Accession	GSE100376
Status	2018/3/22
Title	HIV-1 infection of human monocyte-derived dendritic cells with and without the integrase inhibitor, Raltegravir (ATAC-Seq)
Organism	Homo sapiens
Experiment type	Genome binding/occupancy profiling by high throughput sequencing
Summary	Myeloid dendritic cells (DCs) have the innate capacity to sense pathogens and orchestrate immune responses. However, DCs do not mount efficient immune responses to HIV-1, due to potent restriction at the level of reverse transcription. Here, we uncover that when reverse transcription is allowed to proceed, DCs detect HIV-1 in distinct phases, before and after integration. Blocking integration suppressed, but did not abolish, activation of the transcription factor, IRF3, interferon responses, and DC maturation. The cytoplasmic DNA sensor, cGAS, and the E3 ligase, TRIM5, were both required for these responses. Consistent with two stages of innate activation, HIV-1 altered host chromatin accessibility before and after integration. Our studies support the hypothesis that HIV-1 replication increases the amount of material available for sensing and that cGAS signaling can be tuned by discrete inflammatory inputs to drive DC maturation.
Samples	GSM ID Sample info Characteristics Description GSM2679737 mock_D223 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 0 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx GSM2679738 HIV_16h_D223 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 16 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx GSM2679739 HIV_32h_D223 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 32 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx GSM2679740 HIV_48h_D223 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 48 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx GSM2679741 RAL_D223 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 0 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir GSM2679742 HIV_RAL_16h_D223 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 16 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir GSM2679743 HIV_RAL_32h_D223 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 32 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir GSM2679744 HIV_RAL_48h_D223 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 48 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir GSM2679745 mock_D224 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 0 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx GSM2679746 HIV_16h_D224 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 16 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx GSM2679747 HIV_32h_D224 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 32 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx GSM2679748 HIV_48h_D224 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 48 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx GSM2679749 RAL_D224 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 0 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir GSM2679750 HIV_RAL_16h_D224 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 16 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir GSM2679751 HIV_RAL_32h_D224 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 32 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir GSM2679752 HIV_RAL_48h_D224 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 48 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir GSM2679753 mock_D225 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 0 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx GSM2679754 HIV_16h_D225 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 16 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx GSM2679755 HIV_32h_D225 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 32 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx GSM2679756 HIV_48h_D225 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 48 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx GSM2679757 RAL_D225 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 0 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir GSM2679758 HIV_RAL_16h_D225 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 16 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir GSM2679759 HIV_RAL_32h_D225 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 32 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir GSM2679760 HIV_RAL_48h_D225 cell type:monocyte derived dendritic cells ATAC-Seq of human monocyte-derived DCs 48 hours after infection with HIV-GFP in the presence of virus-like particles packaging Vpx with Raltegravir
Platform	GPL18573  : Illumina NextSeq 500 (Homo sapiens)
Literature	29544097
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