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1 Center for Medical Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji Chuo-ku, Tokyo 104-0045, Japan
2 Laboratory of Molecular and Cellular Pathology, Hokkaido University School of Medicine, N15, W7, Kita-ku, Sapporo 060-8638, Japan
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Abstract |
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 Top Abstract IntroductionResultsDiscussionExperimental proceduresReferences |
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Introduction |
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It was shown that SYT interacts and co-localizes with BRM (Thaete et al. 1999), which is one of components of human SWI/SNF complexes (Wang et al. 1996; Kornberg & Lorch 1999; Vignali et al. 2000). The SWI/SNF complex was first characterized in Saccharomyces cerevisiae and affected transcriptional activity by modifying the chromatin structure in vicinity of target promoters (Vignali et al. 2000). As the activity of yeast SWI/SNF complex is dependent on an ATP-hydrolysis, SWI2 protein, which is a subunit of the complex and has a DNA-dependent ATPase activity, is a key player. Two proteins, BRM and Brg1, closely related to the yeast SWI2 have been identified in humans. These proteins are associated with human SWI/SNF complex, composed of at least eight other proteins, including a yeast SNF5 homologue BAF47b. Within this complex, the two SWI2-related proteins are mutually exclusive, indicating at least two versions of the human SWI/SNF complexes. Both BRM and Brg1 can interact with BAF47b, indicating that the two proteins have common molecular partners of BAF47b (Muchardt et al. 1995). It was known that the human SWI/SNF complexes can positively and negatively regulate gene expressions.
Although it was shown that the SYT is a transcriptional co-activator and interacts with BRM (Thaete et al. 1999), there is no evidence demonstrating the functional effects of BRM on SYT activity. In this paper, we report that BRM and its homologue, Brg1, repress the transactivation of SYT. The repression by BRM or Brg1 correlates with its ATP-hydrolysis activity as a functional component of the human SWI/SNF complex. Interestingly, this repression is independent of HDAC activity.
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Results |
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The human SYT protein is composed of 387 amino acids and has no homology to any known protein. The protein has a C-terminal domain, rich in glycine, proline, glutamine and tyrosine (QPGY domain), that is found in several transcriptional activators. It was shown that SYT is a transcriptional co-activator (Brett et al. 1997; Thaete et al. 1999). Because the SYT lacks obvious DNA binding domains, to find the SYT functional domain in the transactivation, we analysed a luciferase reporter assay by fusing SYT and its deletion mutants to the Gal4 DNA binding domain (Fig. 1A). The transcriptional activity of the C-terminal domain (SYT-E) was strong, but that of the wild-type (SYT-WT) or the N-terminal domain (SYT-A) was weak, in the 293T cell (Fig. 1B). This result suggests that the N-terminal domain negatively regulates the transcriptional activity of the C-terminal domain in SYT, the same as previously reported (Brett et al. 1997).
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Recently, it was shown that a chicken BRM binds to SYT in vitro (Thaete et al. 1999) and that human BRM (amino acid residues 156–205) interacts with SYT N-terminal domain by co-immunoprecipitation analysis (Nagai et al. 2001). BRM is one of components of the SWI/SNF complex, which is involved in chromatin structure remodelling in an ATP-hydrolysis-dependent fashion (Vignali et al. 2000). We found that the interaction domain of BRM with SYT shares homology with Brg1 (Fig. 2A), which is another component of SWI/SNF complexes. To examine the direct interaction between SYT and BRM or Brg1, we analysed a binding activity of the full length of BRM or Brg1 to the SYT N-terminal domain. Gal4-SYT mutants that contain SYT-A (amino acid residues 1–180), SYT-B (amino acid residues 1–70) and SYT-C (amino acid residues 71–180) were fused to GST (glutathione S-transferase) protein. GST-Gal4-SYT mutant proteins purified from Escherichia coli were immobilized on glutathione-sepharose beads and incubated with full-length BRM or Brg1 purified from Sf9 cells. After washing the beads, the bound proteins were separated by SDS–PAGE and detected by anti-BRM and anti-Brg1 antibodies, respectively. BRM and Brg1 interacted with GST-SYT-A and GST-SYT-B, but not GST-SYT-C (Fig. 2B, lanes 7, 8 and 9, and Fig. 2C, lanes 7, 8 and 9). These results suggest that both BRM and Brg1 bind to the N-terminal 70 amino acids of SYT.
