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Direct non-productive HIV-1 infection in a T-cell line is driven by cellular activation state and NFκB Dahabieh, Matthew S; Ooms, Marcel; Brumme, Chanson; Taylor, Jeremy; Harrigan, P R; Simon, Viviana; Sadowski, Ivan Feb 7, 2014

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RESEARCHDirect non-productive HIV4,retrehmlytivated by cellular activation, for example. This results latent state. Nevertheless, known HIV-1 transcriptionalDahabieh et al. Retrovirology 2014, 11:17http://www.retrovirology.com/content/11/1/17Without the ability to identify latently infected cellsearly, and in the absence of activation stimuli, it isbuilding 18-50, New York, NY 10029, USAFull list of author information is available at the end of the articlein proviral transcription and production of new virions[4]. Thus, HIV-1 latency, which allows the virus to per-sist indefinitely during highly active antiretroviral ther-apy (HAART), is one of the most significant barriers toHIV-1 eradication.silencing mechanisms include: 1) suboptimal T-cell acti-vation, 2) low levels of transcriptional activator function,3) restrictive chromatin structure at the site of integra-tion, 4) transcriptional interference at the site of inte-gration, 5) low pTEF-b (CDK9/Cyclin T1) levels, and6) repressive HIV-1 LTR nucleosome positioning andhistone post-translational modifications (reviewed in[1-3]).* Correspondence: marcel.ooms@mssm.edu2Department of Microbiology, The Global Health and Emerging PathogensInstitute; Mount Sinai School of Medicine, 1468 Madison Avenue, Annenbergantly, latent HIV-1 remains functional and can be reac-proviral integration sites and cellular activation state on direct non-productive infections at the single cell level.Proviral integration site mapping of infected Jurkat T-cells revealed that productively and non-productively infectedcells are indistinguishable in terms of genomic landmarks, surrounding epigenetic landscapes, and proviralorientation relative to host genes. However, direct non-productive infections were inversely correlated with bothcellular activation state and NFκB activity. Furthermore, modulating NFκB with either small molecules or byconditional overexpression of NFκB subunits was sufficient to alter the propensity of HIV-1 to directly enter anon-productive latent state in newly infected cells. Importantly, this modulatory effect was limited to a short timewindow post-infection.Conclusions: Taken together, our data suggest that cellular activation state and NFκB activity during the time ofinfection, but not the site of proviral integration, are important regulators of direct HIV-1 non-productive infections.Keywords: HIV-1, Latency, LTR, CMV, Promoter, eGFP, mCherry, Double-label, Silent-infection, NFκBBackgroundIntegrated HIV-1 provirus transcribes messenger andgenomic RNA to produce progeny virions. However,the HIV-1 promoter can also exist in an inactive state,and the subsequent lack of viral products allows la-tently infected cells to escape both immune surveillanceand viral cytopathic effects (reviewed in [1-3]). Import-HIV-1 latency is generally regarded as a product ofproviral transcriptional silencing. Numerous silencingmechanisms have been characterized using in vitro la-tency models that require cellular activation and long-term culturing to identify and isolate latently infectedcells. Given these requirements, the majority of knownsilencing mechanisms pertain to the progressive silen-cing of productive infections and the maintenance of aline is driven by cellular aMatthew S Dahabieh1, Marcel Ooms2*, Chanson Brummeand Ivan Sadowski1AbstractBackground: Molecular latency allows HIV-1 to persist inprovirus integrated into host chromosomal DNA. Multiplehave been described in the context of progressive epigenunderstanding of the determinants critical for the establisResults: In this study, we used a recently described, doub© 2014 Dahabieh et al.; licensee BioMed CentCommons Attribution License (http://creativecreproduction in any medium, provided the orOpen Access-1 infection in a T-cellctivation state and NFκBJeremy Taylor4, P Richard Harrigan4, Viviana Simon2,3sting memory CD4+ T-cells as transcriptionally silentanscriptional regulatory mechanisms for HIV-1 latencytic silencing and maintenance. However, ourent of latency in newly infected cells is limited.fluorescent HIV-1 latency model to dissect the role ofral Ltd. This is an open access article distributed under the terms of the Creativeommons.org/licenses/by/2.0), which permits unrestricted use, distribution, andiginal work is properly cited.Dahabieh et al. Retrovirology 2014, 11:17 Page 2 of 17http://www.retrovirology.com/content/11/1/17difficult to evaluate which HIV-1 transcriptional silen-cing mechanisms are critical for latency establishment innewly infected cells. Thus, we and others have recentlydeveloped double-labeled HIV-1 latency models that candetect both productive and non-productive proviralstates early post-infection [5,6]. Application of thesemodels to both cell lines and activated primary CD4+T-cells suggests that direct non-productive infections(latency) actually represent the majority of HIV-1 infec-tions [5,6]. This conclusion is further supported byother studies identifying silent/inducible infectionsearly in infection [7,8]. Taken together, these studiesprovide significant support for the role of direct silen-cing in HIV-1 latency establishment, and highlight theimportance of studying establishment mechanisms innewly infected cells.In this study, we use our doubly fluorescent HIV-1 re-porter [5] to directly evaluate potential mechanisms re-sponsible for the formation of direct non-productivestates in newly infected Jurkat T-cells. We focus on twohighly variable HIV-1 transcriptional regulatory mecha-nisms: 1) proviral integration site, and 2) cellular activa-tion state and NFκB signaling. First, we show that directnon-productive infections occur at all sites of integra-tion, thereby excluding a role for viral integration sitelocations. Instead, the occurrence of non-productive in-fections was inversely correlated with cellular activationstate and NFκB activity. Moreover, modulating NFκBlevels at the time of infection, either by small moleculesor NFκB subunit overexpression, was sufficient to alterthe occurrence of non-productive infection in newlyinfected cells. Taken together, our data suggest that thecellular level of NFκB activity at the time of infection,rather than the site of viral integration, controls theestablishment of HIV-1 latency in newly infected T-celllines. These findings are of relevance to HIV-1 eradica-tion strategies since they may point to putative targetsfor therapeutic interventions minimizing HIV-1 latencyestablishment rather than latency reactivation.ResultsThe doubly labeled Red-Green-HIV-1 (RGH) molecularclone is a recently described model that enables investiga-tion of HIV-1 transcriptional regulatory mechanisms innewly infected, native state cells. This single-cycle vectorincorporates both an LTR-driven gag-eGFP marker, and aCMV-driven mCherry marker in place of Nef, to allow foridentification of both productively (eGFP+mCherry+) andnon-productively (eGFP- mCherry+) infected cells at sin-gle cell resolution (Figure 1A, [5]). We have previouslyused this vector to determine that the majority of HIV-1proviruses are directly silenced shortly after infection inboth cell lines and primary CD4+ T cells [5]. Since themajority of HIV-1 latency mechanisms described pertainto progressive epigenetic silencing, the determinants ofdirect non-productive infection remain unknown. In thisstudy, we sought to use the recombinant RGH model todissect the roles of proviral integration site and cellular ac-tivation state in regulating direct non-productive infectionin Jurkat T-cells.Both productive and non-productive HIV-1 proviruses areintegrated at similar locationsHIV-1 proviral integration sites are highly variable[1-3,9,10]. In some latency models, proximity to certaingenomic features (alphoid repeats - [11], gene deserts -[12], and very highly expressed genes [7,12]) has beenassociated with proviral transcriptional silencing. How-ever, a recent meta-analysis of integration sites foundthat, in five distinct latency models using either cell-lines or primary T-cells, these associations are not uni-versal properties of HIV-1 latency, but rather are specificto the models in which they were identified [13]. Import-antly, this study highlights the importance of characteriz-ing the effect of integration site in each individual latencymodel. In this light, we sought to determine whetherproviral integration sites were different between product-ively and non-productively RGH-infected Jurkat cells. Wesorted total RGH infected cells into non-productively in-fected ‘red’ (eGFP- mCherry+; ~4% of total), and product-ively infected ‘yellow’ (eGFP+mCherry+; ~2% of total)cell populations with more than 90% purity (Figure 1B).The ‘double negative’ population (eGFP- mCherry-) wasalso sorted and analyzed since we previously estimatedthat ~30% of all RGH infections result in direct repressionof both the LTR and CMV promoters [5]. To identify sitesof viral integration, genomic DNA from each populationwas extracted, digested with MseI, and ligated to adapters[14]. Nested PCR was used to amplify LTR-host chromo-some junctions and resulting amplicons were sequencedby 454 pyrosequencing [14]. Reads were filtered for qualityand mapped to the human genome using the INSIPIDpipeline [15].We mapped 2,900 and 4,271 unique integration sitesin the ‘red’ and ‘yellow’ populations, respectively. Con-sistent with our previous characterization of ‘doublenegative’ RGH infected cells [5], we were also able tomap 1,195 integration sites in this population, whichrepresent proviruses in which both eGFP and mCherrymarkers were silenced directly upon infection.To compare the integration sites between the cell pop-ulations, we first compared the density of integrations(1 Mb windows) across the whole human genome. High-resolution mapping of the integrations found withinchromosome one, as well as within the entire humangenome, revealed that in all cell populations integrationswere largely constrained to gene dense areas, and thatthe integration densities in all three cell populationsDahabieh et al. Retrovirology 2014, 11:17 Page 3 of 17http://www.retrovirology.com/content/11/1/17were largely overlapping (Figure 2A). Quantification ofintegration sites and gene densities showed a highlysignificant correlation for each population (Spearmancorrelation, ‘double negative’, rho = 0.78; ‘red’, rho = 0.83;‘yellow’, rho = 0.85; p < 0.001 in all cases, Figure 2B).This preference for HIV-1 integrations in gene-rich areasis consistent with previous reports [9,10]. Quantificationof integration density across the genome revealed similarintegration site distributions for each of the ‘doublenegative’, ‘red’, and ‘yellow’ populations (Figure 2C). OfFigure 1 Experimental outline for integration site mapping in newly infin this study. The virus contains a Gag fused eGFP marker under the control ounder the control of the CMVIE promoter inserted into the nef position. B: Schinfected (RGH) Jurkat cells used for integration site mapping. Total RGH infectgreater than 90% purity four days post-infection. Genomic DNA from approxito map HIV-1 integration sites by 454 deep sequencing.note, we did observe a minor but statistically significantdecrease in integration density for the ‘red’ population inchromosome 18 (Figure 2C – p < 0.05). We also observed amodest but statistically significant increase in integrationsinto chromosomes 3 and 16, and a decrease in integrationsinto chromosome 6 for the ‘double negative’ population(Figure 2C - p < 0.05, ANOVA for number of integrationsin each chromosome, and Student’s T test for number of'double negative' integrations compared to 'red' and 'yellow'populations).ected cells. A: Schematic representation of Red-Green-HIV-1 (RGH) usedf the LTR promoter as well as a constitutively expressed mCherry markerematic representation for isolation of productively and non-productivelyed Jurkat cells were sorted based on eGFP and mCherry expression tomately 5 x 105 cells of each sorted cell-population was isolated and usedDahabieh et al. Retrovirology 2014, 11:17 Page 4 of 17http://www.retrovirology.com/content/11/1/17High-throughput analysis of HIV-1 integration sites haspreviously revealed genomic preferences for HIV-1 integra-tion in terms of gene density, distance to gene boundariesand transcriptional start sites (TSS), DNaseI hypersensitivity,CpG density, gene expression, and GC content [9,10]. EachFigure 2 Productive and non-productive RGH infections occur at similawere mapped by 454 pyrosequencing in RGH infected Jurkat cells sorted forintegrations, 2,900 eGFP- mCherry+ integrations, and 4,271 eGFP+mCherry+ ited for chromosome one (left panel) and the entire genome (right panel). ThUCSC hg18 reference genome, while the inner tracks (colored line plots) indicagainst gene density (genes per chromosome) for each sample. A linear regrecance by Spearman correlation. Rho coefficients and p values are listed. C: Thsorted cell population. Error bars represent standard deviations of triplicate exof these characteristics are indicative of HIV’s preference tointegrate into nucleosome-associated DNA within theintrons of actively transcribed genes [9,10]. We used the IN-SIPID pipeline (Bushman Lab, University of Pennsylvania)to compare the genomic signatures of integration betweenr viral integration sites across the genome. A: Viral integration siteseGFP and mCherry expression. Data is shown for 1,195 eGFP- mCherry-ntegrations. Integrations and gene density across 1 Mb windows are plot-e outer track (black histogram) depicts gene density as annotated in theate relative numbers of viral integrations. B: Integration density is plottedssion line of the plotted points is shown. Samples were tested for signifi-e proportion of total integrations in each chromosome is shown for eachperiments * p < 0.05 (Student’s T test).each RGH infected population (Figure 3A). As a whole, thegenomic properties of integrations in each population wereconsistent with previous studies [9,10], indicating that theRGH virus integrates into host chromatin similarly to wildtype HIV-1. Importantly, the genomic signatures of the inte-gration events in the ‘red’ population were highly similar tothose in the ‘yellow’ population, indicating that they do notaffect non-productive and productive infections (Figure 3A).Of note, we did observe a minor , but significant decreasein intergenic space (‘intergenic width’ – Figure 3A, p < 0.05,Wald test), and association with highly expressed genes(‘top ½ expr. 1 Mb Unigene’ – Figure 3A, p < 0.05, Waldtest), suggesting that integrations in the ‘red’ population(non-productive infections) may be located in slightly lessgene dense