SKIP interacts with c-Myc and Menin to promote HIV-1 Tat transactivation

Abstract

The Ski-interacting protein SKIP/SNW1 associates with the P-TEFb/CDK9 elongation factor and coactivates inducible genes, including HIV-1. We show here that SKIP also associates with c-Myc and Menin, a subunit of the MLL1 histone methyltransferase (H3K4me3) complex and that HIV-1 Tat transactivation requires c-Myc and Menin, but not MLL1 or H3K4me3. RNAi-ChIP experiments reveal that SKIP acts downstream of Tat:P-TEFb to recruit c-Myc and its partner TRRAP, a scaffold for histone acetyltransferases, to the HIV-1 promoter. By contrast, SKIP is recruited by the RNF20 H2B ubiquitin ligase to the basal HIV-1 promoter in a step that is bypassed by Tat and downregulated by c-Myc. Of interest, we find that SKIP and P-TEFb are dispensable for UV stress-induced HIV-1 transcription, which is strongly upregulated by treating cells with the CDK9 inhibitor flavopiridol. Thus, SKIP acts with c-Myc and Menin to promote HIV-1 Tat:P-TEFb transcription at an elongation step that is bypassed under stress.

Figure 1

SKIP associates with c-Myc and acts downstream of Tat:P-TEFb at the HIV-1 promoter. (A) Co-immunoprecipitation of HeLa SKIP with CycT1 and c-Myc, as shown by immunoblot (lanes 1-3). GST pulldown fractions from HeLa nuclear extract were assessed by immunoblot, using antisera indicated to the left of each panel (lanes 4-18). (B) Analysis of Tat activity in HeLa cells treated with SKIP-siRNA or a control (si-con) siRNA. Inset shows immunoblot analysis of knockdown efficiency. (C) ChIP analysis of the integrated HIV-1 LTR:Luc reporter gene promoter in the presence (+) or absence (−) of transduced recombinant GST-Tat101 protein. Where indicated, the cells were transfected with si-SKIP or si-con RNAs prior to analysis by ChIP. All graphs represent mean and standard error obtained from three independent experiments.

Figure 2

SKIP recruits c-Myc:TRRAP to the Tat-activated HIV-1 promoter. (A) ChIP analysis of the basal and Tat-induced HIV-1 promoter in control or SKIP knockdown HeLa cells. Inset, immunoblot analysis of knockdown efficiency. (B) HeLa HIV-1 LTR:Luc (luciferase) activity induced with 5 ng of transfected Tat101 plasmid in si-control, si-c-Myc, or si-TRRAP transfected cells. Inset, analysis of knockdown efficiency by RT-PCR. (C) RNAi-ChIP analysis of the indicated proteins at the HIV-1 promoter in control or c-Myc knockdown cells. Inset, assessment of knockdown efficiency by immunoblot. All graphs represent mean and standard error obtained from three independent experiments.

Figure 3

SKIP is required for gene-specific H3K4me3, and both SKIP and c-Myc interact with nuclear MLL1:Menin complexes and recombinant Menin in vitro. (A) RNAi-ChIP analysis of the basal and Tat-activated HIV-1 promoter in control or SKIP knockdown cells. All graphs represent mean and standard error obtained from three independent experiments. (B) Immunoblot analysis of global H3K4me3 levels in SKIP or Ash2L knockdown HeLa cells. Total acid-extracted histones were visualized by Coomassie staining. (C) Immunoblot analysis of the binding of MLL complex subunits (input, lanes 1, 5) to GST (lane 2, 6 and 7), GST-SKIP (full-length, FL; lane 3, 8 and 9) or GST-SKIP (N-terminal fragment, NT; lane 4) beads in pull-down experiments from a HeLa nuclear extract. (D) Binding of nuclear MLL1 complex factors (input, lane 1) to GST (lanes 2,3), GST-SKIP (FL; lanes 4,5), GST-c-Myc (FL; lanes 6,7) or GST-Tat101 (lanes 8,9) beads in the presence (+) or absence (−) or HeLa nuclear extract (HNE), as visualized by immunoblot. Analysis of the association of endogenous HeLa SKIP, MLL1, or c-Myc with Menin by co-immunoprecipitation with anti-Menin antisera, as visualized by immunoblot (lanes 10-15). (E) Analysis of the binding of wild-type or truncated GST-SKIP and GST-c-Myc proteins to purified recombinant baculovirus-expressed His-tagged Menin was assessed by immunoblot (lanes 1-13) with an anti-Menin antibody.

