**3. Human lentiviral integration**

The two closely related human lentiviruses HIV-1 and HIV-2 are responsible for the 21th century AIDS pandemic [7-9]. Most current therapeutic approaches use combinations of antiviral drugs that inhibit activities of viral enzymes such as reverse transcriptase, protease and integrase; nevertheless none of those have succeeded in controlling infection [10-12]. One option to overcome the problem is to explore new therapies that include the study of the integration dynamics of human Lentiviruses because it would permit to understand the underpinnings behinds of alterations of cellular homeostasis when a cell is infected [13]. Additionally, analysis of integration process is important in HIV-induced disease and in Lentivirus-based gene therapy [14].

Integration is a crucial step in the life cycle of retrovirus permitting the incorporation of viral cDNA into the host genome [15-17]. cDNA integration is mediated by the virally encoded integrase enzyme and other viral and cellular proteins in a molecular complex called the preintegration complex (PIC) [18]. One cellular factor involved in HIV targeting is the lens epithelium-derived growth factor (LEDGF) [19, 20], which binds to both HIV-1 integrase and chromatin, tethering the viral integration machinery to chromatin [21]. HIV-1 integration has been extensively studied using a wide array of molecular biology, biochemistry and structural biology approaches [22]. However, is critical to directly identify the viral distribution inside human genome in order to understand at genomic level the relationship between the composition and topology of chromatin and the target site selection.

As shown by previous studies, the preferences in target site selection for integration are not entirely random [23-26]; being pronounced favored and disfavored chromosomal regions which differ among retroviruses [27]. These preferential regions of host genomes are characterized by having a high frequency of integrational events, as known as "hotspot" and are distributed along the genome of host cell [28, 29]. In HIV-1, most of proviruses are localized into transcriptionally active regions not only in exons and introns, but also in sequences around start transcription sites [30, 31].

An additional related study performed by Felice et al, 2009 [32] compared and contrasted the chromosomal integration patterns between gamma retrovirus (Moloney Leukemia virus, MLV) and Lentivirus (human immunodeficiency virus type 1, HIV-1), finding that gammaretroviral, but not lentiviral vectors, integrate in genomic regions enriched in cell-type specific subsets of transcription factors binding sites (TFBSs), independently from their relative position with respect to genes and transcription start sites. Therefore, is proposed that TFBSs could be differential genomic determinants of retroviral target site selection in the human genome.

Several *in vitro* and *in vivo* studies have shown that HIV-1 integrate predominantly in active transcription units and in genome zones with high gene density, high frequency of Alu elements, low content of CpG islands and open chromatin regions [33]. Notwithstanding this evidence, the identification of particular characteristics of local chromatin that facilitate integration in a wider genomic manner still remains to be elucidated.

The objective of the this chapter is to show the main results that our group of investigation have obtained of statistically testing those genomic variables that define a preferred genomic environment for human lentiviral integration and localize them in specific chromosome loci; moreover in the construction of gene/protein interaction networks among those cellular genes located around several Lentivirus integration sites in naturally infected humans as a systemic approach to better understand the lentiviral integration process.

To test our hypothesis we conducted *in silico* studies of the integration profile in the genomic DNA of peripheral blood mononuclear cells (PBMCs) and macrophages for both human Lentiviruses (HIV-1 and HIV-2) in a window size analysis of 100K. The statistical analyses included several genomic variables such as the chromosomal loci, the numbers of CpG Island, protein coding genes, transcripts and also the distribution of SINEs, LINEs, LTRs and others; moreover the exploration genomic regions in which epigenetics mechanisms would be associated with the integration process. Together, the results allow us to propose common genomic environments that favor the target chromatin zones for both human Lentiviruses.