and less expressed regions than in the ‘yellow’population. The profile of integrations in the ‘doublenegative’ population were similar to the ‘red’ and ‘yellow’populations but the number of integrations into genes(coding or intronic sequence and irrespective of expression)was significantly increased (‘in gene, refSeq’ – Figure 3A,p < 0.001, Wald test; ‘gene expr. 1 Mb, Unigene’ –Figure 3A, p < 0.05). These findings suggest that, in certaincontexts, integration into genes could repress transcriptionof both the LTR and CMV promoters in the RGH provirus(‘double negative’ population). Of note, the gene expressionprofiles used in this analysis were obtained from previousindependent datasets produced with Jurkat cells [16].We also compared the epigenetic landscape surroundingviral integration sites in the different RGH infected popula-tions using INSIPID’s annotated epigenetic data from inde-pendent Jurkat and CD4+ T-cell experiments [15,17-23].No significant differences were observed between the ‘red’and ‘yellow’ populations (Additional file 1: Figure S1A).Integrations in the ‘double negative’ population were,however, significantly less frequently associated with nu-cleosomes and histone post-translational modifications, ascompared to the ‘red’ or ‘yellow’ populations (Additionalfile 1: Figure S1A). This result, and the increased associ-ation with genes for the ‘double negative’ population(Figure 3A), suggests some effect of integration site onngmrsitls oenDahabieh et al. Retrovirology 2014, 11:17 Page 5 of 17http://www.retrovirology.com/content/11/1/17Figure 3 Productive and non-productive RGH infections are indistias well as proviral orientation. A: Integration sites in each of the eGFP-using the INSIPID heatmap tool for genomic features (Bushman Lab, Univedepletion of each feature, respectively, relative to matched random controrelative to the eGFP+mCherry+ population (dashes). B: The proportion of gpanel) integrations relative to total integrations is shown for each of the eGFPbars represent one standard deviation between triplicate experiments. ‘ns’ nouishable in terms of genomic features at the site of integration,Cherry-, eGFP- mCherry+, and eGFP+mCherry+ samples were comparedy of Pennsylvania). Pink and blue colors represent enrichment andf integration sites. Statistical significance (ranked Wald tests) is shownic (top panel), anti-parallel (bottom left panel) and parallel (bottom right- mCherry-, eGFP- mCherry+, and eGFP+mCherry+ infected cells. Errorn-significant; * p <0.05 (Student’s T test).Dahabieh et al. Retrovirology 2014, 11:17 Page 6 of 17http://www.retrovirology.com/content/11/1/17transcriptional repression. However, this effect is small andlikely does not explain the transcriptional differencesbetween the different RGH infected populations. Moreover,this is likely not an HIV-1 specific effect since both the LTRand CMV promoters are silenced in the ‘double negative’population.In human cells, the occurrence of transcriptionalregulation-associated histone marks is often correlated withnucleosome position relative to gene promoters and genebodies [17]. Therefore, we plotted RGH integration densitiesas a function of both the average distance across genes andthe average distance from gene transcriptional start sites(TSS), however we observed no differences between cellpopulations in either case (Additional file 1: Figure S1B).We next experimentally tested the effect of the epigeneticlandscape on the productivity of RGH infection by utilizingan N74D capsid mutant that causes integration into regionsof lower gene density and increased heterochromatin[24-26]. However, no differences were observed in the ratioof non-productive (‘red’) to productive (‘yellow’) infectionsbetween the RGH N74D capsid mutant and the wild-typeRGH vector, further suggesting that epigenetic profiles sur-rounding integration sites are not major mediators of directnon-productive infection (Additional file 1: Figure S1C).The orientation of proviral integrations within host geneshas also been implicated in HIV-1 transcriptional regulationand latency [27-29]. However, another study did notobserve a role for proviral orientation across multiplelatency models [13]. Therefore, we compared the frequencyof parallel and anti-parallel genic integrations betweenthe RGH infected cell populations. The frequency of paral-lel and anti-parallel intragenic orientations were similar(~40% of total integrations), and not significantly differentbetween cell populations (Figure 3B). Supplementary toproviral orientation, we analyzed the nucleotide sequencesaround the site of integration in RGH infected cells.These sequences were similar between cell populations andconsistent with previously described HIV-1 target sites [9](Additional file 2: Figure S2A). Moreover, gene ontologyanalysis did not reveal any differences in the types of genesharboring integrated provirus between the RGH infectedcell populations (Additional file 2: Figure S2B).Taken together, our data suggests that integration sitesfail to play a significant role in regulating direct non-productive RGH infections in newly infected Jurkat cells.Therefore, alternative mechanisms are likely to dictate thisprocess in this model T-cell system.Direct non-productive HIV-1 infection is associated withlower cellular activation and NFκB signalingHIV-1 transcription is tightly linked to both cellularactivation and the activity of signaling pathways down-stream of the T-cell receptor (reviewed in [1,3]). Moreover,the NFκB pathway is an important and potent regulator ofHIV-1 transcription (reviewed in [30]), and has been previ-ously implicated in mediating early productive HIV-1 infec-tions [7]. Given that direct non-productive RGH infectionis independent of proviral integration sites (Figures 2 and 3,S1 and S2), we speculated that differences in cellular activa-tion state and NFκB signaling around the time of infectioncould be responsible.To analyze the effect of cellular activation on non-productive RGH infection we measured CD69 expression,a well characterized early T-cell activation marker [31], inthe different populations of RGH infected cells. Stainingtotal RGH infected cells for CD69 early post-infection (fourdays) showed that the gated ‘red’ and ‘yellow’ populationsexpressed approximately 2.3 and 4.5 fold more CD69 thanmock-infected cells, respectively (Figure 4A). In contrast,the gated ‘double negative’ population (uninfected andeGFP- mCherry- infected cells) expressed CD69 at levelssimilar to the mock-infected cells (Figure 4A). Importantly,RGH infection itself did not activate Jurkat cells, as we didnot observe substantial differences in CD69 expressionbetween the total RGH infected population and mockinfected cells (Additional file 3: Figure S3A). These datasuggest that differences in LTR transcription from provi-ruses in newly infected cells are, in fact, associated withdifferences in cellular activation state.To specifically address the role of NFκB in the establish-ment of direct non-productive infections, we infected cellswith RGH and examined NFκB levels four days post-infection by intracellular staining for the DNA-binding p50subunit of NFκB and the activated form of the trans-activating p65 subunit (S529-phospho) (Figure 4B). BothNFκB subunit levels were positively correlated with activetranscription, as the gated ‘red’ and ‘yellow’ populationsexpressed approximately 1.3 and 1.5 fold more of both sub-units, respectively, whereas the ‘double