Caracterización genómica de la integración in vitro del VIH-1 en células mononucleares de sangre periférica, macrófagos y células T de Jurkat

Article information

Resumen

Introducción

La mayor parte del genoma celular es accesible a la integración retroviral; sin embargo, se propone que este proceso no es aleatorio y es dependiente de cada retrovirus.

Objetivos

Identificar y caracterizar las regiones del genoma humano en donde ocurre la integración del virus de la inmunodeficiencia humana de tipo 1 (VIH-1) en células mononucleares de sangre periférica, macrófagos y células T de Jurkat infectadas.

Materiales y métodos

Se seleccionaron 300 secuencias de ADN humano obtenidas por el método de ligación mediada por PCR, previamente depositadas en el GenBank. Utilizando el programa BLAST, sólo 264 de ellas se incluyeron en el estudio, pues se pudo obtener información sobre localización cromosómica, genes anotados, secuencias repetidas, número de islas CpG y tiempo medio de replicación, entre otras variables genómicas. Estas secuencias se exportaron a otras bases de datos.

Resultados

El 53% (140/264) de las integraciones se registraron en bandas G. El 70,45% de los provirus se localizaron en los genes humanos anotados, mientras que el restante lo hizo en elementos repetidos. En general, la selección del sitio de integración se relacionó con las características locales genómicas y estructurales de la cromatina, entre las que se incluyen secuencias Alu-Sx y L1, densidad génica y de islas CpG, remodelación de la cromatina y tiempo de replicación. Éstas influenciarían la interacción eficiente del complejo de preintegración con los genomas celulares.

Conclusión

Se determinó que la integración del VIH-1 en los genomas celulares estudiados estaría condicionada por características diferenciales de la cromatina y por procesos epigenéticos que influirían la selección del sitio blanco de integración.

Palabras clave:

virus de la inmunodeficiencia humana 1

integración retroviral

bioinformática

genoma humano.

Abstract

Introduction

Most of the infected host cell genome is available for retroviral integration; however, it has been proposed that this process does not occur at random and depends upon each type of retrovirus.

Objective

The objective is to identify and characterize differences in human genome regions of peripheral blood mononuclear cells, macrophages and Jurkat T cells in which integration of HIV-1 occurs.

Material and Methods

Three hundred human DNA genome sequences, previously deposited in the GenBank, were selected at random. Using program BLAST, only 264 of them were included in the study because relevant information about chromosomal position, associated genes, repetitive sequences, number of CpG islands and average replication time was available; these sequences were exported to other data bases for analysis.

Results

53% (140/264) of integrations were located on G bands. 70.45% of provirus was located in human genes and the rest was located in repetitive elements. In general the integration site selection was correlated with genomics and structural characteristics of cell chromatin including Alu-Sx and L1 sequences, gene and CpG island densities, remodeling of chromatin, and replication time. All of them would influence the efficient interaction between the pre-integration complex and target cell genomes.

Conclusion

It was determined that HIV-1 integration in target cellular genomes would be conditioned by differential characteristics of associated chromatin and by epigenetic processes that would influence the selection of integration sites.

Key words:

Human Immunodeficiency Virus 1

retroviral integration

bioinformatics

human genome

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