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. 2016;2016:2168590.
doi: 10.1155/2016/2168590. Epub 2016 May 12.

Integration of HIV in the Human Genome: Which Sites Are Preferential? A Genetic and Statistical Assessment

Juliana Gonçalves  1 , Elsa Moreira  2 , Inês J Sequeira  2 , António S Rodrigues  1 , José Rueff  1 , Aldina Brás  1
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Integration of HIV in the Human Genome: Which Sites Are Preferential? A Genetic and Statistical Assessment

Juliana Gonçalves et al. Int J Genomics. .
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Abstract

Chromosomal fragile sites (FSs) are loci where gaps and breaks may occur and are preferential integration targets for some viruses, for example, Hepatitis B, Epstein-Barr virus, HPV16, HPV18, and MLV vectors. However, the integration of the human immunodeficiency virus (HIV) in Giemsa bands and in FSs is not yet completely clear. This study aimed to assess the integration preferences of HIV in FSs and in Giemsa bands using an in silico study. HIV integration positions from Jurkat cells were used and two nonparametric tests were applied to compare HIV integration in dark versus light bands and in FS versus non-FS (NFSs). The results show that light bands are preferential targets for integration of HIV-1 in Jurkat cells and also that it integrates with equal intensity in FSs and in NFSs. The data indicates that HIV displays different preferences for FSs compared to other viruses. The aim was to develop and apply an approach to predict the conditions and constraints of HIV insertion in the human genome which seems to adequately complement empirical data.

Figures

Figure 1
Figure 1
Integration of HIV-1 isolated from Jurkat T cells in Giemsa dark bands versus Giemsa light bands. Graphical representation of the results for the intensity number. Each point represents a chromosome whose coordinates are the (x, y) pairs obtained in the measure calculations. The statistical analysis indicates that the virus integrates preferentially in Giemsa light bands (Wilcoxon test, T obs: 59; T critic: 69).
Figure 2
Figure 2
Integration of HIV-1 isolated from Jurkat T cells in FRs versus NFRs. Graphical representation of the results for the intensity number. Each point represents a chromosome whose coordinates are the (x, y) pairs obtained in the measure calculations. The statistical analysis indicates that the virus integrates with equal intensity in FRs and in NFRs (Sign test, p value: 0.202, and Wilcoxon test, T obs: 82; T critic: 62).
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