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The Journal of Immunology, 1998, 161: 2276-2283.
Copyright © 1998 by The American Association of Immunologists

The Role of Enhancer A in the Locus-Specific Transactivation of Classical and Nonclassical HLA Class I Genes by Nuclear Factor {kappa}B1

Sam J. P. Gobin2, Vivian Keijsers, Marlijn van Zutphen and Peter J. van den Elsen

Department of Immunohematology and Blood Bank, Leiden University Medical Center, Leiden, The Netherlands


    Abstract
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
HLA class I expression is tightly controlled at the transcriptional level by several conserved regulatory elements in the proximal promoter region. In this study, the two putative {kappa}B motifs of enhancer A ({kappa}B1 and {kappa}B2) of the classical and nonclassical HLA class I genes were investigated for their binding properties of transcription factors and tested for their contribution to the NF-{kappa}B-induced route of transactivation. It was shown that NF-{kappa}B-induced transactivation through enhancer A is most important for the HLA-A locus, which contains two NF-{kappa}B binding sites. Although the enhancer A of HLA-B contains only one NF-{kappa}B binding site ({kappa}B1), there was still a moderate transactivation by NF-{kappa}B. Since HLA-F, which also possesses one NF-{kappa}B binding site but lacks protein binding to its {kappa}B2 site, was not transactivated by NF-{kappa}B, the NF-{kappa}B-mediated transactivation through the {kappa}B1 motif in HLA-B is most probably facilitated by binding of the transcription factor Sp1 to the upstream {kappa}B2 site. Thus, transcriptional regulation of HLA class I genes by NF-{kappa}B is restricted to the HLA-A and HLA-B loci.


    Introduction
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
The human classical MHC class I genes HLA-A, HLA-B, and HLA-C and the nonclassical MHC class I genes HLA-E, HLA-F and HLA-G differ in their level of expression in different cell types (reviewed in Refs. 1 and 2). The classical MHC class I molecules are crucial for immune recognition, as they present antigenic peptides to cytotoxic T lymphocytes (3). Nonclassical MHC class I molecules, such as HLA-E and HLA-G, are also able to present peptides (reviewed in 4 , but their exact role in the T lymphocyte-mediated immune response remains to be elucidated. However, there is increasing evidence that nonclassical HLA class I molecules are important in protection against NK cell responses (reviewed in 4 . Classical MHC class I molecules are ubiquitously expressed in adult tissues (reviewed in Refs. 1 and 2). In embryonic tissue, there is a general lack of classical MHC class I expression, a characteristic thought to be important for evading a potential maternal immune reaction against the developing fetus (5). In contrast, the nonclassical MHC class I genes HLA-E and HLA-F are expressed in many fetal and in some adult tissue (reviewed in Refs. 2 and 4). HLA-G has the most restricted expression pattern and is only expressed on the cytotrophoblasts at the materno-fetal interface, where it is likely to be important for the protection of the fetus against NK cytolysis (5, 6).

The regulation of MHC class I gene expression is mediated by several conserved cis-acting regulatory elements clustered in the promoter region of MHC class I genes. These include the enhancer A element, the IFN-stimulated response element (ISRE) and site {alpha} (reviewed in Refs. 2, 7, and 8–10).

Enhancer A is the target binding site for transcription factors of the NF-{kappa}B/Rel family and is thought to be essential for constitutive and cytokine-induced gene expression. The {kappa}B motif GGGGATTCCCC in enhancer A of the HLA class I gene promoters is highly conserved, particularly in the HLA-A and HLA-B loci (2). This is a symmetrical variant of the more divergent {kappa}B site in the promoter of the Ig {kappa}-light chain gene (GGGACTTCC (11)). Although the {kappa}B motif is the principal target sequence for proteins of the NF-{kappa}B/Rel family, it is also bound by several other DNA-binding proteins, such as the high mobility group protein I(Y) (HMG I(Y))3 and proteins that belong to the leucine zipper family of transcription factors (reviewed in Refs. 12 and 13). The NF-{kappa}B/Rel family of transcription factors comprises at least five members, p50, p65 (also termed RelA), p52, c-Rel, and RelB, that bind DNA either as homo- or heterodimers (reviewed in Refs. 12 and 13). These dimers posess different binding affinities for {kappa}B sites and their half-sites, as well as different transcriptional properties (12, 13, 14, 15, 16).