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For a further validation of the SYT/BRM and SYT/Brg1 interactions, we determined the subcellular localizations of these proteins using immunofluorescence assay. A full-length SYT was cloned in-frame with the green fluorescent protein (GFP) construct. GFP-SYT was co-transfected with BRM or Brg1 in the SW13 cell. After co-transfection, GFP-SYT was detected by autofluorescence. BRM and Brg1 were detected by specific antibodies, respectively. GFP-SYT green signals and Brg1 red signals were observed in punctate configurations (Fig. 2E, a and b). After overlay, a mixed colour (yellow) was observed for almost every signal (Fig. 2E,c), which is indicative of a co-localization of SYT and Brg1. DAPI counter-staining (Fig. 2E,d) indicated that the co-localizing signals were present in the nucleus. Similar co-localization of SYT and BRM in the nucleus was observed (Fig. 2E,e–h). A punctate pattern of co-localization signals was also observed after transfection with flag-tagged full-length SYT and Brg1 (data not shown).
BRM and Brg1 negatively regulate transcriptional activity of SYT
To examine whether BRM or Brg1 has any effects on the SYT transcriptional activity, we analysed the activities of SYT-WT, SYT-A and SYT-E in the SW13 cell that expresses undetectable levels of BRM and Brg1 (Wang et al. 1996; DeCristofaro et al. 2001). SYT-WT showed strong transcriptional activity similar to SYT-E in both the BRM- and Brg1-deficient cell lines (Fig. 3A). This result suggests that the N-terminal domain (amino acids 1–180) of SYT has no effect on the transcriptional co-activator activity of its C-terminal domain (amino acids 181–379) in the BRM- and Brg1-deficient cells, unlikely in the 293T cell (Fig. 1B). To examine whether the difference of the SYT-WT transcription activity between the SW13 cell and the 293T cell was dependent on expression levels of BRM and Brg1, the SYT-WT activity was analysed by co-transfection of BRM or Brg1 in SW13 and 293T cells. The SYT-WT transcriptional activity was repressed by addition of BRM or Brg1, with dose dependency in the SW13 cell, but not the 293T cell (Fig. 3B,C, and data not shown). In another cell C33A that also expresses undetectable levels of BRM and Brg1 (Wang et al. 1996; DeCristofaro et al. 2001), the same as the SW13 cell, the SYT-WT activity was repressed by addition of BRM or Brg1 (data not shown). These results suggest that BRM or Brg1 negatively regulates the SYT-WT activity in cultured cells. Next, to test whether BRM and Brg1 repress SYT transcriptional activity through the SYT N-terminal 70-amino acid domain that is the binding domain of BRM and Brg1, we analysed the activity of SYT-F in which the N-terminal 70 amino acids were fused to the SYT C-terminal transactivation domain (Fig. 1A) in SW13 and C33A cells. SYT-F transactivation activity was repressed by addition of BRM or Brg1, but that of SYT-E was not affected (Fig. 3D,E, and data not shown). These results suggest that BRM and Brg1 negatively regulate SYT transcriptional activity through their binding to the SYT N-terminal 70-amino acid domain.
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It is known that BRM or Brg1 make SWI/SNF protein complexes with a lot of proteins. To examine whether repression by BRM or Brg1 is dependent on their protein complexes, we analysed the SYT-WT activity in the G401 cell that expresses undetectable levels of BAF47b, one of the subunits in the SWI/SNF complexes (Versteege et al. 1998; DeCristofaro et al. 1999, 2001). The transcriptional activity of SYT-WT was high, the same as that of SYT-E in the BAF47b-deficient cell (data not shown) as previously shown in the BRM- and Brg1-deficient cells, SW13 (Fig. 3A). The SYT-WT activity was repressed by the addition of BAF47b with dose dependency (Fig. 4A). This result suggests that BAF47b also works for the repression of the SYT activity and that BRM and Brg1 regulate SYT transcriptional activity in the SWI/SNF complexes.
