The chromatin landscape at the HIV-1 provirus integration site determines viral expression.

Gerlinde Vansant,Eduard Zorita,Dalibor Miklík,Katerina Trejbalová,Heng-Chang Chen,Guillaume Filion,Zeger Debyser

doi:10.1093/nar/gkaa536

Abstract

HIV-1 persists lifelong in memory cells of the immune system as latent provirus that rebounds upon treatment interruption. Therefore, the latent reservoir is the main target for an HIV cure. Here, we studied the direct link between integration site and transcription using LEDGINs and Barcoded HIV-ensembles (B-HIVE). LEDGINs are antivirals that inhibit the interaction between HIV-1 integrase and the chromatin-tethering factor LEDGF/p75. They were used as a tool to retarget integration, while the effect on HIV expression was measured with B-HIVE. B-HIVE tracks insert-specific HIV expression by tagging a unique barcode in the HIV genome. We confirmed that LEDGINs retarget integration out of gene-dense and actively transcribed regions. The distance to H3K36me3, the marker recognized by LEDGF/p75, clearly increased. LEDGIN treatment reduced viral RNA expression and increased the proportion of silent provirus. Finally, silent proviruses obtained after LEDGIN treatment were located further away from epigenetic marks associated with active transcription. Interestingly, proximity to enhancers stimulated transcription irrespective of LEDGIN treatment, while the distance to H3K36me3 only changed after treatment with LEDGINs. The fact that proximity to these markers are associated with RNA expression support the direct link between provirus integration site and viral expression.

Highlights

During infection with the human immunodeficiency virus type 1 (HIV-1), a DNA copy of the viral genome is inserted as provirus in a host chromosome by the viral integrase
We have previously shown that LEDGIN treatment inhibits HIV-1 integration and that residual integrants are more often in a transcriptionally inactive state that is refractory to reactivation [31]
While on average 10 000 insertion sites were retrieved in the control samples, only 500 were obtained in cells treated with 31.25 ␮M of LEDGIN (Figure 1D)

Summary

Introduction

During infection with the human immunodeficiency virus type 1 (HIV-1), a DNA copy of the viral genome is inserted as provirus in a host chromosome by the viral integrase. Part of the proviruses enter a silent mode without gene expression rendering the virus invisible for the host immune system. These latent HIV proviruses mainly reside in long lived memory CD4+ T cells, that form a latent reservoir with an estimated half-life of 44 months [1,2,3]. Less studied is the role of HIV-1 integration in the host genome and the impact of integration site selection on proviral gene expression. The Bushman lab reported that low-expressing proviruses integrate more often in genomic regions devoid of proteincoding genes and centromeric heterochromatin [17] and are less associated with DNase I sensitive sites, CpG islands and

Methods

Results

Conclusion