HIV-1 integration sites are flanked by potential MARs that alone can act as promoters.

Matrix attachment regions (MARs) are cis regulatory elements that modulate gene expression in a tissue and cell stage specific manner. Recent reports show that viral integration within the genome takes place at nonrandom active genes. We have checked for the presence of MARs in the vicinity of the reported 524 HIV-1 integration sites. Our studies show that in 92.5% cases, MARs flank the integration sites. Similarly, for adeno-associated virus, two potential MARs were present next to the integration site on the human chromosome. Earlier we have shown that short MAR sequences present upstream of HIV-1 LTR promote processive transcription at a distance. Here, using a well-studied IgH-MAR and another potential MAR from p53 promoter, we demonstrate that MARs alone can act as promoters. Thus, we propose that MAR elements near the HIV-1 integration sites can act as potential promoters, which may facilitate proviral integration and transcription.