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2 A Soluble Chromatin-bound MOI HDAC B VprBP HDAC2 Soluble Chromatin-bound NT sirna VprBP sirna Empty Empty WT WT Empty Empty WT WT HDAC8 40 HDAC8 40 GAPDH 35 GAPDH 35 His-H3 His-H3 1.5 HDAC2 HDAC8 1.5 HDAC2 HDAC8 Signal intensity Signal intensity MOI Soluble Chromatin-bound 0.0 VprBP sirna Empty Empty WT WT Empty Empty WT WT NT sirna Soluble Chromatin-bound C Soluble Empty WT Chromatin-bound Empty WT Signal intensity GAPDH His-H Empty WT Empty WT Soluble Chromatin-bound

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4 A Empty WT DMSO SAHA Vpr + SAHA Cell number B GFP Empty Q65R R80A WT Caffeine Empty Vpr Empty Vpr G0/G1 G0/G1 G0/G1 G0/G1 G2/M G2/M G2/M G2/M G2+M:G1= 0.35 G2+M:G1= 1.32 G2+M:G1= 0.36 G2+M:G1= Cell number Cell number C GFP GFP

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6 Untransfected NT sirna sirna sirna Cell number GFP NT sirna sirna sirna Soluble Chromatin-bound GAPDH His-H3 Figure S3. Depletion of and reactivates the latent provirus in J-Lat 6.3. J-Lat 6.3 cells were transfected with sirnas against and. As control, J- Lat 6.3 cells were also transfected with non-targeting sirnas (NT). After 48 h, cells were analyzed for expression of GFP (the upper panel). Some cells were also fractionated and analyzed using Western blot (the lower panel).

7 A : 117 HDAC2: 118 : 111 HDAC8: 119 B Conserved motif selected for mutagenesis 4 x 10 5 Relative light uinit 3 x x Control (No ) Mut + SAHA Mut + SAHA Figure S4. H134/135A -Flag and its histone deacetylase activity. (A) Alignment of class I HDACs showing a conserved motif selected for generating a mutant (B) Comparing histone deacetylase activity of and H134/135A -Flag (mut-). HEK293T cells were transfected with Flag-tagged or mut-. After 48 h, cells were lysed and or mut- were affinity purified. Purified were splitted in two aliquots and treated with SAHA or DMSO. Histone deacetylase activities of the purified and mut- were measured as relative light units. The experiment was repeated 3 times.

8 A Plasma of healthy donor Plasma of HIV-1 infected patient M 1μl 10 μl 100 μl 1 μl 10 μl 100 μl Vpr 10 B C D Marker Lysate Purified protein 1 μg BSA 3 μg BSA 10 μg BSA BSA Marker Serum Purified protein 1 μg BSA 3 μg BSA 10 μg BSA BSA Vpr GFP expression (%) Untreated Serum (Healthy donor) Vpr (Patient) Figure S5. Characterization of Vpr antibody and efficiency of Vpr purification. (A) Plasma was isolated from a healthy donor and an HIV-1 infected patient. Different amounts of plasma were analyzed by Western blot using the homemade antibody. (B) HEK293T cells were transduced with lentiviral vectors expressing. After 48 h, was purified from the cell lysate by affinity chromatography purification and loaded on SDS-PAGE. Gel was stained using Coomassie Blue staining. (C) Vpr from serum of HIV-positive individuals was purified using home-made Vpr antibody conjugated to chromatography columns. Serum-purified Vpr was loaded on SDS-PAGE and stained using Coomassie Blue staining. (D) J-Lat 10.6 cells were treated with 500 ng/ml and serum purified Vpr. After 24 h, cells were analyzed using flow cytometry for expression of GFP.

9 6000 WT lysate Vpr lysate HIV-1 RNA copies/ml Day Figure S6. Release of virion-incorporated Vpr from HIV-1 virions reactivates latently infected cells. PBMCs were isolated from five HAART-treated HIV-1 infected individuals with no detectable viral load. Unstimulated PBMCs were then treated with viral lysates of the WT or Vpr HIV-1. Viral load was measured in the supernatant by quantifying the HIV-1 RNA using quantitative PCR. Asterisks () indicate statistically significant differences between the WT and Vpr lysate treated cells.