Spt6 levels are modulated by PAAF1 and proteasome to regulate the HIV-1 LTR
- Mirai Nakamura†1,
- Poornima Basavarajaiah†1,
- Emilie Rousset1,
- Cyprien Beraud1,
- Daniel Latreille1,
- Imène-Sarah Henaoui2, 3,
- Irina Lassot1, 4,
- Bernard Mari2, 3 and
- Rosemary Kiernan1Email author
© Nakamura et al; licensee BioMed Central Ltd. 2012
Received: 1 December 2011
Accepted: 8 February 2012
Published: 8 February 2012
Tat-mediated activation of the HIV-1 promoter depends upon a proteasome-associated factor, PAAF1, which dissociates 26S proteasome to produce 19S RP that is essential for transcriptional elongation. The effect of PAAF1 on proteasome activity could also potentially shield certain factors from proteolysis, which may be implicated in the transcriptional co-activator activity of PAAF1 towards the LTR.
Here, we show that Spt6 is targeted by proteasome in the absence of PAAF1. PAAF1 interacts with the N-terminus of Spt6, suggesting that PAAF1 protects Spt6 from proteolysis. Depletion of either PAAF1 or Spt6 reduced histone occupancy at the HIV-1 promoter, and induced the synthesis of aberrant transcripts. Ectopic Spt6 expression or treatment with proteasome inhibitor partially rescued the transcription defect associated with loss of PAAF1. Transcriptional profiling followed by ChIP identified a subset of cellular genes that are regulated in a similar fashion to HIV-1 by Spt6 and/or PAAF1, including many that are involved in cancer, such as BRCA1 and BARD1.
These results show that intracellular levels of Spt6 are fine-tuned by PAAF1 and proteasome, which is required for HIV-1 transcription and extends to cellular genes implicated in cancer.
KeywordsLTR transcription Tat Spt6 PAAF1 proteasome
Spt6 is a highly conserved transcription factor that plays a number of distinct roles during transcription. It interacts directly with histones, particularly H3, and possesses nucleosome assembly activity in vitro . Together with FACT, a H2A/H2B chaperone, Spt6 restores chromatin structure in the wake of elongating RNAPII [2, 3]. Loss of Spt6 disrupts normal chromatin structure and leads to the initiation of cryptic transcripts from within the coding region . At inducible genes, Spt6 is required to restore transcriptional repression by promoting nucleosome reassembly over the promoter region [4, 5]. Spt6 is a transcription elongation factor that is associated with the body of genes during transcription [6, 7] and enhances the elongation rate of RNAPII, even on naked DNA [8, 9]. It contains tandem SH2 domains that interact with phosphorylated Ser2 and Ser5 of the carboxy-terminal domain (CTD) of RNAPII [10, 11]. Spt6 is also implicated in mRNA processing through interactions with the nuclear exosome subunit, Rrp6, and Iws1 that recruits RNA processing/export factors Ref1/Aly [11, 12], and prevents premature 3' processing at cryptic, upstream polyadenylation sites . Spt6 controls basal and Tat-mediated transcription from the HIV-1 promoter [13, 14] and controls HIV-1 latency . Thus, Spt6 is required for transcription through chromatin by ensuring proper nucleosome reassembly during elongation and linking transcription to mRNA processing and quality control.
