The molecular biology of HIV latency: breaking and restoring the Tat-dependent transcriptional circuit

Abstract

Purpose of review: Despite the remarkable success of intensive antiretroviral drug therapy in blocking the HIV replication, the virus persists in a small number of cells in which HIV has been transcriptionally silenced. This review will focus on recent insights into the HIV transcriptional control mechanisms that provide the biochemical basis for understanding latency.

Recent findings: Latency arises when the regulatory feedback mechanism driven by HIV Tat expression is disrupted. Small changes in transcriptional initiation, induced by epigenetic silencing, can lead to restrictions in Tat levels and entry of proviruses into latency. In resting memory T-cells, which carry the bulk of the latent viral pool, additional restrictions limiting cellular levels of the essential Tat cofactor P-TEFb and the transcription initiation factors nuclear factor kappa B and nuclear factor of activated T cells ensure that the provirus remains silenced unless the host cell is activated.

Summary: Strategies to purge the latent proviral pool require nontoxic activator molecules. The multiple restrictions imposed on latent proviruses that need to be overcome suggest that proviral reactivation will not be achieved when only a single reactivation step is targeted but will require both removal of epigenetic blocks and the activation of P-TEFb. Alternatively, new inhibitors that block proviral reactivation could be developed.

Figure 1. Reactivation of latent proviruses

(A) Latent HIV provirus. In latent proviruses transcription elongation is very inefficient due to absence of the transcription elongation factor NF-κB as well as chromatin restrictions (not shown for simplicity). The small number of transcription complexes that are able initiate and elongate through TAR are subject to additional elongation restrictions by NELF. NELF forces premature termination leading to an exceptionally low level of transcription from the latent provirus. (B) NF-κB and Tat-activated transcription. Initiation is strongly induced by NF-κB, which acts primarily to remove chromatin restrictions near the promoter through recruitment of histone acetyltransferases. Under these circumstances promoter clearance is also much more efficient and relatively few of the elongation complexes pause near the promoter. After the transcription through the TAR element, both NELF and the Tat/P-TEFb complex (including CDK9 and CycT1 and the accessory elongation ELL2) are recruited to the elongation complex via binding interactions with TAR RNA. This activates the CDK9 kinase and leads to hyperphosphorylation of the CTD of RNA polymerase II, Spt5 and NELF-E. The phosphorylation of NELF-E leads to its release. The presence of hyperphosphorylated RNAP II and Spt5 allows enhanced transcription of the full HIV genome.

Figure 2. Autoregulation of HIV transcription by Tat

Small in initiation efficiency, due to transcriptional interference or epigenetic silencing, reduce Tat levels in the cell and disproportionately inhibit transcription, driving the HIV provirus into latency. Reinitiation stimulates Tat production and restores full transcription efficiency.

Figure 3. Stages in epigenetic silencing

Latent HIV proviruses almost invariably have deacteylated histones, but clones show heterogenous levels of methylated histones and methylated DNA. This suggests that silencing is an ordered and progressive process, with DNA methylation being a sign of the most repressed state.

Figure 4. Control of P-TEFb by Tat

In resting CD4+ T-cells the majority of the P-TEFb in cells is found in a transcriptionally inactive snRNP complex containing 7SK RNA, HEXIM and the RNA binding proteins MePCE and LARP7. Tat disrupts this complex by displacing HEXIM and forming a stable complex with P-TEFb. Prior to recruitment to the transcription complex a larger complex is formed between P-TEFb and transcription elongation factors from the mixed lineage leukemia (MLL) family, including ELL2. A small fraction of the Tat in cell is also able to form a complex with 7SK RNA in the absence of HEXIM1.