The p50-p65 heterodimer, termed NF-{kappa}B, is present in virtually all differentiated cells and is the most abundant of the NF-{kappa}B/Rel dimers (12, 13). NF-{kappa}B is normally retained in the cytoplasm complexed to the inhibitory protein I{kappa}B (reviewed in Refs. 16–18). Following activation by stimuli such as cytokines and phorbol esters, I{kappa}B is inactivated and degraded, after which NF-{kappa}B is released and subsequently translocated to the nucleus (reviewed in Refs. 12 and 13). Interaction of NF-{kappa}B with the {kappa}B site results in transactivation of MHC class I and a variety of other genes, including those encoding cytokines and viral genes.

The level of gene transcription of the various MHC class I loci is determined by tissue-specific levels of expression of the NF-{kappa}B/Rel family proteins, their differential binding affinity for a particular {kappa}B site, and the transactivation capacities of the different dimers (reviewed in Refs. 12 and 13). The NF-{kappa}B subunits p65 and c-Rel both have a transactivation domain, although p65 is the more potent of the two. The NF-{kappa}B subunit p50, lacking such transactivation domain, is thought to have no transactivating capacity as a homodimer but rather to fulfill an ancillary function for the p65 and c-Rel subunits. However, since in cell-free assays the p50 homodimer can transactivate MHC class I (19), its exact role in transactivation is still unclear.

The human classical and nonclassical MHC class I genes differ in their level of constitutive expression in different cell types and also in their cytokine-induced expression patterns (reviewed in 2 . Locus-specific variation in the two putative {kappa}B sites of the enhancer A elements (2, 20, 21) determines their binding capacity and functioning. Locus-specific contribution of the enhancer A element to transactivation may be an important mechanism in the differential regulation of the constitutive and cytokine-induced levels of classical and nonclassical HLA class I expression in various cell types.

In this study, we assessed the capacity of the two putative {kappa}B sites within the enhancer A region in the promoter of the classical and nonclassical HLA class I genes to bind proteins of the NF-{kappa}B/Rel family of transcription factors and to mediate transactivation by NF-{kappa}B. The NF-{kappa}B-mediated transactivation of HLA class I genes is restricted to the HLA-A and HLA-B loci and seems to require binding not only of NF-{kappa}B to the {kappa}B1 site, but also of either NF-{kappa}B or Sp1 to the {kappa}B2 site.


    Materials and Methods
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Cell culture

The cells used were the teratocarcinoma cell line Tera-2 and the B lymphoblastoid cell line CCRF-SB (American Type Culture Collection, Manassas, VA). The cells were grown in Iscove’s modified DMEM supplemented with 10% (v/v) heat-inactivated FCS (Life Technologies, Paisley, Scotland), penicillin (100 IU/ml), and streptomycin (100 µg/ml).

Plasmids

Reporter constructs pGL3-A230 and pGL3-A140 were generated by cloning a 228-bp BglI-AhaII HLA-A*0201promoter fragment or a 143-bp PpuMI-AhaII HLA-A*0201 promoter fragment, respectively, upstream of the firefly luciferase gene in pGL3-Basic (Promega, Madison, WI). Enhancer A-containing reporter constructs were generated by cloning ds-oligonucleotides of the enhancer A sequence (containing both the {kappa}B1 and {kappa}B2 motifs) from the various HLA class I genes upstream of the 143-bp HLA-A*0201 promoter fragment in pGL3-A140.

The expression vector constructs of pRSV-p50 and pRSV-p65 (a kind gift of Dr. L. Struyk, Academic Medical Centre, Amsterdam, The Netherlands) contain the 1.3-kb cDNA and 2.6-kb cDNA fragments encoding NF-{kappa}B-p50 and NF-{kappa}B-p65, respectively, and were generated by inserting the cDNAs into pRSVNeo (22) from which the NeoR gene has been deleted.