negative’ populationexpressed the lowest levels of both subunits (Figure 4B). Ofnote, expression of p50 and p65-S529-phospho increasedconcomitantly in 'red' and 'yellow' cells, suggesting thatproductive infections are associated with higher cellularlevels of the activating form of NFκB (p65-p50) rather thanthe inhibitory p50-p50 form (Figure 4B). Importantly, RGHinfection does not appear to up regulate NFκB, as the totalRGH infected population and mock infected cells expressedsimilar amounts of both NFκB subunits (Additional file 3:Figure S3B).To futher evaluate the role of NFκB signaling in promot-ing productive infection in newly infected cells, we simul-taneously monitored both HIV-1 transcription as well asNFκB signaling at the single cell level. We created an RGHisogenic clone bearing the blue fluorescent protein tagBFPin place of eGFP (Red-Blue-HIV-1, RBH), as well as fiveJurkat NFκB reporter cell lines bearing integrated eGFPconstructs under the control of an NFκB responsive pro-moter (Figure 4C). Infection of Jurkat cells with RBHFigure 4 (See legend on next page.)Dahabieh et al. Retrovirology 2014, 11:17 Page 7 of 17http://www.retrovirology.com/content/11/1/17ceti-C. ErrkarecanBHκBommualysst)tituDahabieh et al. Retrovirology 2014, 11:17 Page 8 of 17http://www.retrovirology.com/content/11/1/17resulted in an infection profile similar to that of RGH i.e.the majority of RBH infections resulted in direct non-productive infection (Figure 4D). Treatment of the NFκB-eGFP reporter cell lines with known NFκB agonistsTNFα and PMA/Iono resulted in 2.2 and 3.7 fold increasesin eGFP mean fluorescence intensity (MFI), respectively(Figure 4E, Additional file 4: Figure S4A). Infection of theNFκB reporter cell lines with RBH virus showed that theproductively infected cells (tagBFP +mCherry+, ‘purple’)were characterized by higher eGFP MFI (indicative of activeNFκB signaling) compared to non-productively infectedcells (tagBFP- mCherry+ ‘red’, or tagBFP- mCherry- ‘doublenegative’, Figure 4F – clone 1, Additional file 4: Figure S4B– clones 2–4). Importantly, RBH infection itself did not upregulate NFκB, as we did not observe substantial differencesin eGFP fluorescence intensity between RBH- and mock-infected total cells (Additional file 3: Figure S3C). Thesedata are consistent with the results of the intracellular NFκBstaining of RGH infected Jurkat cells, and lend further sup-port to the role of NFκB in regulating early RGH productiveinfections.(See figure on previous page.)Figure 4 Non-productive RGH infection inversely correlates with bothdays post-infection) were assayed for cellular activation by staining with antreated with either DMSO or PMA/Ionomycin for 24 hours prior to analysis*** p < 0.001 (Student’s T test). B: Four days post-infection, RGH infected Ju(right panel) subunits and analyzed by flow cytometry. Uninfected cells webars represent standard deviations of triplicate experiments. ‘ns’ non-signifirepresentation of Red-Blue-HIV-1 (RBH) and NFκB-eGFP reporter cell lines. Rreporter cell lines contain a stably integrated eGFP marker driven by an NFupstream of a CMV minimal promoter). D: Jurkat cells were infected with cflow cytometry four days post-infection. Plots shown are representative ofwas treated with DMSO, TNFα, or PMA/Ionomycin for 24 hours prior to anbars represent one standard error of the mean. *** p < 0.001 (Student’s T teflow cytometry at four days post-infection. Cells were gated into their consrepresent one standard error of the mean. *** p < 0.001 (Student’s T test).NFκB modulating drugs administered at the time of infectioncan alter the occurrence of productive RGH infectionOur data indicate that cellular activation and NFκB signal-ing may influence the occurrence of direct non-productiveinfections in RGH infected cells (Figure 4). Therefore, wehypothesized that modulating NFκB activity during infec-tion would affect the formation of direct non-productiveinfections. To test this, we treated Jurkat cells with TNFα(NFκB signaling agonist), BMS-345541 (IκB kinase inhibi-tor), SAHA (HDAC inhibitor) or DMSO (control) duringRGH infection. The infected cells were cultured for threedays, treated with either DMSO or PMA/Iono for 24 hours,and then analyzed by flow cytometry.Cells treated with the DMSO control at the time ofinfection showed the typical higher frequency of non-productively infected cells compared to productively in-fected cells (‘red-yellow ratio’ ~1.7 – Figures 5A and B).Subsequent treatment with PMA/Iono prior to flow cy-tometry strongly induced LTR expression, resulting inan increase in productively infected cells (‘red-yellowratio’ ~0.7, Figures 5A and B). In contrast, TNFα treat-ment at the time of infection reduced the number ofnon-productively infected cells by ~2.3 fold (‘red-yellowratio’ ~0.7), indicating that NFκB up regulation duringinfection largely mitigates the formation of direct non-productive infection. Furthermore, TNFα treatment atthe time of infection prevented LTR transcriptionalsilencing days later, as PMA/Iono treatment prior toanalysis had no further effect in reducing the proportionof non-productively infected cells (Figures 5A and B).TNFα treatment at the time of infection increased thetotal number of both productive and non-productive in-fections, suggesting that proviruses present in the‘double negative population’ were shifted to productive(‘yellow’) and non-productive (‘red’) infections (compareDMSO to TNFα treatment, Figure 5A). Of note, similareffects were observed with PMA/Iono pre-treatmentwhich, in addition to other effects, stimulates NFκB ac-tivity in cells (data not shown). Conversely, down regula-llular activation and NFκB activity. A: RGH infected Jurkat cells (fourD69 antibodies and analysis by flow cytometry. Uninfected cells wereror bars represent standard deviations of triplicate experiments. * p < 0.05,t cells were stained for NFκB p50 (left panel) and p65-S529-phosphotreated with DMSO or PMA/Ionomycin for 30 min prior to analysis. Errort, * p < 0.05, ** p < 0.01, *** p < 0.001 (Student’s T test). C: Schematiccontains tagBFP in place of eGFP but is otherwise isogenic. Jurkat NFκBresponsive promoter (4x tandem NFκB cis-elements ‘GGGACTTTCC’parable amounts of RGH and RBH viral stocks. Cells were analyzed byltiple independent infection experiments. E: Jurkat NFκB reporter clone 1is by flow cytometry for eGFP mean fluorescence intensity (MFI). Error. F: Jurkat NFκB reporter clone 1 was infected with RBH and analyzed byent infected populations and then analyzed for eGFP MFI. Error barstion of NFκB by BMS-345541 treatment at the time ofinfection resulted in a ~2.7 fold increase in the fre-quency of non-productive infections (‘red-yellow ratio’~4.4, Figure 5A and B). This increase in non-productiveinfections was counteracted by subsequent PMA/Ionotreatment prior to flow cytometry, which increased pro-ductive infections by ~4.1 fold (‘red-yellow ratio’ ~1.1,Figure 5A and B). Interestingly, treatment with theHDAC inhibitor SAHA did not mitigate the formationof direct non-productive infection (‘red-yellow ratio ~1.5, Figure 5A and B), despite being a known activator ofLTR transcription in other experimental settings [32,33].This is consistent with previous reports [7], and suggeststhat epigenetic modifications, such as acetylation (sensi-tive to the HDAC1 inhibitor SAHA), are likely not amajor mediator of direct non-productive infections. In-deed, SAHA (and HDAC inhibitors in general) modulatesDahabieh