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

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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.

Original languageEnglish
Article number2168590
Number of pages6
JournalInternational Journal of Genomics
Volume2016
DOIs
Publication statusPublished - 2016

Fingerprint

Human Genome
Viruses
Genes
HIV
Virus Integration
Jurkat Cells
Human Herpesvirus 4
Hepatitis B virus
Computer Simulation
HIV-1

Keywords

  • chromosome fragile
  • gene insertion
  • Giemsa stain
  • human cell
  • human genome
  • Human immunodeficiency virus 1
  • jurkat cell line
  • nonhuman
  • nonparametric test
  • virus DNA cell DNA interaction

Cite this

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title = "Integration of HIV in the Human Genome: Which Sites Are Preferential? A Genetic and Statistical Assessment",
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.",
keywords = "chromosome fragile, gene insertion, Giemsa stain, human cell, human genome, Human immunodeficiency virus 1, jurkat cell line, nonhuman, nonparametric test, virus DNA cell DNA interaction",
author = "Juliana Gon{\cc}alves and Elsa Moreira and Sequeira, {In{\^e}s Jorge da Silva} and Rodrigues, {Ant{\'o}nio S.} and J. Rueff and A. Br{\'a}s",
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T2 - Which Sites Are Preferential? A Genetic and Statistical Assessment

AU - Gonçalves, Juliana

AU - Moreira, Elsa

AU - Sequeira, Inês Jorge da Silva

AU - Rodrigues, António S.

AU - Rueff, J.

AU - Brás, A.

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N2 - 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.

AB - 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.

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KW - nonhuman

KW - nonparametric test

KW - virus DNA cell DNA interaction

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