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Open AccessArticle

Genome-Wide CpG Island Methylation Profiles of Cutaneous Skin with and without HPV Infection

1
Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
2
Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
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Department of Human Anatomy, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia
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Department of Internal Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan
5
Division of Dermatology, Department of Internal Medicine, King Abdullah University Hospital Jordan University of Science and Technology, Irbid 22110, Jordan
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(19), 4822; https://doi.org/10.3390/ijms20194822
Received: 16 August 2019 / Revised: 13 September 2019 / Accepted: 16 September 2019 / Published: 28 September 2019
(This article belongs to the Special Issue Modifications of Molecular Structure and Interactions in Epigenome)
HPV infection is one of the most commonly transmitted diseases among the global population. While it can be asymptomatic, non-genital HPV infection often gives rise to cutaneous warts, which are benign growths arising from the epidermal layer of the skin. This study aimed to produce a global analysis of the ways in which cutaneous wart formation affected the CpG island methylome. The Infinium MethylationEPIC BeadChip microarray was utilized in order to quantitatively interrogate CpG island methylation in genomic DNA extracted from 24 paired wart and normal skin samples. Differential methylation analysis was carried out by means of assigning a combined rank score using RnBeads. The 1000 top-ranking CpG islands were then subject to Locus Overlap Analysis (LOLA) for enrichment of genomic ranges, while signaling pathway analysis was carried out on the top 100 differentially methylated CpG islands. Differential methylation analysis illustrated that the most differentially methylated CpG islands in warts lay within the ITGB5, DTNB, RBFOX3, SLC6A9, and C2orf27A genes. In addition, the most enriched genomic region sets in warts were Sheffield’s tissue-clustered DNase hypersensitive sites, ENCODE’s segmentation and transcription factor binding sites, codex sites, and the epigenome sites from cistrome. Lastly, signaling pathway analysis showed that the GRB2, GNB1, NTRK1, AXIN1, and SKI genes were the most common regulators of the genes associated with the top 100 most differentially methylated CpG islands in warts. Our study shows that HPV-induced cutaneous warts have a clear CpG island methylation profile that sets them apart from normal skin. Such a finding could account for the temporary nature of warts and the capacity for individuals to undergo clinical remission. View Full-Text
Keywords: HPV; warts; DNA methylation; CpG; epigenetics HPV; warts; DNA methylation; CpG; epigenetics
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MDPI and ACS Style

AL-Eitan, L.N.; Alghamdi, M.A.; Tarkhan, A.H.; Al-Qarqaz, F.A. Genome-Wide CpG Island Methylation Profiles of Cutaneous Skin with and without HPV Infection. Int. J. Mol. Sci. 2019, 20, 4822.

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