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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    • "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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    ABSTRACT: Replication-competent latent HIV-1 proviruses that persist in the genomes of a very small subset of resting memory T cells in infected individuals under life-long antiretroviral therapy present a major barrier towards viral eradication. Multiple molecular mechanisms are required to repress the viral trans-activating factor Tat and disrupt the regulatory Tat feedback circuit leading to the establishment of the latent viral reservoir. In particular, latency is due to a combination of transcriptional silencing of proviruses via host epigenetic mechanisms and restrictions on the expression of P-TEFb, an essential co-factor for Tat. Induction of latent proviruses in the presence of antiretroviral therapy is expected to enable clearance of latently infected cells by viral cytopathic effects and host antiviral immune responses. An in-depth comprehensive understanding of the molecular control of HIV-1 transcription should inform the development of optimal combinatorial reactivation strategies that are intended to purge the latent viral reservoir.
    Virology 02/2014; 454-455(1). DOI:10.1016/j.virol.2014.02.008 · 3.32 Impact Factor
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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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    ABSTRACT: Drug abuse alone has been shown to cause epigenetic changes in brain tissue that have been shown to play roles in addictive behaviors. In conjunction with HIV-1 infection, it can cause epigenetic changes at the viral promoter that can result in altered gene expression, and exacerbate disease progression overall. This review entails an in-depth look at research conducted on the epigenetic effects of three of the most widely abused drugs (cannabinoids, opioids, and cocaine), with a particular focus on the mechanisms through which these drugs interact with HIV-1 infection at the viral promoter. Here we discuss the impact of this interplay on disease progression from the point of view of the nature of gene regulation at the level of chromatin accessibility, chromatin remodeling, and nucleosome repositioning. Given the importance of chromatin remodeling and DNA methylation in controlling the retroviral promoter, and the high susceptibility of the drug abusing population of individuals to HIV infection, it would be beneficial to understand the way in which the host genome is modified and regulated by drugs of abuse.
    Journal of Neuroimmune Pharmacology 11/2013; 8(5). DOI:10.1007/s11481-013-9508-y · 4.11 Impact Factor
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    • "Finally, the SWI/SNF chromatin remodeling complex BAF, but not PBAF, was recently shown to facilitate the establishment of latency through repressive nucleosome positioning on the 5’ LTR. BAF knockdown resulted in fewer latent infections in both Jurkat and SupT1 T-cell lines, without affecting levels of productively infected cells [117]. The evidence therefore supports a major role for epigenetic histone modifications and chromatin remodeling leading to provirus silencing and the establishment of latent infection. "
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    ABSTRACT: Latently infected cells represent the major barrier to either a sterilizing or a functional HIV-1 cure. Multiple approaches to reactivation and depletion of the latent reservoir have been attempted clinically, but full depletion of this compartment remains a long-term goal. Compared to the mechanisms involved in the maintenance of HIV-1 latency and the pathways leading to viral reactivation, less is known about the establishment of latent infection. This review focuses on how HIV-1 latency is established at the cellular and molecular levels. We first discuss how latent infection can be established following infection of an activated CD4 T-cell that undergoes a transition to a resting memory state and also how direct infection of a resting CD4 T-cell can lead to latency. Various animal, primary cell, and cell line models also provide insights into this process and are discussed with respect to the routes of infection that result in latency. A number of molecular mechanisms that are active at both transcriptional and post-transcriptional levels have been associated with HIV-1 latency. Many, but not all of these, help to drive the establishment of latent infection, and we review the evidence in favor of or against each mechanism specifically with regard to the establishment of latency. We also discuss the role of immediate silent integration of viral DNA versus silencing of initially active infections. Finally, we discuss potential approaches aimed at limiting the establishment of latent infection.
    Retrovirology 02/2013; 10(1):11. DOI:10.1186/1742-4690-10-11 · 4.19 Impact Factor
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