Transient transfection

Cells were transfected by the calcium phosphate coprecipitation method of Chen and Okayama (23). In each of four wells of a six-well plate, 0.2 x 106 Tera-2 cells were transfected with a DNA mix containing 2.5 µg of pGL3 reporter plasmid, 2.5 µg of pRSV-lacZ plasmid, and 5 µg of pRSV (control) or 2.5 µg of pRSV-p50 and pRSV-p65 (NF-{kappa}B) each and harvested 2 days after transfection. Luciferase activity was determined using a luminometer (Tropix, Badford, MA) and corrected for transfection efficiency by measuring ß-galactosidase activity. Transfection of pGL3-Basic was used as a reference to correct for the possible effects of cotransfection with the expression vectors. The relative luciferase values are given as mean relative light units ± SD (n = 4).

Preparation of nuclear extracts

Nuclear extracts were prepared from 10 x 106 cells. The cells were harvested, washed with PBS, taken up in 300 µl (three cell volumes) of hypotonic solution (20 mM HEPES, pH 8.0, 10 mM KCl, 0.15 mM EGTA, 0.15 mM EDTA, 1 mM DTT, 0.5 mM 4-(2-aminoethyl)-benzenesulfonylfluoride (AEBSF)), and then left on ice for 15 min. The cells were lysed with Nonidet P-40 (final concentration of 0.1% for CCRF-SB cells; 0.2% for Tera-2) for 3 to 5 min. Then, 80 µl (80% of the cell volume) of a sucrose solution (50 mM HEPES, pH 8.0, 10 mM KCl, 0.25 mM EDTA, 1 mM DTT, 0.5 mM AEBSF, 70% (w/v) sucrose) was added, and the nuclei were centrifuged at 5000 rpm for 5 min at 4°C. The supernatant was discarded, and the pellet was gently taken up in 300 µl (three cell volumes) of solution B (10 mM HEPES, pH 8.0, 100 mM NaCl, 0.1 mM EDTA, 1 mM DTT, 0.5 mM AEBSF, 25% (v/v) glycerol) and centrifuged at 5000 rpm for 5 min at 4°C. After the supernatant was discarded, the cell pellet was taken up in 200 µl (2 cell volumes) of extraction solution (10 mM HEPES, pH 8.0, 400 mM NaCl, 0.1 mM EDTA, 1 mM DTT, 0.5 mM AEBSF, 25% glycerol) and left on ice for 30 min with intermittent vortexing. The extracted nuclei were centrifuged at 14,000 rpm for 5 min at 4°C, and the supernatant was aliquoted and stored at -80°C. The total amount of protein was determined using the BCA (bicinchoninic acid) Protein Assay Reagent kit (Pierce, Rockford, IL) according to the manufacturer’s instructions.

Electrophoretic mobility gel shift assay (EMSA)

Nuclear extracts (~5 µg protein) were incubated in DNA/protein-binding buffer (20 mM HEPES, pH 7.9, 50 mM KCl, 10% (v/v) glycerol, 0.5 mM DTT, 0.1 mM EDTA), with 250 ng poly(dI · dC), 100 ng sonicated herring sperm ssDNA, and 1 ng 32P-radiolabeled probe for 15 min at 4°C. The samples were run on a 6% nondenaturing polyacrylamide gel in 0.25x TBE (0.89 M Tris-borate, 0.89 M boric acid, and 0.02 M EDTA) at 200 V for 2 h. The gels were fixed with a 10% methanol, 10% acetic acid solution, dried onto Whatmann 3M paper, and exposed to an x-ray film. The ds-oligonucleotides containing the individual {kappa}B1 and {kappa}B2 sites from the various HLA class I genes were used as probes (see Table IGo).


