Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data
Abstract 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 ),...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Publishing Group
2023-05-01
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| Series: | Oncogenesis |
| Online Access: | https://doi.org/10.1038/s41389-023-00476-0 |
| _version_ | 1797817782923952128 |
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| author | Manqiu Yang Shufan Zhang Rong Jiang Shaomu Chen Moli Huang |
| author_facet | Manqiu Yang Shufan Zhang Rong Jiang Shaomu Chen Moli Huang |
| author_sort | Manqiu Yang |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-03-13T08:58:34Z |
| format | Article |
| id | doaj.art-82a703b381114e989f5b963f3a74711d |
| institution | Directory Open Access Journal |
| issn | 2157-9024 |
| language | English |
| last_indexed | 2024-03-13T08:58:34Z |
| publishDate | 2023-05-01 |
| publisher | Nature Publishing Group |
| record_format | Article |
| series | Oncogenesis |
| spelling | doaj.art-82a703b381114e989f5b963f3a74711d2023-05-28T11:27:59ZengNature Publishing GroupOncogenesis2157-90242023-05-0112111210.1038/s41389-023-00476-0Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq dataManqiu Yang0Shufan Zhang1Rong Jiang2Shaomu Chen3Moli Huang4School of Biology and Basic Medical Sciences, Soochow UniversitySchool of Biology and Basic Medical Sciences, Soochow UniversitySchool of Biology and Basic Medical Sciences, Soochow UniversityDepartment of Thoracic Surgery, The First Affiliated Hospital of Soochow UniversitySchool of Biology and Basic Medical Sciences, Soochow UniversityAbstract 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.https://doi.org/10.1038/s41389-023-00476-0 |
| spellingShingle | Manqiu Yang Shufan Zhang Rong Jiang Shaomu Chen Moli Huang Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data Oncogenesis |
| title | Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data |
| title_full | Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data |
| title_fullStr | Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data |
| title_full_unstemmed | Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data |
| title_short | Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data |
| title_sort | circlehunter a tool to identify extrachromosomal circular dna from atac seq data |
| url | https://doi.org/10.1038/s41389-023-00476-0 |
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