Repressive LTR nucleosome positioning by the BAF complex is required for HIV latency

Fred Hutchinson Cancer Research Center, United States of America
PLoS Biology (Impact Factor: 9.34). 11/2011; 9(11):e1001206. DOI: 10.1371/journal.pbio.1001206
Source: PubMed


Persistence of a reservoir of latently infected memory T cells provides a barrier to HIV eradication in treated patients. Several reports have implicated the involvement of SWI/SNF chromatin remodeling complexes in restricting early steps in HIV infection, in coupling the processes of integration and remodeling, and in promoter/LTR transcription activation and repression. However, the mechanism behind the seemingly contradictory involvement of SWI/SNF in the HIV life cycle remains unclear. Here we addressed the role of SWI/SNF in regulation of the latent HIV LTR before and after transcriptional activation. We determined the predicted nucleosome affinity of the LTR sequence and found a striking reverse correlation when compared to the strictly positioned in vivo LTR nucleosomal structure; sequences encompassing the DNase hypersensitive regions displayed the highest nucleosome affinity, while the strictly positioned nucleosomes displayed lower affinity for nucleosome formation. To examine the mechanism behind this reverse correlation, we used a combinatorial approach to determine DNA accessibility, histone occupancy, and the unique recruitment and requirement of BAF and PBAF, two functionally distinct subclasses of SWI/SNF at the LTR of HIV-infected cells before and after activation. We find that establishment and maintenance of HIV latency requires BAF, which removes a preferred nucleosome from DHS1 to position the repressive nucleosome-1 over energetically sub-optimal sequences. Depletion of BAF resulted in de-repression of HIV latency concomitant with a dramatic alteration in the LTR nucleosome profile as determined by high resolution MNase nucleosomal mapping. Upon activation, BAF was lost from the HIV promoter, while PBAF was selectively recruited by acetylated Tat to facilitate LTR transcription. Thus BAF and PBAF, recruited during different stages of the HIV life cycle, display opposing function on the HIV promoter. Our data point to the ATP-dependent BRG1 component of BAF as a putative therapeutic target to deplete the latent reservoir in patients.

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Available from: Yuri M Moshkin
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    • "HIV-1 chromatin structure at the 5′ LTR, the HIV-1 promoter, is highly organized into specifically deposited nucleosomes: in its latent state, the 5'LTR is organized into nuc-0 and nuc-1, two strictly positioned nucleosomes that are separated by DHS1, a region sensitive to nuclease digestion, which encompasses a loosely positioned nucleosome (Verdin, 1991; Verdin and Van Lint, 1995; Rafati et al., 2011). The positioning of nuc-1, downstream of the core promoter transcription start site, is the hallmark of the repressed 5′ LTR. "
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    ABSTRACT: Persistence of latently infected cells in presence of Anti-Retroviral Therapy presents the main obstacle to HIV-1 eradication. Much effort is thus placed on identification of compounds capable of HIV-1 latency reversal in order to render infected cells susceptible to viral cytopathic effects and immune clearance. We identified the BAF chromatin remodeling complex as a key player required for maintenance of HIV-1 latency, highlighting its potential as a molecular target for inhibition in latency reversal. Here, we screened a recently identified panel of small molecule inhibitors of BAF (BAFi's) for potential to activate latent HIV-1. Latency reversal was strongly induced by BAFi's Caffeic Acid Phenethyl Ester and Pyrimethamine, two molecules previously characterized for clinical application. BAFi's reversed HIV-1 latency in cell line based latency models, in two ex vivo infected primary cell models of latency, as well as in HIV-1 infected patient's CD4+ T cells, without inducing T cell proliferation or activation. BAFi-induced HIV-1 latency reversal was synergistically enhanced upon PKC pathway activation and HDAC-inhibition. Therefore BAFi's constitute a promising family of molecules for inclusion in therapeutic combinatorial HIV-1 latency reversal.
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    • "Maintenance of HIV latency requires BAF, which helps position the repressive Nuc-1. Upon activation, BAF is lost from the HIV promoter, while PBAF is selectively recruited to reposition Nuc-1 and facilitate LTR transcription (Rafati et al., 2011). The NF-κB p65 subunit is itself subject to acetylation by p300/ CBP which serves to maintain it in the nucleus by inhibiting interaction with IκBα (Chen et al., 2001; Furia et al., 2002). "
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    • "Our previous review (Aliya et al. 2012) provides a comprehensive account of the epigenetics of HTLV-1 infection. Thus far there is no report about the effect of any drugs of abuse on HTLV-1 promoter; therefore, we will base our discussion on the HIV-1 LTR (Rafati et al. 2011; Treand et al. 2006), which is known to be affected by drugs of abuse (Molina et al. 2011; Reynolds et al. 2006). We will also elaborate on the epigenetic effects among overlapping populations of virus infected-and individual-drug abusers. "
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