Figure 4

SKIP, c-Myc and Menin are required for Tat transactivation, but act independently of MLL1-mediated H3K4me3. (A) ChIP analysis of the integrated HIV-1 LTR:Luc promoter in control, SKIP- or MLL1-knockdown cells, as indicated below each panel. Right panel, immunoblot analysis of total cell extracts to assess knockdown efficiency (lanes 1-3). Global H3K4me3 levels were assessed by immunoblot and Coomassie staining from cells transfected with each si-RNA. (B) ChIP analysis at the HeLa HIV-1 LTR:Luc promoter in cells treated with control, SKIP- or c-Myc-specific siRNAs, as indicated below each panel. Right panel, immunoblot analysis of knockdown efficiency (lanes 1-3). (C) Luciferase analysis of the HIV-1 Tat transactivation efficiency in cells transfected either with 2 ng of an empty or a Tat expression vector and treated with control or factor-specific siRNAs, as indicated below each panel. Right panel, immunoblot analysis of total cell extracts to assess the efficiency of knockdown for each factor (lanes 1-8). All graphs represent mean and standard error from three independent experiments.

Figure 5

RNF20 is required for basal HIV-1 transcription and to load transcription factors to the LTR:luc promoter. (A) ChIP analysis of H2Bub levels at the HeLa HIV-1 LTR:Luc promoter in si-con and si-SKIP transfected cells. (B) qRT-PCR analysis of basal HIV-1 LTR:Luc mRNA levels, normalized to beta-actin mRNA, in si-control, si-SKIP, or si-RNF20 silenced cells (left panel). The efficiency of SKIP or RNF20 knockdown was assessed by qRT-PCR analysis of the endogenous genes in the middle and right panels, respectively. (C) Analysis of basal and Tat-activated transcription from the integrated HIV-1 LTR:Luc reporter gene in HeLa cells transfected with control, SKIP-, or RNF20-specific siRNAs. (D) ChIP analysis of the integrated HIV-1 promoter (top panel) and PABPC1 gene (bottom panel) in si-con (black) and si-RNF20 (gray) transfected HeLa cells using the factor-specific antisera listed below the bottom panel. Top right panel shows the efficiency of the RNF20 knockdown by immunoblot (lanes 1, 2). Bottom right panel, qRT-PCR analysis of PABPC1 mRNA levels, normalized to beta-actin mRNA, in control and RNF20 knockdown cells. All graphs represent mean and standard error obtained from three independent experiments. (E) Immunoblot analysis of the binding of indicated HeLa proteins to chromatin fractions derived from control or RNF20 knockdown cells (lanes 1-8). Fractions tested were: WCE, whole cell extract; S2, cytoplasmic fraction; S3, soluble nuclear fraction; and P3, chromatin-associated protein fraction. Global H2Bub levels in total acid-extracted histones were assessed by immunoblot and Coomassie staining (lanes 9-12). (F) Immunoblot analysis of H2Bub levels in GST-SKIP (FL), Gst-Tat101, or GST-c-Myc (FL) protein pulldown fractions from a HeLa core histone preparation (lanes 1-5), using an anti-H2Bub antibody.

Figure 6

UV-induced basal HIV-1 LTR:Luc transcription does not require SKIP, CycT1 (P-TEFb), Menin, or RNF20, and is repressed by c-Myc and TRRAP. (A) Analysis of basal and UV-induced HIV-1 LTR:Luc transcription in cells treated with control or various factor-specific siRNAs, as indicated. Bottom panels, immunoblot analysis of knockdown efficiency in this experiment (lanes 1 to 33). (B) ChIP analysis of the HIV-1 LTR:Luc promoter (top panel) or coding region (bottom panel) in control (black) or UV-induced (gray) cells. (C) qRT-PCR analysis of HIV-1 luciferase mRNA levels in control or UV-treated cells, normalized to beta-actin mRNA, for this experiment. All graphs represent mean and standard error obtained from three independent experiments.

Figure 7

The CDK9 inhibitor, flavopiridol, strongly increases basal HIV-1 mRNA levels in UV-treated cells, but inhibits Tat-induced HIV-1 transcription. (A) qRT-PCR analysis of HIV-1 LTR:Luc (luciferase) mRNA levels, normalized to beta-actin mRNA, in control cells or cells exposed to UV, Tat101 (20 ng), or flavopiridol (FP – 500 nM). (B) Analysis of HeLa HIV-1 LTR:Luc (luciferase) activity in the presence of UV, Tat101 (20 ng), or FP (500 nM), as indicated. Inset, immunoblot analysis of the effect of FP on RNAPII Ser2P levels. (C) ChIP analysis of the HIV-1 LTR:Luc promoter and coding region in control, UV-induced and FP (300 nM)-treated cells. All graphs represent mean and standard error obtained from three independent experiments. (D) Model diagram depicting the role of SKIP, c-Myc and Menin in HIV-1 Tat transactivation and induction of MLL1-mediated H3K4me3 at the integrated HIV-1 promoter. See text for details.