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Table I. Oligonucleotides representing the {kappa}B1 and {kappa}B2 sites in enhancer A of the HLA class I loci used for EMSA

 
For the supershift assays, 1 µg of each Ab specifically directed against a member of the NF-{kappa}B/Rel family of transcription factors was added to the nuclear extract and probe mixture and incubated for 1 h at 4°C. The Abs used were anti-p50 Ab (sc-114), anti-p65 Ab (sc-109), anti-c-Rel Ab (sc-71), anti-Sp1 Ab (sc-59), anti-Fra1 Ab (sc-605), anti-Fra2 Ab (sc-171), anti-Fos Ab (sc-413), anti-Jun Ab (sc-44), and anti-IRF-1 Ab (sc-640), all from Santa Cruz Biotechnology (Santa Cruz, CA), and an anti-HMG I(Y) antiserum (24) (kindly provided by Dr. Dimitris Thanos, Columbia University, New York, NY).


    Results
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Locus-specific variation of NF-{kappa}B/Rel protein binding to the {kappa}B sites in enhancer A of the classical and nonclassical HLA class I genes

The promoter regions of classical and nonclassical HLA class I genes contain two putative {kappa}B sites, {kappa}B1 and {kappa}B2, in their enhancer A elements. The {kappa}B1 site in enhancer A of HLA-A(GGGGATTCCCC; Table IGo) is the most conserved throughout the MHC class I loci and was used as reference to test for binding of proteins of the NF-{kappa}B/Rel family in EMSAs. Using nuclear extracts from the B lymphoblastoid line CCRF-SB, which constitutively expresses proteins of the NF-{kappa}B/Rel family, this {kappa}B motif was found to bind several protein complexes: an upper complex consisting of two closely migrating bands, designated complex 1 and complex 2; and a lower complex, designated complex 3 (Fig. 1GoA). Employing antisera specific for p50, p65, and c-Rel (25, 26), the proteins contained in these complexes could be identified (Fig. 1Go, A and B). The uppermost band in the duplex (complex 1) was shown to contain p65. This protein/DNA complex probably represents the p50-p65 heterodimer, although the presence of p65-p65 homodimers cannot be excluded. The lower band of the two closely migrating protein/DNA complexes (complex 2) was shown to contain c-Rel. Complex 2 could be either the p50-c-Rel or the p65-c-Rel heterodimer. Finally, the lower band (complex 3), shown to contain the p50 subunit, is most probably the p50-p50 homodimer (Fig. 1Go, A and B). No supershift was obtained with an irrelevant Ab (Fig. 1GoC).



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FIGURE 1. Binding of p50, p65, and c-Rel to the conserved {kappa}B site in enhancer A of HLA class I. EMSA analysis of nuclear extracts from the B lymphoblastoid cell line CCRF-SB incubated with the {kappa}B1 probe of HLA-A ({kappa}B1-A). Three complexes were found to bind, which could be shown to contain p65 (complex 1), c-Rel (complex 2), and p50 (complex 3) with supershift analysis. For supershift analysis, anti-p50, anti-p65, and anti-c-Rel Abs were used (25, 26); supershifted complexes are indicated by an asterisk. A short (6 h; A) and a normal exposure (overnight; B) are shown. No supershift was obtained with an irrelevant (anti-mouse IRF-1) Ab (C).

 
Next, a panel of probes representing the individual {kappa}B motifs of all HLA class I loci (Table IGo) was used to perform a complete analysis of their binding properties for proteins of the NF-{kappa}B/Rel family using nuclear extracts from B cells. In Figure 2Go, A and B, it is shown that, similar to the conserved {kappa}B1 site of the HLA-A locus, the {kappa}B1 site of the HLA-B locus (GGGGATTCCCC), was bound by the complexes containing the p50, p65, and c-Rel subunits. The {kappa}B2 site in HLA-A (GGGGAGTCCCA) was also bound by these complexes, but with an apparently weaker binding affinity (Fig. 2Go, A and B). No binding of proteins of the NF-{kappa}B/Rel family was detected for the {kappa}B2 sites of HLA-B(GGGGAGGCGCA) and the {kappa}B1 and {kappa}B2 sites of HLA-C(GAGGATTCTCC and GGGGAGGCGCC, respectively) under these experimental conditions (Fig. 2GoA). EMSAs with {kappa}B1 and {kappa}B2 probes of the nonclassical HLA class I genes revealed that the {kappa}B1 site in HLA-F (GAGAATTCCCC) was bound by the p50, p65, and c-Rel subunits (Fig. 2GoA), while both the {kappa}B1 and {kappa}B2 sites in HLA-G (GGGGATTCTCT and GGGGAGGCCCC, respectively) were bound only by the p50-containing complex (complex 3; Fig. 2Go, A and B); binding of the p65-containing complex was hardly detectable and only after long exposure times (data not shown). No NF-{kappa}B complex could be detected binding to the {kappa}B2 site of HLA-F (TTGGAAGGCTC) nor to the {kappa}B1 and {kappa}B2 sites of HLA-E (GGGAAACTCTG and AAGAACTGCTG, respectively) (Fig. 2GoA).



