f6be,
title = "Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure",
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.",
keywords = "Chromatin accessibility, ecDNA, mA, Methylation, Methyltransferase",
author = "Weitian Chen and Zhe Weng and Zhe Xie and Yeming Xie and Chen Zhang and Zhichao Chen and Fengying Ruan and Juan Wang and Yuxin Sun and Yitong Fang and Mei Guo and Yiqin Tong and Yaning Li and Chong Tang",
note = "Publisher Copyright: {\textcopyright} 2021, The Author(s).",
year = "2021",
doi = "10.1186/s13072-021-00416-5",
language = "English",
volume = "14",
journal = "Epigenetics & Chromatin",
issn = "1756-8935",
publisher = "BioMed Central Ltd.",

}

RIS

TY - JOUR

T1 - Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure

AU - Chen, Weitian

AU - Weng, Zhe

AU - Xie, Zhe

AU - Xie, Yeming

AU - Zhang, Chen

AU - Chen, Zhichao

AU - Ruan, Fengying

AU - Wang, Juan

AU - Sun, Yuxin

AU - Fang, Yitong

AU - Guo, Mei

AU - Tong, Yiqin

AU - Li, Yaning

AU - Tang, Chong

N1 - Publisher Copyright: © 2021, The Author(s).

PY - 2021

Y1 - 2021

N2 - 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.

AB - 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.

KW - Chromatin accessibility

KW - ecDNA

KW - mA

KW - Methylation

KW - Methyltransferase

U2 - 10.1186/s13072-021-00416-5

DO - 10.1186/s13072-021-00416-5

M3 - Journal article

C2 - 34425889

AN - SCOPUS:85113777682

VL - 14

JO - Epigenetics & Chromatin

JF - Epigenetics & Chromatin

SN - 1756-8935

M1 - 40

ER -

ID: 279119757