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Nucleic Acids Research, 2003, Vol. 31, No. 12 3248-3256
© 2003 Oxford University Press

Stimulation of Tat-independent transcriptional processivity from the HIV-1 LTR promoter by matrix attachment regions

Shravanti Rampalli, Asavari Kulkarni, Pavan Kumar, Devraj Mogare, Sanjeev Galande, Debashis Mitra and Samit Chattopadhyay

National Center for Cell Science, Pune University Campus, Ganeshkhind, Pune 411007, India

*To whom correspondence should be addressed. Tel: +91 20 569 0922; Fax: +91 20 569 2259; Email: samit{at}nccs.res.in

The chromatin environment and the sites of integration in the host genome are critical determinants of human immunodeficiency virus (HIV) transcription and replication. Depending on the chromosomal location of provirus integration within the genome, HIV-1 long terminal repeat (LTR)-mediated transcription may vary from 0- to 70-fold. Cis-elements such as topoisomerase II cleavage sites, Alu repeats and matrix attachment regions (MARs) are thought to be targets for retroviral integration. Here we show that a novel MAR sequence from the T-cell receptor ß locus (MARß) and the IgH MAR mediate transcriptional augmentation when placed upstream of the HIV-1 LTR promoter. The effect of transcriptional augmentation is seen in both transient and stable transfection, indicating its effect even upon integration in the genome. MAR-mediated transcriptional elevation is independent of Tat, and occurs synergistically in the presence of Tat. Further, we show that MAR-mediated transcriptional elevation is specific to the HIV-1 LTR and the Moloney murine leukemia virus LTR promoter. In a transient transfection assay using over-expressed I{kappa}B, the inhibitor of NF-{kappa}B, we show that MAR-induced processive transcription is NF-{kappa}B dependent, signifying the role of local enhancers within the LTR promoter. Furthermore, by RNase protection experiments using proximal and distal probes, we show that MAR-mediated transcriptional upregulation is more prominent at the distal rather than the proximal end, thus indicating the potential role of MARs in promoting elongation.


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