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FIGURE 2. Differential binding properties of NF-{kappa}B/Rel complexes to the {kappa}B1 and {kappa}B2 probes of the various classical and nonclassical HLA class I loci. A, EMSA analysis with nuclear extracts from the B lymphoblastoid cell line CCRF-SB were incubated with a panel of {kappa}B1 and {kappa}B2 probes of the various HLA class I genes (see Table IGo). Three NF-{kappa}B/Rel complexes were found to bind (complex 1, 2, and 3) as well as two additional nucleoprotein complexes (complex A and B). B, Supershift analysis identifying p65 (complex 1), c-Rel (complex 2), and p50 (complex 3) with anti-p65, anti-c-Rel, and anti-p50 Abs. Complex A and B do not contain p50, p65, or c-Rel. The arrowhead indicates supershifted complexes.

 
Several {kappa}B site probes were seen to bind proteins not belonging to the NF-{kappa}B family of transcription factors for which we were testing. For example, a slowly migrating complex (referred to as complex A) was found to bind the {kappa}B2 sites of HLA-B, HLA-C, and HLA-G, which all share the GGGGAGGCG/CC sequence (Table IGo). The specificity of the binding was tested by competition with cold {kappa}B probes. Cold {kappa}B2 probe of HLA-C or of HLA-G competed with the {kappa}B2 site of HLA-C for binding of complex A, whereas cold {kappa}B1 probe of HLA-A did not compete (Fig. 3GoA). Conversely, binding of complex A to the {kappa}B2 site of HLA-G was inhibited when using cold {kappa}B2 probe of HLA-C or of HLA-G, but not when using the {kappa}B1 probe of HLA-A (data not shown). Since the sequence of these {kappa}B2 sites is homologous to an Sp1 binding site (27, 28, 29), we tested for binding of Sp1 to the {kappa}B2 site of HLA-C. Using an anti-Sp1-specific Ab in supershift assays, complex A was shown to contain Sp1 (Fig. 3GoB). The complex could not be supershifted with an irrelevant Ab (Fig. 3GoB). Similarly, Sp1 binding could also be demonstrated to the {kappa}B2 sites of HLA-B and HLA-G (data not shown).



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FIGURE 3. Complex A binds specifically to the {kappa}B2 sites of HLA-C and contains Sp1. A, EMSA analysis with nuclear extracts from the B lymphoblastoid cell line SB to demonstrate the specificity of complex A binding to the {kappa}B2 probe of HLA-C ({kappa}B2-C). Cold {kappa}B1-A, {kappa}B2-C, or {kappa}B2-G probe was added in 25-, 50-, and 100-fold excess as competitor. The cold {kappa}B2-C and {kappa}B2-G probes competed well for binding of complex A, whereas cold {kappa}B1-A probe was unable to compete. B, Supershift analysis demonstrating the presence of Sp1 in complex A. The asterisk indicates supershifted complexes. No supershift was obtained with an irrelevant Ab (anti-mouse IRF-1).