et al. Retrovirology 2014, 11:17 Page 9 of 17http://www.retrovirology.com/content/11/1/17approximately 10-20% of genes non-specifically without af-fecting T cell receptor pathways [34].Taken together, these results suggest that direct non-productive RGH infection is regulated by the action ofNFκB signaling at the time of infection and that thepropensity to form a non-productive infection can bemodulated by NFκB agonists (TNFα and PMA/Iono) andantagonists (BMS-345541).Figure 5 The frequency of non-productive RGH infection can be alteredinfection. A: Jurkat cells were treated with DMSO, TNFα, BMS-345541, or SAHwith either DMSO or PMA/Ionomycin for 24 hours and analyzed by flow cytoB: Data from panel A is enumerated as the red-yellow ratio of infected cells. Esignificant, *** p < 0.001 (Student’s T test).Specifically modulating NFκB is sufficient to modulate theoccurrence of productive RGH infectionWhile the major target of TNFα signaling is NFκB, TNFαcan also affect the stress response related JNK-MAPKpathway and its downstream factor AP-1 (reviewed in [35]).Although TNFα-mediated reduction of RGH latency canlikely be attributed to NFκB (Figures 4 and 5), it is possiblethat other pleiotropic effects may be contributing to theby treatment of cells with NFκB modulating drugs at the time ofA at the time of RGH infection. Four days post-infection cells were treatedmetry. Plots shown are representative of triplicate infection experiments.rror bars represent standard deviations of triplicate experiments. ‘ns’ non-observed results. To test NFκB signaling in a more specificand temporal fashion, we generated Jurkat cell-lines bearingdoxycycline inducible versions of a dominant negative(DN) form of the IκBα repressor (S32A/S36A - [36]), or theNFκB p65 subunit to allow direct down- or up-regulationof NFκB signaling, respectively.We infected Jurkat cells containing the doxycyclineinducible constructs with RGH and cultured the cells in thepresence of doxycycline for 24 hours (day 1 to day 2 post-infection). Cells were washed and cultured in fresh completemedia until flow cytometry at four and seven dayspost-infection (Figure 6A). Expression of DN IκBα resultedin a ~1.8 fold increase in the occurrence of non-productiveinfections, relative to empty vector control cells (‘red-yellowratio’ ~3.4, Figure 6B). Of note, cells expressing the DN IκBαconstruct showed a ~1.5 fold increase in non-productivelyinfected cells even in the absence of doxycycline (‘red-yellowratio’ ~2.9, Figure 6B), which suggests leaky expression ofthe DN IκBα construct. In contrast to DN IκBα, cells ex-pressing the p65 expression construct resulted in a ~2.6 folddecrease in the proportion of non-productively infectedcells, relative to the empty vector control (‘red-yellow ratio’~0.7, Figure 6B). Importantly, these changes in productivelyand non-productively infected cells persisted even whencells were cultured in the absence of doxycycline for anadditional three days (day 7 post-infection, Figure 6B). Theseresults suggest that modulating NFκB near the time of infec-tion exerts a lasting effect on the establishment of directnon-productive infections and that the observed effects arenot due to continual modulation of NFκB signaling. Tofurther test this, we measured IκBα and p65 levels byimmunoblotting at two, four, and seven days post infection.Concurrent with the end of doxycycline treatment, weobserved a transient increase in IκBα and p65 protein levelsat day two post-infection (Figure 6C). This increase wasspecific to cells containing the expression construct andtreated with doxycycline (Figure 6C). IκBα and p65 proteinlevels decreased substantially in the absence of doxycyclinetreatment four days post-infection, and returned to baselineat seven days post-infection (Figure 6C). Importantly, cellsnlata dtheatiDahabieh et al. Retrovirology 2014, 11:17 Page 10 of 17http://www.retrovirology.com/content/11/1/17Figure 6 Direct alteration of NFκB activity near the time of infectioinfection. A. Experimental outline for doxycycline-inducible NFκB moduintegrated, doxycycline-inducible expression construct containing eitherRGH. Cells were cultured with or without doxycycline for 24 hours, andat four and seven days post-infection. Error bars represent standard devi*** p < 0.001 (Student’s T test). C: Immunoblot analysis of cells used in panto nitrocellulose membrane, and blotted with antibodies against IκBα or p6is sufficient to modulate the frequency of non-productive RGHion and RGH infection of Jurkat cells. B: Jurkat cells bearing a stablyominant negative IκBα or p65 open reading frame were infected withn washed and cultured in fresh media until analysis by flow cytometryons of triplicate experiments. ‘ns’ non-significant, * p < 0.05, ** p < 0.01,el B. Jurkat whole cell extracts were separated by SDS-PAGE, transferred5.Dahabieh et al. Retrovirology 2014, 11:17 Page 11 of 17http://www.retrovirology.com/content/11/1/17bearing the DN IκBα and p65 expression constructs stillshowed a significant change in the occurrence of product-ively and non-productively infected cells (‘red-yellow-ratio’)seven days post-infection (Figure 6B). This further supportsthe idea that modulating NFκB activity near the time ofinfection alters the fate of productive RGH infection on apermanent basis.The determination of productive RGH infection occursaround the time of infectionModulating NFκB activity at the time of infection alteredthe proportion of non-productive RGH infections days later(Figures 5 and 6). Therefore, we wanted to determine thetime frame in which infection productivity is amenable topermanent modification by TNFα treatment. We reasonedthat if a window of opportunity existed to alter the infectionproductivity, treatment of cells with TNFα outside of thiswindow should only have transient effects on the product-ivity of RGH infection. To test this, we infected cells withRGH and treated them with either DMSO or TNFα at fourdays post-infection rather than at the time of infection.24 hours post TNFα treatment, a portion of cells were ana-lyzed by flow cytometry (to check for LTR induction), whilethe remaining cells were allowed to recover for anotherfour days. Similar to TNFα treatment at the time ofinfection (Figures 5A and B), treatment with TNFα fourdays post-infection was able to reactivate a large proportionof non-productive proviruses, as demonstrated by a de-crease in the size of the ‘red’ population, and a correspond-ing increase in the number of ‘yellow’ cells (Figure 7A).However, after a four day recovery, the DMSO and TNFαtreated samples were largely indistinguishable in terms ofthe sizes of the ‘red’ and ‘yellow’ populations, suggestingthat TNFα treatment at day four post-infection had notpermanently altered the proportion of non-productivelyinfected cells (Figure 7A). This data stands in contrast tothe effect of treating cells with TNFα at the time of infec-tion (Figures 5A and B), which suggests that the formationof direct non-productive infection occurs during, or shortlyafter, proviral integration.To further explore the timing of RGH infection prod-uctivity, and to minimize the confounding impact ofviral state on cellular outgrowth in a mixed population,we repeated the TNFα-treatment-recovery experimentwith RGH infected Jurkat cells sorted into their constitu-ent ‘double negative’, ‘red’, and ‘yellow’ subpopulations.In each of the ‘double negative’ and ‘red’ populations,TNFα treatment of sorted cells activated a