26S proteasome, the major pathway of degradation for ubiquitinated proteins in cells, consists of two large subcomplexes, 19S regulatory particle (19S RP) and 20S core particle (20S CP) . 19S RP recognizes polyubiquitinated substrates that are subsequently degraded by the 20S catalytic particle (20S CP) in an energy-dependent manner. Previous studies have highlighted a role for proteasome in controlling transcription . Transcription-coupled proteolytic destruction of activators facilitates gene activation at certain promoters . Other studies, by contrast, suggest that 19S RP positively affects transcription through mechanisms that are independent of proteolysis but may require the ATPase-dependent chaperonin activity of 19S RP [19–21]. Indeed, proteolytic activity is excluded from regions that are highly transcribed, but can become associated with such regions under conditions that lead to transcriptional stalling . Alternatively, the degradation of transcription factors can be more specifically controlled in several ways. Most simply, the ubiquitinated lysine residue can also be an acceptor residue for acetylation. Thus, factor degradation is controlled via cycles of acetylation/deacetylation, as shown for Foxo3 and RelA [23, 24]. In other cases, interaction with another factor can control the rate of substrate degradation. For example, interaction with FANCJ prevents proteolytic degradation of Blm . Similarly, HSP70 protects ATF5 from rapid degradation by proteosome in glioma cells . Thus, the proteolytic degradation of certain factors can be specifically and reversibly controlled, which has important implications for a number of cellular processes, including transcription.
We have previously demonstrated that transcription from the HIV-1 promoter is controlled by proteasome . In the absence of the viral transactivator, Tat, 26S proteasome is associated with the promoter and represses basal transcription. In the presence of Tat, however, 19S RP is recruited to the HIV-1 promoter where it facilitates an early step in transcriptional elongation in a non-proteolytic manner. This switch is dependent on a proteasomal ATPase-associated factor, PAAF1. Originally identified through its binding to a 19S RP subunit, PAAF1 was shown to regulate proteasome assembly and activity [27, 28]. PAAF1 and its yeast homologue, Rpn14, were subsequently characterized as 19S RP chaperones [29, 30]. Since PAAF1/Rpn14 associates with the fully assembled base of 19S ATPases, but dissociates prior to association of 20S CP, it is not detected in association with 26S proteasome [28, 31]. PAAF1 is physically associated with HIV-1 chromatin and regulates 26S proteasome dynamics to produce 19S RP that is essential for transcriptional elongation in the presence of Tat [27, 28]. Since both 19S RP and 20S CP are present on the HIV-1 promoter in the absence of PAAF1, it seems likely that promoter-associated proteasome activity is enhanced under these conditions . This raises the possibility that PAAF1 might shield certain factors from proteasomal degradation, which could have consequences for HIV-1 transcription. Here, we show that PAAF1 specifically protects Spt6 from proteasomal degradation, which is crucial for nucleosome assembly during transcription at the HIV-1 promoter. Since regulation of the LTR is often a paradigm for cellular genes, we wondered if this mechanism operating at the LTR extends to cellular genes. Transcriptional profiling in either PAAF1 or Spt6 knockdown cells followed by ChIP analysis at selected genes revealed an important role for Spt6 and PAAF1 in controlling the expression of a subset of genes involved in cancer.
Spt6 level is modulated by PAAF1 in proteasome dependent-manner
We then asked whether diminution of Spt6 following PAAF1 depletion might affect Spt6 recruitment to chromatin. Control or PAAF1 RNAi cells containing a stably integrated LTR linked to a Luciferase reporter (HeLa-LTR-luc) were analyzed by chromatin immunoprecipitation (ChIP) to detect Spt6 association with the HIV-1 promoter and luciferase region. Spt6 association was reduced to almost the same extent by PAAF1 RNAi as by Spt6 RNAi (Figure 1C). In contrast, Spt6 recruitment to GAPDH was not affected indicating that the effect might be restricted to specific genes (Additional file 3, Figure S3). Since the Spt6 level in cell extract was partially recovered by MG132, we asked if Spt6 recruitment to the LTR was also rescued. MG132 treatment significantly enhanced Spt6 association with HIV-1 chromatin in PAAF1 RNAi cells but had no effect in control cells (Figure 1D). These data suggest that PAAF1 stabilizes Spt6 to levels that are sufficient for its association with HIV-1 chromatin.
