Project description:This study examine the transcriptional profiling of HIV dual reporter non-infected, latetnly infected and productively infected Jurkat T cells.

2021-01-21 | GSE149492 | GEO

HiC and H3K27ac HiChIP of clonal Jurkat T cells infected HIV-1 model NL4-3-D6-drEGFP

Project description:HIV-1 integration introduces ectopic transcription factor binding sites into host chromatin. We postulate that the integrated provirus serves as an ectopic enhancer that recruits additional transcriptional factors to the integration locus, increases chromatin accessibility, changes 3D chromatin interactions, and enhances both retroviral and host gene expression. We used 4 well-characterized HIV-1-infected cell line clones having unique integration sites and low to high levels of HIV-1 expression. Using single-cell DOGMA-seq, which captured the heterogeneity of HIV-1 expression and host chromatin accessibility, we found that HIV-1 transcription correlated with HIV-1 accessibility and host chromatin accessibility. HIV-1 integration increased local host chromatin accessibility within ~5–30 kb distance. CRISPRa and CRISPRi-mediated HIV-1 promoter activation and inhibition confirmed integration site-dependent HIV-1-driven changes of host chromatin accessibility. HIV-1 did not drive chromatin confirmation changes at the genomic level (by Hi-C) or the enhancer connectome (by H3K27Ac HiChIP). Using 4C-seq to interrogate HIV-1-chromatin interactions, we found that HIV-1 interacted with host chromatin ~100–300 kb from the integration site. By identifying chromatin regions having both increased transcription factor activity (by ATAC-seq) and HIV-1-chromtain interaction (by 4C-seq), we identified enrichment of ETS, RUNT, STAT, and ZNF transcription factor binding that may mediate HIV-1-host chromatin interactions. Our study found that HIV-1 promoter activity increased host chromatin accessibility, increased HIV-1-host chromatin interactions in an integration site dependent manner, within the existing chromatin boundaries without impacting broader host chromatin structure.

2023-05-01 | GSE230313 | GEO

Transcriptional Profiling of Untreated, HIV-1 Vector-Infected and TNFalpha-treated Jurkat T cells

Project description:Jurkat T cells (in triplicate per treatment group) were left untreated in culture, infected with VSV-G-pseudotyped HIV-based vector (which transduces Tat and eGFP) or treated with TNFalpha. Keywords: parallel sample

2005-04-07 | GSE2504 | GEO

Expression profiling of Jurkat cells infected with HIV-1 and treated with digoxin or DMSO

Project description:To determine changes of gene expression in human CD4+ T cells (Jurkat) infected with HIV-1 and treated with digoxin. Cells were infected (MOI 0.01) with a single cycle HIV-1 delta env expressing GFP and pseudotyoed with VSV-G in the presence of 400nM digoxin or DMSO. Cells were harvested 36 hours post-infection and processed for RNAseq

2017-08-19 | E-MTAB-5982 | biostudies-arrayexpress

HIV-1 NL4-3

Project description:A population of HIV-1 NL4-3 sequences from an evolution experiment (raw sequence reads)

| PRJNA304947 | ENA

Transcription profiling of untreated, HIV-1 vector-infected and TNFalpha-treated human Jurkat T cells

2007-08-25 | E-GEOD-2504 | biostudies-arrayexpress

Single Cell Multiome of isogenic HIV-1-infected Jurkat T cells

2023-05-01 | GSE229928 | GEO