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On-line Access: 2019-07-05

Received: 2018-08-30

Revision Accepted: 2019-02-27

Crosschecked: 2019-06-10

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Journal of Zhejiang University SCIENCE B 2019 Vol.20 No.8 P.637-646

http://doi.org/10.1631/jzus.B1800453


DNA sequences homologous to hepatitis C virus (HCV) in the extrachromosomal circular DNA in peripheral blood mononuclear cells of HCV-negative subjects


Author(s):  Reinhard H. Dennin, Jian-Er Wo

Affiliation(s):  Formerly Department of Infectious Diseases and Microbiology, University of Lübeck, University Hospital Schleswig-Holstein, 23538 Lübeck, Germany; more

Corresponding email(s):   rh.dennin@t-online.de

Key Words:  Hepatitis C virus (HCV), 5'-Non-coding region (5'-NCR), Human genome, Extrachromosomal DNA, Circular DNA, Pattern of methylation


Reinhard H. Dennin, Jian-Er Wo. DNA sequences homologous to hepatitis C virus (HCV) in the extrachromosomal circular DNA in peripheral blood mononuclear cells of HCV-negative subjects[J]. Journal of Zhejiang University Science B, 2019, 20(8): 637-646.

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author="Reinhard H. Dennin, Jian-Er Wo",
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doi="10.1631/jzus.B1800453"
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%T DNA sequences homologous to hepatitis C virus (HCV) in the extrachromosomal circular DNA in peripheral blood mononuclear cells of HCV-negative subjects
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%A Jian-Er Wo
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T1 - DNA sequences homologous to hepatitis C virus (HCV) in the extrachromosomal circular DNA in peripheral blood mononuclear cells of HCV-negative subjects
A1 - Reinhard H. Dennin
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PB - Zhejiang University Press & Springer
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DOI - 10.1631/jzus.B1800453


Abstract: 
Objective: This study aimed to investigate DNA sequences that are substantially homologous to the corresponding RNA sequence sections of the hepatitis C virus (HCV). These DNA sequences are present in the whole DNA extracted from peripheral blood mononuclear cells (PBMCs) of HCV-negative subjects. We presumed that these experimentally proven 5'-noncoding region (5'-NCR) homologous DNA sequences could be contained in the extrachromosomal circular DNA (eccDNA) fraction as part of the whole cellular DNA. Methods: Home-made polymerase chain reaction (PCR) with whole cellular and isolated eccDNA, nucleotide basic local alignment search tool (BLASTn) alignments, and tests for patterns of methylation in selected sequence sections were performed. Results: The PCR tests revealed DNA sequences of up to 320 bp that broadly matched the corresponding sequence sections of known HCV genotypes. In contrast, BLASTn alignment searches of published HCV 5'-NCR sequences with human genome databases revealed only sequence segments of up to 36 bp of the 5'-NCR. The composition of these sequences shows missing base pairs, base pair mismatches as well as complete homology with HCV reference sequences. These short sequence sections are present in numerous copies on both the same and different chromosomes. The selected sequence region within the DNA sequences of the 5'-NCR revealed a broad diversity of individual patterns of methylation. Conclusions: The experimental results confirm our assumption that parts of the HCV 5'-NCR genomic RNA sequences are present at the DNA level in the eccDNA fraction of PBMCs. The tests for methylation patterns therein revealed individual methylomes which could represent an epigenetic feature. The respective sequence section might be subject to genetic regulation.

HCV阴性者外周血单核细胞的染色体外环状DNA中与HCV同源的DNA序列

目的:研究与丙型肝炎病毒(HCV)基因RNA序列同源的人染色体外环状DNA(eccDNA)序列.
创新点:首次从HCV阴性者eccDNA中检测到HCV 5’-非编码区(5’-NCR)基因组RNA序列,验证了我们的假设: HCV同源DNA序列存在于人的外周血单核细胞的eccDNA组分中.
方法:用分离的eccDNA进行HCV特异的聚合酶链反应(PCR),采用核苷酸序列同源性搜索分析软件(BLASTn)对测序结果进行比对分析,并检测其甲基化模式.
结论:实验结果证实了我们的假设:即部分HCV 5’-NCR基因组RNA序列存在于外周血单核细胞的eccDNA组分.同时,甲基化分析结果显示了个体间的甲基化模式所代表的受遗传调控的表观遗传特征.

关键词:丙型肝炎病毒(HCV);5’-非编码区;人类基因组;染色体外DNA;环状DNA;甲基化模式

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

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