Supplementary MaterialsS1 Table: List of statistically significant differentially expressed genes between unstimulated and stimulated peripheral CD4+ T cells from your Resting-cell model

Supplementary MaterialsS1 Table: List of statistically significant differentially expressed genes between unstimulated and stimulated peripheral CD4+ T cells from your Resting-cell model. genes (FDR 0.05) in stimulated vs. unstimulated peripheral CD4+ T cells from your Resting-cell model, the Wild-type model (wtNL4.3) and CD4+ T cells NSC 663284 from ART-suppressed individuals. Genes are ranked alphabetically and the average log2 fold switch (FC) is shown for each model.(PDF) ppat.1009060.s004.pdf (187K) GUID:?A1AC5FF6-0D7B-46A7-81D1-A9D2FF7AAB64 S1 Fig: Progression through HIV transcription stages. This schematic representation shows relative levels of HIV transcription initiation, elongation, completion, and multiple splicing quantified in latently/unstimulated and productively/stimulated HIV infected cells from your Dual-reporter, Resting-cell, and Wild-type main cell HIV latency models and from CD4+ T cells from HIV-infected NSC 663284 ART-suppressed individuals. The level depicts the maximal block to transcription BTF2 (reddish) to no transcriptional block (green), and the blue arrow indicates the comparative progression through each stage of HIV transcription.(TIF) ppat.1009060.s005.tif (3.3M) GUID:?C231B0F8-3D17-49B0-A723-6847551EC4D4 S2 Fig: The Wild-type computer virus model using integrase inhibitors. (A) Diagram of the model, (B) total HIV NSC 663284 DNA, (C) level of HIV transcripts million cells, (D) level of HIV transcripts per provirus, (E) progression through HIV transcription stages. Individual values per donor (dots), and median and range (bars) are shown. Unstimulated cells at days 10 and 12 post-infection are shown in light colors and stimulated cells at day 12 in dark color.(TIF) ppat.1009060.s006.tif (4.9M) GUID:?AEFFA2E9-ABB8-4140-87B1-17F99C232A21 S3 Fig: The Resting-cell model in tonsil-CD4+ T cells. (A) Level of HIV transcripts per million cells, (B) progression through HIV transcription stages. Individual values per donor (dots), and median and range (bars) are shown. Unstimulated cells are shown in light color and stimulated cells in dark color.(TIF) ppat.1009060.s007.tif (2.8M) GUID:?F887EB91-111D-4ECB-A365-B7BD7155537A S4 Fig: Effect of bound virions around the Resting-cell model. (A) Diagram of the model, (B) total HIV DNA, (C) level of HIV transcripts per million cells, (D) level of HIV transcripts per provirus, (E) progression through HIV transcription stages. Individual values per donor (dots), and median and range (bars) are shown. Non-pronase treated cells are shown in light color and pronase treated cells in dark color.(TIF) ppat.1009060.s008.tif (2.9M) GUID:?586241EC-B13F-4739-9385-699114CFE204 S5 Fig: The Dual-reporter computer virus model time course. (A-B) Level of HIV transcripts per million cells at days 3 and 10 after contamination, (C-D) Level of HIV transcripts per provirus at days 3 and 10 after contamination, (E-F) progression through HIV transcription stages at days 3 and 10 after contamination. Individual values per donor (dot) are shown. Double unfavorable and latent cells are shown in light colors and productive cells in dark color.(TIF) ppat.1009060.s009.tif (4.2M) GUID:?E7DE6E4C-4A0C-4E36-A85D-DD47A5F1E7BE S6 Fig: Comparison of HIV transcriptional initiation, elongation, completion, and multiple splicing across all donors. Levels of HIV transcriptional initiation, elongation, completion, and multiple splicing are shown in the latent (unstimulated) and productive (stimulated) populations from all donors used in the three main models (Figs ?(Figs22C4) plus supplementary experiments (S2CS4 Figs). Bars show the median; P-values were calculated using the Wilcoxon signed rank test.(TIF) ppat.1009060.s010.tif (828K) GUID:?5C880BB8-53F4-4CC4-9970-B2F8E9F4C3AD Data Availability StatementRNA-sequencing datasets were submitted to the NCBI Gene Expression Omnibus (GEO) repository under accession number GSE144585 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144585). All other relevant data are within the manuscript and its Supporting Information files. Abstract It is unclear what mechanisms govern latent HIV contamination or in main cell models. To investigate these questions, we compared the HIV and cellular transcription profile in three main cell models and peripheral CD4+ T cells from HIV-infected ART-suppressed individuals using RT-ddPCR and RNA-seq. All main NSC 663284 cell models recapitulated the block to HIV multiple splicing seen in cells from ART-suppressed individuals, suggesting that this may be a key feature of HIV latency in main CD4+ T cells. Blocks to HIV transcriptional initiation and elongation were observed more variably among models. A common set of 234 cellular genes, including users of the minor spliceosome pathway, was differentially expressed between unstimulated and activated cells from main cell models and ART-suppressed individuals, suggesting these genes may play a.