Transcription silencing and sub-nuclear positioning of the HIV-1 provirus

The human immunodeficiency virus (HIV-1) is a retrovirus that integrates into host cell’s chromatin for gene expression and replication. As integrated provirus HIV-1 is able to persist for long periods of time during antiretroviral therapy in quiescent memory T cells reservoirs. Understanding how these reservoirs are established, maintained, and reactivated is essential for developing methods to target and eventually eradicate HIV-1 infection. Latency is likely established and maintained by numerous blocks at multiple steps in the HIV-1 gene expression pathway, which potentially complicates eradication strategies that aim at the purging of HIV-1 reservoirs from the infected patient. Recently, it has been proposed that the spatial distribution of genes within the nucleus contributes to transcriptional control allowing optimal gene expression as well as constitutive or regulated gene repression. Hence, the position of the provirus within the nucleus and its long-range interaction with other genomic regions could be another unexplored level of HIV-1 transcription control. In order to gain insight in the conformation of chromatin at the site of HIV-1 integration we exploited seven different cell lines carrying a single latent provirus, which represent well-characterized models of HIV-1 latency. In the silenced state, the provirus was consistently found at the nuclear periphery. After induction of transcription the location of the transcribing provirus remained peripheral. Furthermore, in the J-lat A1 cell line, chromatin conformation studies revealed that the proviral vector is associated to a pericentromeric region of chromosome 12 (Ch12q12) located at the periphery of the nucleus. Even though the location of the provirus did not change in transcriptionally active cells, the association between these two loci was lost. These results reveal a new mechanism of transcriptional silencing involved in HIV-1 post-transcriptional latency and reinforce the notion that gene transcription can occur also at the nuclear periphery.