Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data.
Journal
Oncogenesis
ISSN: 2157-9024
Titre abrégé: Oncogenesis
Pays: United States
ID NLM: 101580004
Informations de publication
Date de publication:
22 May 2023
22 May 2023
Historique:
received:
05
08
2022
accepted:
05
05
2023
revised:
04
05
2023
medline:
23
5
2023
pubmed:
23
5
2023
entrez:
22
5
2023
Statut:
epublish
Résumé
In cancer, extrachromosomal circular DNA (ecDNA), or megabase-pair amplified circular DNA, plays an essential role in intercellular heterogeneity and tumor cell revolution because of its non-Mendelian inheritance. We developed circlehunter ( https://github.com/suda-huanglab/circlehunter ), a tool for identifying ecDNA from ATAC-Seq data using the enhanced chromatin accessibility of ecDNA. Using simulated data, we showed that circlehunter has an F1 score of 0.93 at 30× local depth and read lengths as short as 35 bp. Based on 1312 ecDNAs predicted from 94 publicly available datasets of ATAC-Seq assays, we found 37 oncogenes contained in these ecDNAs with amplification characteristics. In small cell lung cancer cell lines, ecDNA containing MYC leads to amplification of MYC and cis-regulates the expression of NEUROD1, resulting in an expression pattern consistent with the NEUROD1 high expression subtype and sensitive to Aurora kinase inhibitors. This showcases that circlehunter could serve as a valuable pipeline for the investigation of tumorigenesis.
Identifiants
pubmed: 37217468
doi: 10.1038/s41389-023-00476-0
pii: 10.1038/s41389-023-00476-0
pmc: PMC10202962
doi:
Types de publication
Journal Article
Langues
eng
Pagination
28Subventions
Organisme : National Natural Science Foundation of China (National Science Foundation of China)
ID : 31971117
Informations de copyright
© 2023. The Author(s).
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