Differences in Cpg Island Distribution Between Subgenotypes of the Hepatitis B Virus Genotype

Chen, Lin; Shi, Yi; Yang, Wanrong; Zhang, Yafei; Xie, Qinxiu; Li, Yunsong; Xu, Li; Li, Jun; Zhang, Zhenhua

doi:10.12659/msm.910049

Cited by 4 publications

(5 citation statements)

References 35 publications

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“…This variation may be attributed to different mucocutaneous tropisms of various human Papillomavirus genotypes, potentially influencing the CpG island positions within the genome. These findings align with the work of Chen and colleagues, who observed differences in CpG island profiles in hepatitis B virus (7).…”

Section: Discussionsupporting

confidence: 92%

“…Indeed, 7 different species of Alphapapillomaviruses were found, which included 5 major and 10 minor Papillomavirus types. A total of 15 viruses had a CpG island; among these genotypes, 46.66% were high-risk (26, 30, 51, 59, 66, 69, 82) and low-risk (6,7,11,32,43,54,91). The vast majority of the CpG islands were identified in the E2 genes in almost 80% of the cases.…”

Section: Profile Of Hpv With a Single Cpg Islandmentioning

confidence: 99%

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Epigenetic Peculiarity of Alphapapillomavirus Genus Based on the CpG Dinucleotides’ Island Variability

Elisee Libert,

Christian Kitchener,

Halidou

et al. 2024

Gene Cell Tissue

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Background: Methylation plays a crucial role in genome regulation, serving as an essential epigenetic mechanism. CpG islands, which are regions of DNA rich in CpG dinucleotides, are ubiquitous epigenetic regulatory features that can modulate the functional dynamics of genes, thereby influencing the pathophysiology of pathogenic organisms within a host. Objectives: In this study, we aimed to investigate the distribution of CpG islands on Papillomavirus genomes and assess their potential impact on the neoplastic progression of different Alphapapillomavirus genera within host cells. Methods: We conducted an analysis of dinucleotide frequencies in DNA sequences from various Alphapapillomavirus genera. The sequences for our analysis were sourced from the specialized HPV (human papillomavirus) database (pave.niaid.nih.gov). Following a comprehensive comparative examination of entire genomes from different HPV species, we specifically focused on 63 genomes belonging to the Alphapapillomavirus genus to identify internal CpG island profiles. These investigations were conducted using online bioinformatics software (DBCAT), and statistical analysis was performed using GraphPad Prism v. 8.0.1. Results: Our preliminary findings revealed that 76.1% of the viruses in our study had fewer than 3 CpG islands but multiple CpG sites, while fewer than 25% of the viruses possessed at least 3 CpG islands. High-risk viruses were identified in 68.42% of genotypes with fewer than 3 CpG islands, whereas low-risk genotypes were observed in 15.7% of cases. Notably, some oncogenic viruses lacked CpG islands entirely, and this pattern was also observed in viruses with a single CpG island, occurring in 50% of cases. Based on the absence of CpG islands, genotypes such as HPV 67, HPV 97, and HPV 34 could potentially be classified as carcinogenic. Additionally, the distribution of CpG islands across HPV genes did not appear to be random. Genes like L2 and E2 contained a CpG island in 50% of cases, whereas oncogenes E6 and E7 consistently had a CpG island in 100% of cases in high-risk genotypes. Conclusions: Our findings suggest that the loss of 1 or more CpG islands could potentially transform an HPV genotype into a high-risk genotype. This process may be accelerated in the presence of host-related risk factors. Further research is required to validate whether CpG island distribution can aid in identifying oncogenic viruses.

