Detection of HERV-K6 and HERV-K11 transpositions in the human genome

Abstract

Mobile genetic elements classed as transposons comprise an estimated 45% of the human genome, and 8% of these elements are human endogenous retroviruses (HERVs). Endogenous retroviruses are retrotransposons, containing 5' and 3' long terminal repeat sequences and encoding envelope, group-specific antigen and DNA polymerase proteins. The aim of the present study was to analyse genome integration polymorphisms of HERV type K member 6 (HERV-K6) and HERV-K11 by using the retrotransposon based molecular marker technique, inter-retrotransposon amplified polymorphism (IRAP). For this purpose, blood samples of 18 healthy individuals within the age range of 10-79 years (10 females and 8 males) were collected, genomic DNAs were isolated and IRAP-polymerase chain reaction (PCR) was performed. IRAP-PCR analyses demonstrated that there were 0-70% polymorphism rates for HERV-K6, and 0-38% polymorphism rates for HERV-K11 among all the samples. Furthermore, the polymorphism rates were 0-70% among females and 11-60% among males for HERV-K6, and 0-38% among females and 0-25% among males for HERV-K11. Age-associated polymorphism was also investigated, but no age-associated polymorphism was observed among the samples. Therefore, HERV-K6 and HERV-K11 polymorphisms may arise on an individual-specific basis. Various previous studies have investigated the associations between the expression of HERVs and cancer or other major diseases. However, few reports have analysed HERV-K movements among individuals. This is the first report to investigate HERV-K6 and HERV-K11 retrotransposon polymorphisms between the genders and different age groups.

Keywords: human endogenous retrovirus type K; human genome; mobile genetic elements; polymorphism.

Figure 1.

Inter-retrotransposon amplified polymorphism-polymerase chain reaction amplification using human endogenous retrovirus type K member 6-specific primers. Lane numbers correspond to the subjects listed in Table I. M, marker (GeneRulerTM100 bp plus; Fermentas; Thermo Fisher Scientific, Inc., Waltham, MA, USA); NC, negative control (no template DNA). Arrows indicate polymorphic bands.

Figure 2.

Inter-retrotransposon amplified polymorphism-polymerase chain reaction amplification using human endogenous retrovirus type K member 11-specific primers. Lane numbers correspond to the subjects listed in Table I. M, marker (GeneRulerTM100 bp plus; Fermentas; Thermo Fisher Scientific, Inc., Waltham, MA, USA); NC, negative control (no template DNA). Arrows indicate polymorphic bands.

Figure 3.

Clustering of subjects based on inter-retrotransposon amplified polymorphism-polymerase chain reaction amplification using human endogenous retrovirus type K member 6 primers (UPGMA analysis). Lane numbers correspond to the subjects listed in Table I.

Figure 4.

Clustering of subjects based on inter-retrotransposon amplified polymorphism-polymerase chain reaction amplification using human endogenous retrovirus type K member 11 primers (UPGMA analysis). Lane numbers correspond to the subjects listed in Table I.