Detection of Alkali-Labile Sites on Satellite DNA by DNA Breakage Coupled with Fluorescence in Situ Hybridization (DNA-FISH) Monitor DNA Damage in Cervical Epithelial Cells

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Satellite DNA is the main component of functional centromeres and forms the main structural constituent of heterochromatin. The presence of alkali-labile sites (ALSs) is a feature inherent to chromatin structure. Here we aimed to characterize ALSs in different satellite DNA loci in cervical epithelial cells using DNA breakage detection coupled with fluorescence in situ hybridization (DBD–FISH). Cervical epithelial cells embedded in an agarose matrix were deproteinized and exposed to alkaline denaturation, which generated single-stranded DNA (ssDNA) starting from the ends of spontaneous basal DNA breaks and ALSs. The amount of ssDNA produced within a specific sequence area could be detected by DBD–FISH using specific probes. The DBD–FISH signals, which were corrected for respective FISH signals during metaphase, were remarkably stronger in the 5 bp classical satellite DNA domains analyzed (D1Z1, D9Z3, and D16Z3) compared with alphoid satellite regions (D3Z1, D8Z2, and DXZ1). D1Z1 locus of chromome-1 being the most affected by alkali denaturation, and contrary, D3Z1 locus of chromosome–3 was the least sensitive to alkali treatment. These findings suggest a high density of constitutive ALSs—probably abasic sites—within the 5 bp satellite DNA sequences in cervical epithelial cells. The presence and relative abundance of ALSs might help explain the high frequency of spontaneous breakage and rearrangements in the pericentromeric heterochromatin of chromosomes 1, 9, and 16 when this chromatin region is undercondensed spontaneously or via induction, such as following viral infections. ALSs in these sequences could be useful tools to monitor DNA damage in cases of cervical carcinogenesis. ALSs on these sequences could be useful tools to monitor DNA damage in cases of cervical carcinogenesis.