PAAF1 physically interacts with Spt6
PAAF1-mediated Stabilization of Spt6 Facilitates Nucleosome Reassembly during Transcription
PAAF1-dependent stabilization of Spt6 is required to suppress aberrant HIV-1 transcription
The uncoupling of HIV-1 transcript synthesis and protein production in PAAF1 and Spt6 knockdown cells suggests that, although transcription is increased, the transcripts may be aberrant. RT-Q-PCR analysis was thus performed in the case of PAAF1 RNAi using primer pairs spanning the transcript (Figure 5B). Amounts of transcripts were normalized to the value obtained in the TAR region, a RNA hairpin located at the 5' end of initiated HIV-1 transcripts, in order to assess the efficiency of transcription elongation. In the absence of Tat (siScr + GST), transcripts were poorly elongated since more transcripts contained TAR than luc 3' sequences. As expected, transcripts were efficiently elongated in the presence of Tat since equivalent amounts of TAR and products up to the 3' end of luciferase could be detected. In PAAF1 knockdown cells, by contrast, transcripts were poorly elongated, in both the presence and absence of Tat (Figure 5B). Additionally, transcripts that were elongated up to the 3' end of luciferase were presumably incompetent for protein synthesis, which may be in part due to the function of Spt6 in mRNA 3' processing [6, 7] export . Thus, transcripts synthesized in the absence of PAAF1 are aberrant, likely due to a combination of defects in elongation and RNA processing/export. We next asked whether the transcriptional defect in PAAF1 knockdown cells could be suppressed by Spt6. Ectopic expression of Spt6 had no effect on HIV-1 transcription in control cells (Figure 5C). In contrast, expression of HA-Spt6 partially reversed the increase in transcription induced following loss of PAAF1. Taken together, these data show that Spt6 is required for repression of basal transcription, and loss of Spt6 following PAAF1 knockdown permits aberrant transcription that is highly inefficient for protein synthesis.
Regulation of Cellular Genes by PAAF1 and/or Spt6
We have previously demonstrated that PAAF1, a modulator of proteasome activity, is required for HIV-1 transcription . In this study, we show that PAAF1 specifically protects Spt6, a key factor in nucleosome reassembly, transcription elongation and RNA processing, from proteasomal degradation. PAAF1 interacts with Spt6 and both factors localize at the HIV-1 promoter. The level of Spt6 in cells, and also its association with HIV-1 chromatin are modulated by PAAF1 in a proteasome-dependent manner. Ablation of either PAAF1 or Spt6 led to loss of histones from HIV-1 chromatin, concomitant association of RNAPII and the induction of transcripts that were largely defective for protein synthesis.
As nucleosomes present a barrier to the passage of RNAPII, many factors, including histone chaperones, are required to coordinate their removal ahead of RNAPII, and their redeposition in the wake of elongating RNAPII . The repositioning of nucleosomes can prevent cryptic transcription that may have deleterious effects. Loss of nucleosomes can deregulate transcription. For example, depletion of histone H4 increased transcription from a subset of genes in yeast , and reassembly of nucleosomes is required to repress transcription under non-inducing conditions . Nucleosome reassembly requires the concerted action of chaperones, Spt6 and FACT, which interact with histones to restore chromatin structure in the wake of RNAPII. Interestingly, PAAF1 knockdown did not affect occupancy of the Spt16 subunit of FACT at HIV-1 chromatin suggesting that, while PAAF1 regulates Spt6, Spt16 is not subject to the same regulatory mechanism even though both chaperones frequently function at the same genes. Our findings indicate that modulation of Spt6 by PAAF1 and proteasome controls transcription at the HIV-1 promoter by facilitating the restoration of chromatin structure.
