Background: In order for HIV to successfully replicate, the proviral DNA must integrate into human DNA. Previously we reported mapping 524 sites of HIV cDNA integration on the human genome sequence using a human T-cell line. We have extended the study by using human primary cells, peripheral blood mononuclear cells (PBMCs).

Methods: Forty-eight (48) hours after infection with an HIV-based vector, the proviral-containing chromosomal DNA was isolated. This DNA was cleaved with restriction enzymes and the resulting DNA fragments ligated to linkers. The HIV-genome junction sequences were amplified with primers complementary to the linker and the HIV cDNA end. The PCR product was cloned, sequenced, and chromosomal location of the HIV cDNA end determined. Gene activity in the target cells is also monitored by transcriptional profiling using Affymetrix Chips.

Results: Genes were strongly favored as integration acceptor sites. Global analysis of cellular transcription will be performed to see if, as in the earlier study, active genes are preferential integration targets.

Conclusions: The previous finding that genes are favored target sites for HIV integration has been found to also be true in cells that are more physiologically relevant to a human HIV infection. As more genes are identified in the human genome and as the functions of more genes are determined we will be able to ascertain whether HIV integration is favored in particular types of genes.