Repressive LTR Nucleosome Positioning by the BAF Complex Is Required for HIV Latency

Abstract

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.

Stable Phenotypic Changes of the Host T Cells Are Essential to the Long-Term Stability of Latent HIV-1 Infection

“…While chromatin and histone modifications have been reported for some latent HIV-1 LTRs (77-79), the nature of these modifications and their downstream effects are not unique to the latent LTR but are shared with many cellular gene promoters that are transcriptionally silent in quiescent T cells but are induced upon T cell activation. For example, Rafati et al reported that for latent HIV-1 infection events, the two nucleosomes that are found at the LTR are actively repositioned away from their predicted DNA binding sites as a function of the presence of BAF or PBAF, respectively, so as to possibly restrict the access of activating transcription factors to the LTR (80). Similar findings have been reported previously for many inactive but inducible cellular promoters (for recent reviews, see references 81 and 82).…”

Quantification of HIV-1 latency reversal in resting CD4 + T cells from patients on suppressive antiretroviral therapy

“…Alternatively, preactivation latency has also been described, where HIV-1 DNA can be integrated into quiescent rCD4 cells via interactions of chemokines with CCR7, CXCR3, and CCR6 in the absence of productive infection (21). Independently of whether productive infection has occurred, the G 0 resting state in rCD4 cells contributes to the inhibition of HIV-1 transcription and translation through a variety of mechanisms, including the sequestration of transcription factors NF-κB and NFAT (22,23); association of P-TEFb with the inhibitory 7SK snRNA complex (24,25); and association of the BAF complex and histone deacetylases with the HIV long terminal repeat (26,27). In addition to transcriptional blocks, posttranscriptional nuclear sequestration of the spliced tat and rev HIV-1 mRNAs in latently infected rCD4 cells prevent productive infection (28).…”

Glioma tumor suppressor candidate region gene 1 (GLTSCR1) and its paralog GLTSCR1-like form SWI/SNF chromatin remodeling subcomplexes

“…ARID1A is the most commonly mutated SWI/SNF subunit in cancer, due to transcriptional functions that are non-redundant with ARID1B (21,22); however, cancers with deletions in ARID1A are dependent on ARID1B for viability (23) due to redundant, essential functions at enhancers (22). Additionally, homologous complexes can display transcriptionally antagonistic roles, as has been observed for ARID1A and ARID2-containing complexes at specific gene targets (8,20,24). Targeting specific SWI/SNF complexes has been proposed both for alleviating subunit-specific pathogenic function as well as to target essential redundant functions in cancers with mutations in the genes for specific subunits (25,26).…”