 
A fast migrating complex (complex B) was found to bind specifically to the {kappa}B1 sites of HLA-C and HLA-G (Fig. 2Go, A and B), which share the GGATTCTC sequence. The specificity of the binding was also tested by competition with cold {kappa}B probes, and binding of complex B was competitive when using the cold {kappa}B2 probe of HLA-C or of HLA-G (containing the homologous sequence), but only weakly competitive with the divergent {kappa}B1 probe of HLA-A (data not shown). These characteristics suggest that complex B contains the high mobility group I(Y) protein (HMG I(Y)). Using an HMG I(Y)-specific Ab (24), a supershift was obtained (data not shown), strongly suggesting that this complex contains HMG I(Y) protein.

Recently, the Fos/Jun family protein Fra-2 has been shown to bind the {kappa}B binding site of porcine MHC class I (30). Since this {kappa}B binding site is homologous to the {kappa}B2 site of HLA-A, we tested for binding of members of the Fos/Jun family of transcription factors to the {kappa}B1 and {kappa}B2 sites of HLA-A. However, we were unable to detect Fra-2 or other factors of the Fos/Jun family in the complex binding to the {kappa}B1 site or {kappa}B2 site of HLA-A, using nuclear extracts of CCRF-SB or EBV-transformed B cell nuclear extracts (data not shown).

Locus-specific HLA class I transactivation mediated by enhancer A

Having determined the binding properties of NF-{kappa}B/Rel proteins to the {kappa}B1 and {kappa}B2 sites of enhancer A, we evaluated the contribution of the enhancer A elements of the various HLA class I loci to transactivation in transient cotransfection experiments. For these experiments, reporter constructs were generated containing the enhancer A sequence of the various HLA class I genes in front of a minimal promoter fragment of HLA-A2.1 (Fig. 4GoA).



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FIGURE 4. NF-{kappa}B is only able to induce HLA-A and HLA-B. A, Enhancer A sequences of the various classical and nonclassical HLA class I genes and the cloning of the panel of enhancer A containing luciferase reporter plasmid constructs based on pGL3-Basic. The sequences in bold type indicate the two putative {kappa}B sites, {kappa}B1 and {kappa}B2. The double-stranded enhancer A oligonucleotides were cloned upstream of a 143-bp HLA-A2.1 promoter fragment in the reporter plasmid pGL3-Basic. B, Transient cotransfection assay of the control construct pGL3-A230, containing the HLA-A2.1 promoter, together with the expression vector of p50, p65, or both in Tera-2 cells. The luciferase activity values were normalized with the ß-galactosidase activity and are expressed as mean ± SD of n = 4. C, The relative contribution of enhancer A to transactivation was tested by transient cotransfection experiments in Tera-2 cells, with the panel of luciferase reporter constructs containing the enhancer A region of the various HLA class I loci linked to the minimal promoter of HLA-A(see description in A) together with the expression vectors of p50 and p65. The luciferase activity values were normalized with the ß-galactosidase activity and are expressed as mean ± SD of n = 4.

 
First, we determined the transactivation capacity of the NF-{kappa}B subunits using pGL3-A230, containing the 228-bp HLA-A2.1 promoter fragment. As shown in Figure 4GoB, cotransfection with the p50 subunit alone did not result in an increase of HLA-A2.1-driven transcription in Tera-2 cells, whereas cotransfection with p65 resulted in a 6-fold induction. Together, p50 and p65 were able to induce HLA-A2.1-driven transactivation to an even higher level (14-fold), which supports the suggestion that they act synergistically (Fig. 4GoB).

Subsequently, the reporter constructs containing the enhancer A sequence of the various HLA class I genes in front of a 143-bp HLA-A2.1 promoter fragment were transiently cotransfected with expression vectors of p50 and p65 in Tera-2 cells. Figure 4GoC shows a typical transient cotransfection experiment. Enhancer A of HLA-A, containing two {kappa}B sites able to bind NF-{kappa}B, gave rise to a significant transcriptional activity when cotransfected with p50 and p65 (15-fold induction), whereas transactivation of enhancer A of HLA-B (containing only one {kappa}B binding sequence) was relatively low (3-fold induction; Fig. 4GoC). The enhancer A of HLA-C did not give rise to any significant NF-{kappa}B-induced transactivation activity, which is in accordance with the inability of the {kappa}B1 and {kappa}B2 motifs of HLA-C to bind NF-{kappa}B subunits. None of the enhancer A elements of the nonclassical HLA class I genes HLA-E, HLA-F, or HLA-G gave rise to any significant NF-{kappa}B-induced transactivation activity (Fig. 4GoC). Despite the binding activity of the p50 and p65 to the {kappa}B1 of HLA-F, no transactivation of HLA-F was observed; this could be attributed to the lack of binding to the {kappa}B2 site. As expected, binding activity of p50 to both the {kappa}B1 and {kappa}B2 of HLA-G did not result in transactivation. Similar results were obtained in HeLa cells (data not shown).