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It is known that some of the SWI/SNF complexes contain HDAC (histone deacetylase) protein and show the repression activity for several gene transcriptions (Zhang et al. 2000; Kuzmichev et al. 2002). To examine whether the histone deacetylase activity has any effects on the SYT repression activity by BRM and Brg1, we analysed the SYT-WT activity by addition of TSA (trichostatin A), which is a histone deacetylase inhibitor, in SW13 cell. However, TSA has no effect on the repression (data not shown). This result indicates that repression of SYT activity by BRM or Brg1 was independent of the histone deacetylase activity.
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Discussion |
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TopAbstractIntroductionResultsDiscussionExperimental proceduresReferences |
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As the SYT lacks obvious DNA binding domains, we analysed the activity of SYT using a luciferase reporter assay with fusing to the Gal4 DNA binding domain (Fig. 1). We have found that the activity of the full-length SYT is weaker than that of the N-terminal domain deleted mutant in the 293T cell (Fig. 1B), indicating that the activity of SYT was negatively regulated through its N-terminal domain in the 293T cell. Recently, it was shown that the SYT-SSX1 fusion protein has a colony-forming activity and the activity is suppressed by the over-expression of the SYT binding domain of BRM (Nagai et al. 2001). These findings led us to hypothesize that BRM or Brg1 may negatively regulate the SYT activity through its binding. Therefore, we analysed the activity of SYT in BRM- and Brg1-deficient cells (SW13 and C33A). The activity of the full-length SYT is strong, the same as the N-terminal domain deleted mutant in these cells (Fig. 3A, and data not shown), indicating that the N-terminal domain did not inhibit activity in BRM- and Brg1-deficient cells (SW13 and C33A). This indicates that BRM and Brg1 could be candidates for repressor of the activity of SYT. In these cells, we have found that the activity of the full-length SYT is repressed by addition of BRM and Brg1, but that of the N-terminal domain deleted mutant is not (Fig. 3B–E). These findings indicate that BRM and Brg1 negatively regulate SYT transcriptional activity through their binding to the SYT N-terminus.
The ATP-hydrolysis-dependent chromatin structure remodelling factors were originally described as the yeast SWI/SNF complex, which is composed of several subunits and positively regulates an HO gene (Stern et al. 1984). Human homologues of these subunits, which have an ATPase domain, have been identified as BRM and Brg1 (Khavari et al. 1993; Muchardt & Yaniv 1993). We have found that negative regulation of the activity of SYT is needed for ATP hydrolysis of BRM or Brg1(Fig. 4B,C). Like this repression, it was shown that Brg1 negatively regulates the gene expression of cyclin-A and c-fos genes using ATP hydrolysis of Brg1 (Murphy et al. 1999; Strobeck et al. 2000). The repression of the cyclin-A gene by Brg1 was also dependent on HDAC activity (Zhang et al. 2000). We then analysed the effects of a histone deacetylase inhibitor TSA on the repression of the SYT activity by BRM and Brg1. However, TSA had no effect on the repression (data not shown). These results suggested that SWI/SNF complexes have at least two pathways to repress gene expression in dependence or independence on HDAC activity. We speculate that SWI/SNF complexes negatively regulate the transcriptional co-activator activity of SYT by recruiting transcriptional negative factors to the promoter, or by masking or changing the structure of the C-terminal active domain of SYT using ATP-hydrolysis energy.
Recently, it has been shown that SYT also interacts with a putative transcriptional factor AF10 through the N-terminal 90-amino acid residue of SYT, and with an acetyl transferase/transcriptional co-factor p300 through the N-terminal 250-amino acid residue of SYT (Eid et al. 2000; de Bruijn et al. 2001a). However these binding domains of SYT are overlapped, it is unknown whether these proteins interact together with SYT or compete for the binding. It has been shown that p300 interacts with SYT only during the G1 cell cycle phase (Eid et al. 2000), and that human SWI/SNF complexes are inactivated prior to chromosome condensation in the G2/M phase and re-activated during the G1 phase (Muchardt et al. 1996). These findings suggested that the transcriptional co-activator activity of SYT may be regulated in the cell cycle phase.
