Genomic profiling of HIV-1 integration in microglia cells links viral integration to the topologically associated domains

HIV-1 encounters the hierarchically organized host chromatin to stably integrate and persist in anatomically distinct latent reservoirs. The contribution of genome organization in HIV-1 infection has been largely understudied across different HIV-1 targets. Here we determine HIV-1 integration sites (IS), associate them to chromatin and expression signatures at different genomic scales in a microglia cell model and profile them together with the primary T cell reservoir. HIV-1 insertions into introns of actively transcribed genes with IS hotspots in genic- and super-enhancers, characteristic of blood cells, are maintained in the microglia cell model. Genome organization analysis reveals dynamic CCCTC-binding factor (CTCF) clusters in cells with active and repressed HIV-1 transcription, while CTCF removal impairs viral integration. We identify CTCF-enriched topologically associated domain (TAD) boundaries with signatures of transcriptionally active chromatin as HIV-1 integration determinant in microglia and CD4+ T cells, highlighting the importance of the host genome organization in HIV-1 infection. Overall design: For single cell RNA-Seq (scRNA-Seq), iPSC-derived microglia cells (~0.5 million cells) were pre-treated with Human Fc block (BD, Catalog # 564219) for 10 min at room temperature, then incubated on ice for 40 min with a cocktail of oligo-indexed antibodies to 41 surface marker proteins. The cocktail included 30 antibodies from the BD ABseq Immune Discovery panel (BD,Catalog # 625970) supplemented with 11 antibodies to microglia-specific antigens as prescribed by the manufacturer (see table below). After a total of three washes with BD Stain buffer (Catalog # 554656), cells were applied to the cartridge of the BD Rhapsody system for single-cells RNAseq/ABseq. After single cell capturing with barcoded beads, we performed reverse transcription and generated Whole Transcriptome and ABseq libraries. Sequencing was performed at Medgenome, Inc. using the Illumina HiSeq X system, PE150.