    Discussion
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Variation in the nucleotide sequence of the {kappa}B binding sites determines both the binding affinity of the various NF-{kappa}B dimers and conformational changes in the nucleoprotein complex (19, 31, 32, 33, 34). Since the various NF-{kappa}B complexes differ in their transactivation capacities (12, 13), this could result in differences in activation of gene transcription. Therefore, locus-specific variations in the nucleotide sequences of the {kappa}B binding sites in HLA class I genes could be at the heart of their differential NF-{kappa}B-mediated regulation via enhancer A. In this study, the {kappa}B sites in enhancer A of the promoter region of classical and nonclassical HLA class I genes were investigated for their capacity to bind proteins of the NF-{kappa}B/Rel family of transcription factors and their contribution to transactivation.

Locus-specific binding properties of NF-{kappa}B to the {kappa}B1 and {kappa}B2 sites in enhancer A of HLA class I

The enhancer A element in HLA class I contains a palindromic {kappa}B site, GGGGATTCCCC, referred to as {kappa}B1. This site is conserved in the HLA-A and HLA-B loci but is also found, albeit with nucleotide alterations, in the promoters of the other HLA class I loci. In addition, upstream of the {kappa}B1 site is the {kappa}B2 site GGGGAGTCCC, which is found in the HLA-A alleles and also, with minor to major nucleotide variations, in the promoters of the other HLA class I loci. Both the {kappa}B1 and {kappa}B2 sites of the enhancer A region of HLA-A have been shown to be occupied, as determined by in vitro footprinting (35). In this study, the {kappa}B1 site of HLA-A and HLA-B (GGGGATTCCCC) was found to bind three complexes containing members of the NF-{kappa}B/Rel family of transcription factors, which is in general agreement with findings by others (21, 29, 36). Supershift assays indicated that the three complexes that were found to bind the {kappa}B1 site contained p50, p65, and c-Rel subunits. These complexes could represent the p50-p65 heterodimer, the p50-c-Rel or p65-c-Rel heterodimer, and the p50-p50 homodimer. Although in HLA-A the {kappa}B2 site (GGGGAGTCCCA) differs by only two nucleotides (underlined) from the {kappa}B1 site, it displayed a reduced binding affinity for all three complexes under these experimental conditions. The central nucleotides (ATT) in a {kappa}B site function as the binding site for HMG I(Y) proteins, which play a role in the DNA bending and the ultimate structure of the nucleoprotein complex and also act as coactivators in NF-{kappa}B-mediated transactivation (24, 37). These central nucleotides are rarely guanines, and it is therefore likely that the central guanine in the {kappa}B2 site of HLA-Ais responsible for this weaker binding affinity. No binding of any NF-{kappa}B complexes could be detected to the {kappa}B2 site of HLA-B or to either of the {kappa}B sites of HLA-C.

Two of the nonclassical HLA class I genes were bound by NF-{kappa}B complexes. The {kappa}B1 site of HLA-F (GAGAATTCCCC) was bound by the three p50-, p65-, and c-Rel-containing complexes, despite two nucleotide differences from the consensus sequence. The {kappa}B1 site of HLA-G(GGGATTCTCT) showed binding of only p50, whereas binding of the other NF-{kappa}B subunits (p65 and c-Rel) was barely detectable. The specificity of the {kappa}B2 site of HLA-Gfor p50 is in agreement with in vitro DNA binding studies in which it was shown that the otherwise perfect {kappa}B motif GGGGAGGCCCC is bound only by p50 (33). No binding of any {kappa}B-specific complexes could be detected to both {kappa}B sites of HLA-E or to the {kappa}B2 site of HLA-F. Together, these data argue that only the {kappa}B2 site of HLA-A is a true NF-{kappa}B binding site and that the putative {kappa}B2 site in the promoter of the other HLA class I loci cannot be termed a {kappa}B site.