The BRM and Brg1 interacting region (amino acids 1–70) of SYT contains the so-called SYT N-terminal homology (SNH) domain (Fig. 1). Originally, the SNH was identified in EST sequences derived from a wide variety of species ranging from plants to human (Thaete et al. 1999). These EST sequences indicate that some of them are derived from SYT orthologs in mouse, rat, zebrafish and xenopus, while others are derived from novel SYT homologous genes from human, mouse and rat (Thaete et al. 1999; de Bruijn et al. 2001a). Two human genes of these homologues, SS18L1 and SS18L2, were mapped in chromosome 20q13.3 and 3p21 [PDB] , respectively. The SS18L1 protein has two functional domains; the N-terminal SNH domain and the C-terminal glycine, proline, glutamine and tyrosine-rich (QPGY) domain, the same as SYT, and has 63% sequence homology of SYT (Thaete et al. 1999; de Bruijn et al. 2001b). Recently, it was found that the SS18L1 gene was fused to the SSX1 gene in synovial sarcoma (Storlazzi et al. 2003). These findings may indicate that SS18L1 functions in normal tissue, the same as SYT, and the activity is regulated by BRM and Brg1 complexes. In contrast, the SS18L2 protein has the N-terminal SNH domain but not the C-terminal QPGY domain (Thaete et al. 1999; de Bruijn et al. 2001b), which is a transcriptional co-activator activity domain in SYT. This may indicate that the SS18L2 can bind to BRM and Brg1 and functions as a positive regulator (anti-repressor) of the transcriptional co-activator activity of SYT and SS18L1. A consensus tyrosine phosphorylation site was found in the SNH domains of SYT and its homologues (de Bruijn et al. 2001a). As tyrosine phosphorylation may play an important role in protein–protein interaction and protein trafficking (Pawson 1995), this conserved tyrosine phosphorylation site may serve to modulate the various interactions.
SYT is originally identified as a fusion partner to SSX1 in t(X;18) synovial sarcomas and AF10 is also identified as a fusion partner to MLL in t(10;11)-positive acute leukaemias. BAF47b, which is a subunit of the human SWI/SNF complexes, is known to be a susceptive gene in rhabdoid tumours (Versteege et al. 1998). Interaction of these proteins with SYT suggested that target genes of SYT may not only have implications for synovial sarcoma but also for development of other tumours. Therefore, it is important to find the target genes of SYT and to analyse the regulation of the genes by SYT through BRM, Brg1 and other binding proteins for understanding synovial sarcoma development.
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Experimental procedures |
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SYT mutant cDNAs fused to Gal4 DNA binding domain (DBD) were inserted in the EcoRI and HindIII sites of pCI-Neo (Promega) and pGEX23b (Amersham Pharmacia Biotech). Flag-tagged SYT mutants also are constructed with pCMV-Tag2 (Stratagene) without GAL4 DBD. The BRM cDNA was inserted in the EcoRI site of pCI-NEO and Brg1 was inserted in the BamHI and XhoI sites of pcDNA3.1 (Invitrogen). The ATPase mutants of BRM (K751A) and Brg1 (K785A) were made by PCR, sequenced and inserted in pcDNA3.1. HA-tagged BRM and Brg1 were also constructed by inserting in pcDNA3.1. BAF47b cDNA was inserted in the BamHI and SalI sites of pcDNA3.1. pG5luc (Promega) contains five Gal4 binding sites and the adenovirus major late promoter upstream of firefly luciferase gene. pRL-TK (Promega) is used as a measure of transfection efficiency to normalize the firefly luciferase values. The GFP-SYT-WT expression vector was constructed by inserting in the KpnI and NotI sites of pQBI 25-fC2 (WAKO Chemical USA Inc.). Anti-Gal4 DBD antibody (Santa-Cruz, sc-577) and anti-flag antibody M2 (Sigma) were purchased.
Cell culture, reporter assay and expression of human BRM and Brg1 in insect cell
293T, SW13 and C33A cells were maintained in Dulbecco's modified Eagle's medium (DMEM). Cells were grown supplemented with 10% fetal calf serum. G401 cell was cultured in RPMI medium-1640 (Invitrogen) supplemented with 10% calf serum. Transfections of all expression vectors, pG5luc and pRL-TK, were carried out by using Lipofectamine Plus reagent (Invitrogen). After 36 h of transfection, the cells in 24-well plates were washed by phosphate-buffered saline (PBS) and analysed for luciferase activities in triplicate in each transfection experiment by using Dual-Luciferase Reporter Assay System (Promega). Sf9 insect cell was grown in Grace's Insect Medium (Invitrogen) supplemented with 10% fetal calf serum. Expression procedure of human BRM or Brg1 in Sf9 insect cell was performed using Bac-to-Bac Baculovirus Expression System (Invitrogen).