Transcriptional profiling following PAAF1 or Spt6 RNAi showed that, among genes that are deregulated by PAAF1 knockdown, more than 50% were also deregulated following Spt6 knockdown. Since the involvement of PAAF1 in transcription is not as widespread as Spt6, it suggests that additional factors may determine which of the Spt6-regulated genes are also regulated by PAAF1. Genes that are commonly deregulated may be those that are highly sensitive to reduced levels of Spt6 in cells. Gene ontology analysis revealed that many of the differentially expressed genes following either PAAF1 or Spt6 knockdown are implicated in cancer. Among the genes deregulated PAAF1 or Spt6 RNAi cells were several oncogenes, such as NOV and MET, whose expression was increased. In contrast, a subset of genes including tumor suppressors, such as BRCA1, BARD1 and BLM, were highly deregulated by loss of Spt6 but were only modestly affected or unaffected by loss of PAAF1, even though Spt6 level in these cells was significantly diminished. Since Spt6 is associated with all of the genes analyzed, the results suggest that certain genes, such as INHBA, NOV and MET may be highly sensitive to loss of Spt6, whereas others such as BLM, FANCA and TOP2A, may be more resistant to loss of Spt6 and can tolerate modest reductions in Spt6 expression levels. Thus, Spt6 appears to control the expression of a number of genes, including several that are involved in cancer.
We show that the HIV-1 transcriptional coactivator, PAAF1, specifically protects Spt6, a key factor in nucleosome reassembly, transcription elongation and RNA processing, from proteasomal degradation, and is thus required for transcription from the HIV-1 LTR.
Cell culture, antibodies and plasmids
HeLa-LTR-luc cells that contain luciferase under the control of an integrated HIV-1 LTR were obtained from K.-T. Jeang (NIAID, NIH, USA) and propagated in Dulbecco's modified Eagle's medium (DMEM, Lonza) supplemented with 10% FBS and antibiotics. The cells were treated with MG132 (Sigma) for 8 h, where indicated. U2OS cells containing a stably integrated HIV-1 LTR linked a reporter containing binding sites for MS2 protein  were obtained from E. Bertrand (IGMM, Montpellier) and propagated in DMEM supplemented with 10% FBS and antibiotics. Antibody recognizing human PAAF1 was raised in rabbits against an immunogenic peptide (Abnova). Antibodies used were anti CDK9, p53, NOV, BARD1 and BLM (SCBT), RNAPII, H3, H2B, Spt6, PAF1 and TOP2A (Abcam), Spt6 for IP (Bethyl Laboratories), Tubulin and Flag M2 (Sigma). pcDNA3-Flag-Spt6-HA  and pMyc-Spt6  were gifts from H. Handa and K.A. Jones, respectively. pTat-Flag has been described previously .
RNAi and transfection experiments
HeLa LTR-Luc cells were transfected using Interferin (PolyPlus Transfection) with 5 nM double-stranded siRNAs following the manufacturer's instructions. At 48 hr after transfection, cells were treated with GST or GST-Tat as previously described . Luciferase activity was measured 48 hr after transduction according to the manufacturer's protocol (Promega). Luciferase activity was normalized to protein concentration using Bradford (BioRad). Double stranded RNA oligonucleotides directed against target sequences in PAAF1 (AGC CUG UUC UCU GGA GGA A) , Spt6 (GAA GCC UCA UGU AGU GAC A), Cdk9 (CUA GGG CUC UUG UGU UUU U), and a control siRNA (Scrambled)  were purchased from Eurofins MWG Operon.
HeLa cells were transfected with 5 nM of a control siRNA (Ambion #1 Silencer select), or siRNAs targeting PAAF1 or Spt6 (modified by Silencer, Ambion). To prepare samples, total RNAs were extracted using Trizol (Invitrogen) and quantified by nanodrop spectrophotometry. RNA quality was evaluated using the Agilent Bioanalyzer 2100 and Lab-on-Chip Nano 6000 chip (ratio of the 28S/18S RNA ≥ 1.5). RNA samples from knockdown experiments were labeled with Cy3 dye using the low RNA input QuickAmp kit (Agilent) as recommended by the supplier. 825 ng of labeled cRNA probe were hybridized on a 8x60K high density SurePrint G3 gene expression human Agilent microarray. Two biological replicates were performed for each comparison. The experimental data have been deposited in the NCBI Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/) under series record GSE32033. Normalization was performed using the Limma package available from Bioconductor (http://www.bioconductor.org). Inter-slide normalization was performed using the quantile methods. Means of ratios from all comparisons were calculated and B test analysis was performed. Ontologies attached to each modulated gene were then used to classify them according to main biological themes using Ingenuity software (http://www.ingenuity.com/).