substantialproportion of non-productive proviruses, as reflected inthe increase in the number of ‘yellow’ cells (Figure 7B).As expected, TNFα treatment of the ‘yellow’ populationhad a minimal effect, as the majority of proviruses werealready transcriptionally active (Figure 7B). Interestingly,when the sorted populations were left to recover for fourdays, the ‘double negative’, ‘red’, and ‘yellow’ TNFαtreated cells all became indistinguishable from theirmatched DMSO treated pairs (Figure 7B). This data isconsistent with results from the bulk RGH infected cells(Figure 7A). Of note, we did not observe major differ-ences in the ratio of live cells (FSC/SSC) between DMSOand TNFα treatments, suggesting that HIV-induced cell-toxicity is not a substantial issue (data not shown).Furthermore, these findings collectively support the ideathat non-productive RGH infection is established early(within four days post-infection) and permanently, suchthat TNFα treatment applied after the infection canno longer permanently alter the proportion of non-productively infected cells.DiscussionDespite extensive knowledge of individual mechanisms ofHIV-1 transcriptional regulation, our understanding of thecritical determinants for HIV-1 latency establishment innewly infected cells is limited. This knowledge gap islargely due to the inability to accurately identify latentlyinfected cells early post-infection, and in their native state(i.e. without inducing cellular and viral activation). Tocircumvent these road-blocks, we and others have recentdeveloped ‘double-labeled’ HIV-1 vectors incorporatingconstitutive markers of infection [5,6]. Initial studies withthese models have revealed that a large proportion ofHIV-1 infections result in a direct latent state, howeverthe mechanisms by which these infections form remainsunknown. In this study we used a doubly labeled HIV-1latency model [5] to show that the cellular activation stateand NFκB activity around the time of infection, but notviral integration site, are important for regulating directnon-productive infections in Jurkat T-cells.Although primary CD4+ T-cells are considered to be thegold standard for HIV-1 latency models, we note a numberof technical issues precluding the precise and unbiasedevaluation of direct non-productive RGH infection in rest-ing CD4+ T-cells. Nevertheless, we previously observedthat RGH infection of activated primary CD4+ T-cellsfrom three donors results in a high degree of directnon-productive infection, comparable to Jurkat cells [5].Furthermore, another group also noted a high degree oflatency in activated primary CD4+ T-cells [8]. This suggeststhat activated primary CD4+ T-cell infections may beaccurately recapitulated in Jurkat cells. Thus, the resultsobtained with Jurkat cells in this study are likely to hold inprimary T-cells, especially if primary cells must be activatedin order to render them permissive to infection.Previous reports have implicated integration site variabil-ity as a determinant for HIV-1 latency. Most notably,latency was correlated with integration into gene deserts,highly transcribed genes (high transcriptional interference)and alphoid repeats [11,12,37]. However, high-throughputDahabieh et al. Retrovirology 2014, 11:17 Page 12 of 17http://www.retrovirology.com/content/11/1/17analysis of HIV-1 integration sites indicates that integra-tions into such regions are highly disfavored [9,10]. Instead,most proviruses are located within actively transcribedgenes that are enriched for histone marks associated withactive chromatin (H3K4me3, lysine acetylation), anddepleted for marks associated with repressive chromatin(H3K9me3, H3K27me3) [9,10,12,38,39]. We speculate thatlatency models using cellular activation and long-termFigure 7 The productivity of RGH infection is determined within fourpost-infection, cells were treated with either DMSO or TNFα for 24 hours bprior to re-analysis by flow cytometry. The percentage of cells in each of thshown in the circle plots. Data shown is representative of duplicate experimpost-infection into eGFP- mCherry-, eGFP- mCherry+, and eGFP+mCherry+DMSO or TNFα for 24 hours prior to analysis by flow cytometry. Treated ceanalysis. Data are representative of duplicate experiments.culturing to identify and establish latency could select forthe most strongly repressed latent proviruses, therebyresulting in an over-representation of such disfavored inte-gration locations. Our analysis of proviral locations in RGHinfected Jurkat cells shows little evidence for integrationsites regulating the difference between ‘red’ (eGFP-mCherry+) and ‘yellow’ (eGFP+mCherry+) cells (Figures 2and 3, S1, and S2). Furthermore we did not find anydays post-infection. A: Jurkat cells were infected with RGH. Four daysefore analysis by flow cytometry. Cells were left to recover for four dayse eGFP- mCherry-, eGFP- mCherry+, and eGFP+mCherry+ quadrants isents. B: Jurkat cells were infected with RGH and sorted three days(>90% purity). After 24 hours, the sorted cells were treated with eitherlls were left to recover for four days prior to further flow cytometryevidence for enrichment of the aforementioned rare typesof integration sites. Moreover, the frequency at which thesetypes of integrations occur is incompatible with the degreeof direct non-productive infections observed in the RGHmodel [5] and by other groups [6-8]. Our conclusions arein agreement with a recent meta-analysis of HIV-1 integra-tion sites in five primary and cell line latency models [13].In this study, the authors found no genomic predictors oflatency and, interestingly, only little overlap of chromo-somal features between latency models [13]. This highlightsthe intrinsic mechanistic variability of HIV-1 latencymodels, as well as the need to fully characterize determi-nants of latency in each model.In the absence of a role for integration sites in regulatingdirect non-productive RGH infection in newly infectedJurkat cells, the data presented in this study suggest thatproductive infection is positively correlated with cellular ac-tivation and NFκB activity (Figures 4, 5, 6, 7, and 8). Despitethis understanding, it remains to be determined what drivesfluctuations in cellular activity and corresponding NFκBactivity within any given population of newly infected cells.In the physiological context of T-cells, the timing of infec-tion during cellular deactivation (reversion from activatedstate to memory state) is a plausible driver of activationstate heterogeneity [1]. Depending on the time of infection,Dahabieh et al. Retrovirology 2014, 11:17 Page 13 of 17http://www.retrovirology.com/content/11/1/17cells may be at different points in the deactivation processFigure 8 Model of NFκB mediated effects on RGH productivityin newly infected cells. Schematic representation of productiveinfection determination in RGH infected Jurkat cells. In cells with lowNFκB activity, the majority of RGH infected cells exist in a non-productive state (eGFP- mCherry+, ‘red’) four days post infection,whereas cells with high NFκB activity have a greater propensity toexist in a productive state (eGFP+mCherry+, ‘yellow’) and persistover time. TNFα stimulation of non-productively infected cells fourdays post infection only temporarily reactivates HIV-1, which revertsto its non-productive state days later.and newly integrated proviruses may be exposed to highlyvariable T-cell signaling states and/or transcription factorpools. Complementary to this, thermodynamically