Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data.
Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data.
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DOI：
10.1038/s41389-023-00476-0
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发表时间：
2023-05-22
期刊：
影响因子：
6.2
通讯作者：
Huang, Moli
中科院分区：
文献类型：
--
作者：
Yang, Manqiu;Zhang, Shufan;Jiang, Rong;Chen, Shaomu;Huang, Moli
在癌症中，染色体外环状DNA（ecDNA）或巨碱基对扩增环状DNA，由于其非孟德尔遗传，在细胞间异质性和肿瘤细胞革命中起着至关重要的作用。我们开发了circlehunter（https：//github.com/suda-huanglab/circlehunter），这是一种使用增强的ecDNA染色质可及性从ATAC-Seq数据中鉴定ecDNA的工具。使用模拟数据，我们表明circlehunter在30×局部深度处的F1得分为0.93，读取长度短至35 bp。基于ATAC-Seq分析的94个公开数据集预测的1312个ecDNA，我们发现这些ecDNA中含有37个具有扩增特征的癌基因。在小细胞肺癌细胞系中，含有MYC的ecDNA导致MYC扩增并顺式调节NEUROD 1的表达，导致与NEUROD 1高表达亚型一致的表达模式，并对Aurora激酶抑制剂敏感。这表明circlehunter可以作为研究肿瘤发生的有价值的管道。
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.
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影响因子：
14.9
作者：
Gene Ontology Consortium
通讯作者：
Gene Ontology Consortium
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通讯作者：
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