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Section: Discussionsupporting

confidence: 92%

Section: Profile Of Hpv With a Single Cpg Islandmentioning

confidence: 99%

Epigenetic Peculiarity of Alphapapillomavirus Genus Based on the CpG Dinucleotides’ Island Variability

Elisee Libert,

Christian Kitchener,

Halidou

et al. 2024

Gene Cell Tissue

View full text Add to dashboard Cite

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“…Based on more than 3000 hepatitis B virus (HBV) sequences reported from different countries, our team has divided HBV isolates into 31 different HBV subtypes established by selecting nucleotide with the highest frequency in each position. Using infectious plasmids constructed based on A2, B2, C2, and D1 subtype‐specific reference sequences, in vitro and in vivo studies have confirmed complete biological functions of these reference sequences 21,22 …”

Section: Discussionmentioning

confidence: 86%

“…Using infectious plasmids constructed based on A2, B2, C2, and D1 subtype-specific reference sequences, in vitro and in vivo studies have confirmed complete biological functions of these reference sequences. 21,22 Using the same approaches, in this study, the reference sequence for SARS-CoV-2 was constructed based on genomic sequence of 63 isolated strains. The genome size of the reference strain was 29870 bp.…”

Section: Discussionmentioning

confidence: 99%

The establishment of reference sequence for SARS‐CoV‐2 and variation analysis

Wang

Liu

Chen

et al. 2020

Journal of Medical Virology

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489

498

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Starting around December 2019, an epidemic of pneumonia, which was named COVID-19 by the World Health Organization, broke out in Wuhan, China, and is spreading throughout the world. A new coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the Coronavirus Study Group of the International Committee on Taxonomy of Viruses was soon found to be the cause. At present, the sensitivity of clinical nucleic acid detection is limited, and it is still unclear whether it is related to genetic variation. In this

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“…Viral gene expression is thought to be partially regulated by DNA methylation, which contributes to transcriptional silencing and gene suppression through multiple mechanisms in host tissues (LaMere et al 2019). Several studies found CpG islands in the HBV genomes of different strains, some of which were located at transcription start sites or upstream and downstream of promoters (Vivekanandan et al 2008, Chen et al 2018. In human liver tissues, HBV DNA can be methylated, which plays an important role in the regulation of HBV gene expression (Vivekanandan et al 2008(Vivekanandan et al , 2009.…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of CpG islands in two genotypes of African swine fever virus

Liu

2022

Polish Journal of Veterinary Sciences

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African swine fever (ASF) is an acute, hemorrhagic, and devastating viral infectious disease that causes important economic losses to the swine industry. Currently, there are no effective vaccines or drugs available. Epigenetic mechanisms, especially cytosine methylation of cytosine--phosphate-guanine (CpG) islands, have a significant impact on the life cycle of several viruses. Hence, drugs targeting DNA methylation may potentially be used for the treatment of ASF. Here, we selected the inner core, core shell, inner membrane, capsid, and external envelope membrane, to analyze the characteristics of CpG islands in the ASF virus (ASFV) genomes. Furthermore, we analyzed the promoters and CpG islands in the upstream regions of these genes. Results showed that the CpG islands of seven genes were conserved in the genomes of two genotype of ASFV strains, whereas the CpG islands of other genes were relatively conserved (ASFV strains differed mainly in the quantity of CpG islands). The different distribution of CpG islands in the genomes of different ASFV strains may affect their methylation status, which may in turn affect the regulation of viral gene expression, leading to different clinical outcomes. In addition, the predicted promoter regions based on the upstream sequences of most genes overlapped with CpG island positions. Methylation of the binding sites of the promoter regions inhibits the binding of the transcription factors to the promoters, thus inhibiting the activation of the promoters and limiting the synthesis of viral proteins. The results of this study provide a basis for exploring new antiviral therapeutic strategies from an epigenetic perspective.

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Differences in Cpg Island Distribution Between Subgenotypes of the Hepatitis B Virus Genotype

Cited by 4 publications

References 35 publications

Epigenetic Peculiarity of Alphapapillomavirus Genus Based on the CpG Dinucleotides’ Island Variability

Epigenetic Peculiarity of Alphapapillomavirus Genus Based on the CpG Dinucleotides’ Island Variability

The establishment of reference sequence for SARS‐CoV‐2 and variation analysis

Comparative analysis of CpG islands in two genotypes of African swine fever virus

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