drivenstochastic fluctuations in cellular processes, which can drivephenotypic asymmetry in clonal cells (reviewed in [40,41]),may impact NFκB activity. Indeed, the NFκB and SP1 sitesof the LTR have been implicated in controlling stochasticHIV-1 gene expression noise [42]. Other potential mecha-nisms of NFκB fluctuation include oscillatory behavior inresponse to TNFα signaling [43], and rapid nuclear shut-tling of NFκB p65 and IκBα [44]. NFκB p65 shuttling wasshown to provide low-level basal HIV-1 transcription in in-fected resting CD4+ T-cells [44], while shuttling of IκBαwas shown to dampen leaky NFκB signaling by removingactive NFκB p65 from the nucleus [44,45]. Taken together,the cumulative action of several sources of fluctuationcould contribute to a wide spectrum of cellular activationand NFκB activity in vivo. Further work is needed to eluci-date exactly what cellular state and NFκB activity level isdeterministic for primary latency establishment.Our data indicate that direct non-productive infectionsare established around the time of infection, and that thisprocess is fundamentally different from latency in whichproductive infections are silenced over time (Figures 5, 6, 7,and 8). We note that treatments with NFκB agonists andantagonists early during infection could profoundly alterthe occurrence of non-productive infection days later,whereas treatment four days post-infection did not result inlong term modulation (Figures 7 and 8). This indicates thatonce a non-productive state is established during initial in-fection, it becomes ‘imprinted’, possibly through subsequentepigenetic modifications (Figure 8).Our results contribute to an emerging body of work thatlinks cellular activation state and transcription factor avail-ability with the formation of HIV-1 latency. Althoughevidence is mounting that NFκB contributes to latencydetermination in newly infected cells (this study and [7]),we cannot exclude the actions of other transcription factorsand/or upstream regulators in modulating latency. Mostnotably, the factors SP1 [42], AP1 [46], and the JunN-terminal protein kinase (JNK) [47,48] have all beenimplicated in HIV-1 latency. It will be of great benefit toreconcile these studies and develop a comprehensiveunderstanding of how individual factors/mechanisms actcumulatively to establish latency in newly infected cells.Indeed, fully understanding this process is paramount tosuccessfully devising biologically relevant model sys-tems suitable for screening novel latency modulatingtherapeutics.ConclusionsHIV-1 infection of Jurkat T-cells results in both productiveand non-productive proviral states shortly after infection.Our data indicate that the differences between productiveDahabieh et al. Retrovirology 2014, 11:17 Page 14 of 17http://www.retrovirology.com/content/11/1/17and non-productive infections are not caused by the loca-tion or orientation of viral integrations. Instead, the cellularactivation state and NFκB activity around the time of infec-tion determine the outcome of viral infections and, in turn,early latency.MethodsViral vectors and constructsThe Red-Green-HIV-1 (RGH) molecular clone was used aspreviously described [5]. To construct the gag-N74D RGHclone, the mutation was created by PCR mediated sitedirected mutagenesis and cloning of the amplicon into theBspQI/ApaI sites of the previously described RGHconstruct [5]. The Red-Blue-HIV-1 (RBH) molecular clonewas created by cloning a synthesized tagBFP construct(GeneWiz) into the SapI/SphI sites of RGH.pTRIPz-EV, pTRIPz-DN-IκBα and pTRIPz-p65 arederivatives of the commercial doxycycline-inducible lenti-viral vector pTRIPZ-Ctrl (Thermo Fisher). pTRIPz-EV(empty vector) was created by digestion with AgeI/MluI, blunting with Klenow polymerase, and re-ligation.pTRIPz-DN-IκBα contains the S32A/S36A mutant ver-sion of the IκBα repressor PCR amplified from pSVK3-IKBα-2N [36], which was cloned into the AgeI/MluI sitesof pTRIPz-Ctrl. pTRIPz-p65 contains a PCR amplifiedNFκB p65 open reading frame cloned into the AgeI/MluIsites of pTRIPz-Ctrl.Cell culture, virion production, and transductionJurkat E6-1 [49], HEK293T (ATCC), and derivative celllines created in this study were cultured as previously de-scribed [5]. VSV-G pseudotyped viral stocks were createdby transfecting HEK293T cells with envelope deleted viralmolecular clones and pHEF-VSVg [50] in a 10:1 ratio aspreviously described [5]. Unless otherwise indicated,Jurkat E6-1 cells were spinoculated as previously described[5]. Briefly, 5 ×105 cells in 1 mL culture media (+ 4 μg/mLpolybrene) were spin-infected (1.5 hr, 500 × g, roomtemperature) with 25 μL of viral stock, so as to yield anaverage infection rate of than 10-15% and ensure single-copy integrations.NFκB-eGFP viral stocks were produced in HEK293T cellsby co-transfecting pGreenFire1-NF-κB (Systems Biosci-ences), pHEF-VSVg [50], pLP1-gag/pol, pLP2-Rev, andpcDNA3.1+-Tat (2 μg each, 30 μg polyethyleniminereagent). Purified and concentrated viral stocks wereprepared as previously described [5]. NFκB reporter celllines were created by transducing Jurkat cells withNFκB-eGFP virus (MOI ~ 4), followed by puromycinselection (1 μg/mL - Clontech). Resistant cells were sub-sequently maintained in complete media supplementedwith 0.5 μg/mL puromycin.pTRIPz viral stocks and stable cell lines were producedas described above for NFκB-eGFP, except that the lentiviralvectors pTRIPz-EV, pTRIPz-DN-IκBα or pTRIPz-p65were used.Flow cytometry and stainingAnalysis of infected cells by flow cytometry and live cellsorting were performed as previously described [5]. Ofnote, in all experiments, analysis was limited to live cellsby FSC/SSC gating at the time of data acquisition. Un-less otherwise stated, infected cells were analyzed fourdays post-infection. Jurkat E6-1 cells were stained andanalyzed for CD69 as previously described [51] exceptthat antibodies were conjugated to PE-Cy7 and 1 μL ofantibody was used per 1 × 105 cells (BD Biosciences).Jurkat cells were stained with PE-Cy7-NFκB p65 (pS529)(BD Biosciences) and NFκB p50 (Abcam) with PacificBlue conjugated secondary antibody (Life Technologies)as previously described [52].Compound treatmentsInfected cells were treated with the various compoundsfor the times and durations indicated in individualexperiments. Compounds were added at the listed con-centrations to complete media. Unless otherwise stated,compounds were used at the following concentrations:TNFα, 10 ng/mL (Sigma); SAHA, 0.5 μM [53]; PMA,4 ng/mL (Sigma); Ionomycin, 1 μM (Sigma), BMS-345541, 5 μM (Sigma).Pyrosequencing of integration sitesHIV-1 integration sites were analyzed by 454 deep-sequencing as previously described [14]. Briefly, Jurkatcells were infected with RGH and sorted into constituentpopulations three days post-infection (eGFP- mCherry-,eGFP- mCherry+, eGFP+mCherry+). Genomic DNA wasextracted from ~ 5×105 cells of each population, digestedwith MseI and ligated to adaptors. Nested PCR withadapter and LTR specific primers was performed toamplify the HIV-host genome junctions. After gel extrac-tion of 100–600 bp fragments, amplicons were subjectedto pyrosequencing on a 454 GS Junior machine (Roche). Datawas analyzed using the Integration Site Pipeline and Database(INSIPID) web tool (Bushman Lab - http://microb215.med.upenn.edu/Insipid/ - [10,15], Circos [54], SeqMonksoftware (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), WebLogo3 (http://weblogo.threeplusone.com/create.cgi), and the R/Bioconductor