Total RNA was extracted from HeLa LTR-luc cells using Trizol (Invitrogen) and reverse-transcribed using Superscript First-strand Synthesis System for RT-PCR (Invitrogen). RT products were amplified by quantitative PCR on a LightCycler LC480 (Roche) by using the oligonucleotides shown in Additional file 7, Table S1. TAR, early, luc and luc 3' and GAPDH primers have been described previously [27, 32]. Q-PCR cycling conditions are available on request.
Chromatin immunoprecipitation (ChIP)
HeLa-LTR-Luc cells were treated for 4 hr with DMEM containing 100 μM chloroquin (Sigma), and 2 mg/ml of GST or GST-Tat. ChIP analysis was performed as described previously , except using Dynabeads A or G (Invitrogen) for immunoprecipitation. Normal IgA or IgG (SCBT) was used as a negative control (mock sample). Quantification of immunoprecipitated material was performed by quantitative PCR using LightCycler LC480 (Roche) and normalized for input DNA. Sequences of oligonucleotide primers are shown in Table S1. LTR prom and coding primers have been described previously [27, 32]. Primers were mixed with Quanti Tect Sybr Green (Qiagen), Biorad SYBR green (BioRad) or LightCycler LC480 SYBR Green I Master (Roche). Q-PCR cycling conditions are available on request.
Results were calculated as follows: the value obtained using the specific antibody, expressed as a percentage of input DNA, was divided by the value obtained for the mock IgA or IgG sample. The value obtained for the control sample, usually siScr, was set to 1. The test samples were expressed as a ratio of the control.
U2OS cells containing the HIV-LTR fused to 24 bacteriophage MS2-binding sites  were plated on coverslips and transfected with siRNA using Oligofectamine (Invitrogen). After 24 h, cells were transfected with vectors expressing Tat and MS2-GFP using Lipofectamine2000 (Invitrogen). For single MS2 staining, cells were washed once with PBS, and fixed with 4% paraformaldehyde (PFA, Sigma) for 20 min at room temperature, followed by DNA staining using Hoechst (Sigma). For immunofluorescence, cells were pre-permeabilized with 0.05% Triton-X-100 (Sigma) prior to fixation with 2 or 4% PFA for 5 min on ice. After a PBS wash, coverslips were incubated with blocking buffer (5% bovine serum albumin (BSA)/PBS) for 1 h at room temperature. Blocking buffer containing primary antibodies was overlaid onto a coverslip and incubated for 1 h at room temperature. After washing three times with PBS, cells were treated with secondary antibodies conjugated with Alexa488 or Cy5 (Invitrogen) in blocking buffer for 1 h at room temperature. After 3 PBS washes, samples were counterstained for DNA. Fluorescent images of fixed cells were imaged on a Leica DM 6000-1 microscope (Leica) using MetaMorph software (Molecular Devices).
We thank the Nice-Sophia Antipolis Transcriptome Platform of the Marseille-Nice Genopole in which microarray experiments were performed, A. Bucheton and M. Benkirane for their support, J.T. Lis, W. Tansey and X. Contreras for comments on the manuscript, H. Handa and K.A. Jones for the gifts of pFlag-Spt6-HA and pMyc-Spt6, respectively, and E. Bertrand for U2OS-LTR-MS2 cells. Grants from ANRS and SIDACTION supported this work. MN was supported by ANRS and SIDACTION, PB and DL by ANRS.
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