Genome-wide identification of methylated CpG sites in nongenital cutaneous warts

Laith N Al-Eitan; Mansour A Alghamdi; Amneh H Tarkhan; Firas A Al-Qarqaz

doi:10.1186/s12920-020-00745-6

Genome-wide identification of methylated CpG sites in nongenital cutaneous warts

BMC Med Genomics. 2020 Jul 8;13(1):100. doi: 10.1186/s12920-020-00745-6.

Authors

Laith N Al-Eitan^{1

2}, Mansour A Alghamdi^{3

4}, Amneh H Tarkhan⁵, Firas A Al-Qarqaz^{6

7}

Affiliations

¹ Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan. lneitan@just.edu.jo.
² Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid, 22110, Jordan. lneitan@just.edu.jo.
³ Department of Anatomy, College of Medicine, King Khalid University, Abha, 61421, Saudi Arabia.
⁴ Genomics and Personalized Medicine Unit, College of Medicine, King Khalid University, Abha, 61421, Saudi Arabia.
⁵ Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan.
⁶ Department of Internal Medicine, Jordan University of Science and Technology, Irbid, 22110, Jordan.
⁷ Division of Dermatology, Department of Internal Medicine, King Abdullah University Hospital Jordan University of Science and Technology, Irbid, 22110, Jordan.

Abstract

Background: Low-risk HPV infection has not been the subject of epigenetic investigation. The present study was carried out in order to investigate the methylation status of CpG sites in non-genital cutaneous warts.

Methods: Genomic DNA was extracted from 24 paired epidermal samples of warts and normal skin. DNA samples were bisulfite converted and underwent genome-wide methylation profiling using the Infinium MethylationEPIC BeadChip Kit.

Results: From a total of 844,234 CpG sites, 56,960 and 43,040 CpG sites were found to be hypo- and hypermethylated, respectively, in non-genital cutaneous warts. The most differentially methylated CpG sites in warts were located within the C10orf26, FAM83H-AS1, ZNF644, LINC00702, GSAP, STAT5A, HDAC4, NCALD, and EXOC4 genes.

Conclusion: Non-genital cutaneous warts exhibit a unique CpG methylation signature.

Keywords: CpG; DNA methylation; Epigenetics; HPV; Warts.

MeSH terms

CpG Islands*
DNA Methylation*
Epigenesis, Genetic*
Female
Genome, Human*
Humans
Male
Promoter Regions, Genetic
Skin Diseases / genetics*
Warts / genetics*

Grants and funding

177/2017/Jordan University of Science and Technology/International