package ‘goProfiles’(http://bioconductor.org/packages/2.11/bioc/html/goProfiles.html).ImmunoblottingRGH infected Jurkat cells were lysed in NP-40 lysisbuffer (50 mM Tris, pH 8.0, 150 mM NaCl, 1% (v/v)NP-40, 0.1% (w/v) SDS) supplemented with 1x proteaseinhibitor cocktail (Roche). Lysates were cleared byDahabieh et al. Retrovirology 2014, 11:17 Page 15 of 17http://www.retrovirology.com/content/11/1/17centrifugation (10 min, 16000 × g, 4°C), mixed with 4×SDS-PAGE sample buffer, and boiled for 5 min. Wholecell extracts (40 μg) were separated on a 12% SDS-PAGEgel and then transferred to nitrocellulose membrane.Membranes were blocked with 2% (w/v) BSA in PBS-Tween (0.05% v/v) and then incubated with primaryantibody overnight at 4°C. Antibodies used were asfollows: IκBα – Abcam 32518 [1:5000], NFκB p65 –Abcam 7970 [1:500], GAPDH – Abcam 9484 [1:4000].After washing and incubation with HRP conjugatedsecondary antibody, membranes were washed and signalwas developed with SuperSignal West Femto chemi-luminescent substrate (Thermo Fisher).Statistical analysisUnless otherwise stated, experiments were performed inbiological triplicate. Where appropriate, statistical infer-ence was performed on quantitative data. Two grouptesting was performed using the Student’s T-test, whilecomparison between multiple groups was made usingone-way-ANOVA followed by pairwise two-grouptesting (Student’s T-test). Statistical analysis was per-formed in R 2.15.1 (http://www.r-project.org/). Integrationsite analysis heatmaps were created using the INSIPIDpipeline (Figures 3A and Additional file 1: Figure S1B) util-izing previously described statistical methodology [10,15].Briefly, for each identified integration site, matchedrandom controls were created in silico. This pairing ofexperimental and control sites allows for computationof relative enrichment and de-enrichment profiles usinga receiver operating characteristic framework. Compari-sons between sets of integration sites (samples) forstatistical significance are performed by calculatingWald-type test statistics, which are then tested usingChi Square methods.Additional filesAdditional file 1: Figure S1. Productive and non-productive RGHinfections occur regardless of epigenetic properties at sites of integrationA: Epigenetic properties of identified integration sites were comparedbetween samples using the INSIPID heatmap tool for epigenetic features(Bushman Lab, University of Pennsylvania). Included features were limitedto those identified in high-throughput studies of Jurkat and primaryCD4+ T-cells. Yellow and blue colors represent depletion and enrichmentof each feature, respectively, relative to matched random controls ofintegration sites. Statistical significance (ranked Wald tests) is shownrelative to the eGFP+ mCherry+ population (dashes). B: Proviralintegrations across the entire human genome are plotted as a functionof the average distance across gene bodies (5’ to 3’ – top panel), and theaverage distance from gene transcriptional start sites (TSS – bottompanel). Data are plotted as pale filled circles with darker smoothed lines(Loess) overlaid. C: Jurkat cells were infected with equal amounts of wild-type RGH or an RGH version containing an N74D mutation in Capsid.Cells were analyzed by flow cytometry four days post-infection. Represen-tative plots (left) and graphical quantitation (right) are shown. Error barsrepresent standard deviations of triplicate experiments. ‘ns’ non-significant.Additional file 2: Figure S2. Productive and non-productive RGHinfections occur regardless of DNA sequence at the point of integration,or functional annotation of host genes. A: Weblogo3 analysis of the DNAsequence (+/− 20 bp) surrounding each integration site in theeGFP- mCherry- (‘double negative’), eGFP- mCherry+ (‘red’), and eGFP+mCherry+ (‘yellow’) populations. B: Gene ontology analysis of integrationsites in the eGFP- mCherry- (‘double negative’), eGFP- mCherry+ (‘red’),and eGFP+mCherry+ (‘yellow’) populations, using goProfiles.Additional file 3: Figure S3. RGH infection does not induce cellularactivation or NFκB signaling. A. Mock- and total-RGH-infected Jurkatcells were stained for CD69 four days post-infection. Data shown isrepresentative of triplicate experiments. B. Mock- and total-RGH-infectedJurkat cells were stained for either NFκB p50 or NFκB p65-S529phosphofour days post-infection. Data shown is representative of triplicateexperiments. C. Mock- and total-RBH-infected Jurkat NFkB-eGFP reportercell lines 1–5 were analyzed by flow cytometry four days post-infection.Data shown is representative of multiple experiments.Additional file 4: Figure S4. Characterization of RBH infection andJurkat NFκB reporter cell lines. A: Jurkat NFκB reporter clones 2–5 weretreated with DMSO, TNFα, or PMA/Ionomycin for 24 hours prior toanalysis by flow cytometry for eGFP mean fluorescence intensity (MFI).Error bars represent one standard error of the mean. B: Jurkat NFκBreporter clones 2–5 were infected with RBH viral stock and analyzed byflow cytometry at four days post-infection. Cells were gated into theirconstituent infected populations and then analyzed for eGFP MFI. Errorbars represent one standard error of the mean.Competing interestsThe authors declare that they have no competing interests.Authors’ contributionsMSD and MO conceived, designed and performed the experiments andanalyzed the data. MSD, MO, VS and IS wrote the manuscript. CB, JT and PRHperformed 454 deep sequencing. All authors read and approved the finalmanuscript.AcknowledgementsWe thank Andy Johnson and Justin Wong of the UBC Flow CytometryFacility for live cell sorting and analysis. We thank Winnie Dong andDennison Chan for assistance with pyrosequencing. We thank Nirav Milanifor help with the INSIPID pipeline. We gratefully acknowledge PaulineJohnson for the lentiviral packaging accessory plasmids and Amy Saundersfor assistance with CD69 staining. We thank Jacob Hodgson, AdamChruscicki, Kevin Eade, Benjamin Martin, and Nicolas Coutin for thoughtfuldiscussions and review of this manuscript.The following reagents were obtained through the AIDS Research andReference Reagent Program, Division of AIDS, NIAID, NIH: Jurkat CloneE6-1 from Dr. Arthur Weiss, SAHA (Vorinostat), and pHEF-VSVG fromDr. Lung-Ji Chan.This work was supported by Canadian Institute of Health Research (CIHR)grants to I.S. (MOP-77807, HOP-120237), NIH/NIAID grants to V.S. (AI064001,AI104406, AI90935). M.S.D is supported by a CIHR fellowship (CGD-96495).P.R.H. is supported by a CIHR/GSK chair in clinical virology at the Universityof British Columbia.Author details1Biochemistry and Molecular Biology, University of British Columbia,Vancouver, BC V6T1Z3, Canada. 2Department of Microbiology, The GlobalHealth and Emerging Pathogens Institute; Mount Sinai School of Medicine,1468 Madison Avenue, Annenberg building 18-50, New York, NY 10029, USA.3Division of Infectious Diseases, Department of Medicine, Mount Sinai Schoolof Medicine, New York, NY 10029, USA. 4BC Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z1Y6, Canada.Received: 20 August 2013 Accepted: 4 February 2014Published: 7 February 2014References1. Donahue DA, Wainberg MA: Cellular and molecular mechanisms involvedin the establishment of HIV-1 latency. Retrovirology 2013, 10:11.Dahabieh et al. Retrovirology 2014, 11:17 Page 16 of 17http://www.retrovirology.com/content/11/1/172. Siliciano RF, Greene WC: HIV latency. 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