GST pull-down assay
GST-Gal4-SYT mutant DNAs were transformed in BL21 pLys-S (Novagen). Bacterial cells that expressed GST fusion proteins were harvested and re-suspended in buffer A [50 mM Tris-HCl (pH 7.5), 1 mM EDTA, 500 mM NaCl, protease inhibitors]. After sonication, the lysates were centrifuged for 30 min at 8000 rpm. The supernatants were incubated with glutathione sepharose 4B beads (Amersham Pharmacia Biotech) at 4 °C for 1 h and the beads were washed with buffer A for four times. The Sf9 cells expressed flag tagged BRM or Brg1 were washed with PBS and resuspended in buffer B [10 mM Tris-HCl (pH 8.0), 10 mM glycerol, 0.15 M NaCl, 0.1% nonidet P-40, 5 mM 2-mercaptoethanol, protease inhibitors]. After sonication, the lysates were centrifuged for 30 min at 15 000 rpm. The supernatants were incubated with 30 µL of anti- flag M2 Agarose (Sigma) at 4 °C for overnight and washed five times with buffer B. Bound proteins were eluted with buffer B containing 0.2 mg/mL of flag peptide (Sigma). The elutes were incubated with GST-beads immobilized GST-Gal4-SYT mutants in buffer B at 4 °C for 4 h. The beads were washed four times with buffer B without 2-mercaptoethanol and re-suspended in sample buffer. The bound proteins were separated by 8% SDS–PAGE (sodium dodecyl sulfate—polyacrylamide gel electrophoresis) and analysed with anti-BRM (sc-6450, Santa Cruz) and anti-Brg1 (sc-8749, Santa Cruz) antibodies, respectively. The ECL System (Amersham Pharmacia Biotech) was used for detection on RX-U X-ray films (Fuji).
Immunoprecipitation
The expression vectors of flag-tagged SYT mutants (without GAL4 DNA binding domain), no-tagged BRM and Brg1 were transfected to 293T by Lipofectamine Plus reagent. After 36 h, the cells were washed and suspended in NP-40 lysis buffer [10 mM Tris-HCl (pH 7.8), 1% nonidet P-40, 0.15 M NaCl, 1 mM EDTA, protease inhibitors]. Then lysates were centrifuged for 30 min at 15 000 rpm. The supernatants were incubated with 30 µL of anti-flag M2 agarose at 4 °C for overnight and washed four times with NP-40 lysis buffer. The bound proteins were detected by Western blot.
Immunofluorescence microscopy
Expression vectors of GFP-SYT-WT, HA-tagged BRM or Brg1 were transfected in SW13 using the same method of immunoprecipitaion. After 24 h, the cells were removed to a chamber slide, incubated a further 24 h, fixed with 3% formaldehyde in PBS for 10 min. After washing by PBS, the cells were permeabilized with 0.1% polyoxyehylene octylphenyl ether (10) in PBS for 5 min and washed with PBS. The slide was incubated in blocking buffer (2% normal swine serum in PBS) for 20 min. Cells were incubated overnight with primary antibody at 4 °C, washed three times with PBS and incubated with secondary antibody for 40 min at 25 °C. As primary antibodies, we used anti-BRM (sc-6450 and sc-6449, Santa Cruz), anti-Brg1 (sc-8749, Santa Cruz). As secondary antibodies, we used rhodamine-conjugated donkey anti-goat (sc-2094, Santa Cruz). Finally, the slide was mounted with DAPI and visualized under Leica DM IBD microscope with appropriate filters and images were acquired by Leica Qfluoro.
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Acknowledgements |
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Footnotes |
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* Correspondence: Email: cota{at}gan2.res.ncc.go.jp
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References |
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Received: 6 November 2003
Accepted: 12 February 2004
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