Two other complexes, designated complex A and B, were found to bind to some of the {kappa}B motifs of HLA class I loci; these complexes did not contain any of the {kappa}B/Rel family proteins for which we were testing. The slower migrating complex A had an apparent binding specificity for the GGGGAGGCG/CC sequence. This sequence has been proposed as a binding site for Sp1 in HLA-B(28, 29). Furthermore, both half-sites of this sequence are homologous to zinc finger binding sites: the 5' half-site is homologous to the binding site for the myeloid zinc finger protein MZF1 (38), and the 3' half site is homologous to the binding site for the zinc finger protein ZFX, identified in the promoters for HLA-A genes (39, 40). In this study, we demonstrated that complex A contained Sp1; but since the supershift was not complete with the Ab used, the possibility cannot be excluded that other (zinc finger) proteins are contained in the complex. The faster migrating complex B had an apparent binding specificity for the GGATTCTC sequence. These characteristics, and the fact that a supershift could be obtained using an anti-HMG I(Y) antiserum (24), strongly suggest that complex B consists of HMG I(Y) proteins (24, 37). It is possible that in the absence of NF-{kappa}B binding, such as to the {kappa}B1 sites of HLA-C and HLA-G, formation of a complex with HMG I(Y) proteins is more prominent.

NF-{kappa}B-induced transactivation through enhancer A is limited to the HLA-A and HLA-B loci

Transactivation by NF-{kappa}B dimers is dependent on the subunits they contain. Both the p65 and c-Rel subunits possess transactivation domains, but p65 has been shown to be the more potent transactivator of the two (12, 13). Experiments in mice have shown that a transgene driven by a promoter containing multiple {kappa}B sites was not transcribed in organs in which only the p50 subunit was expressed; the transgene was found to be transcribed only in those organs in which both p65 and p50 were expressed (41). Moreover, p50 alone does not activate transcription in transient transfection assays (this study and Refs. 29, 42, and 43). The p50 subunit has therefore been attributed an ancillary function in DNA binding of the dimer and in transactivation by the p65 or c-Rel subunits.

The enhancer A elements of classical HLA class I genes HLA-A and HLA-B were, in accordance with their ability to bind the p50-p65 heterodimer, mediators of NF-{kappa}B-induced transcription. Enhancer A of HLA-A, which contains two {kappa}B sites binding the different NF-{kappa}B dimers, displayed the strongest transactivation capacity of all of the HLA class I loci. Multiple {kappa}B binding sites that are occupied by NF-{kappa}B, as is the case for HLA-A, can lead to a synergistic transcriptional effect (44) and are thought to be required for transcriptional induction (21, 45). Less marked was the transactivation through the enhancer A region of HLA-B, which contains only one NF-{kappa}B binding site ({kappa}B1). In this locus, the {kappa}B2 site is bound by Sp1 (this study and Refs. 28 and 29), a transcription factor that is shown able to interact with NF-{kappa}B (46, 47). Sp1 binding to the {kappa}B2 site may assist in the NF-{kappa}B-mediated transactivation through the {kappa}B1 site by allowing protein/protein interactions, leading to transactivation through the enhancer A of HLA-B (28, 48). This would explain why there is still transactivation through the single NF-{kappa}B-occupied {kappa}B1 site in this locus (this study and Refs. 28 and 29). In support of this hypothesis is the lack of NF-{kappa}B-mediated transcriptional activity through the {kappa}B1 site in the enhancer A region of HLA-F, because unlike the HLA-B gene, HLA-F does not bind transcription factors to the upstream {kappa}B2 site. These findings are corroborated by the observation that the single {kappa}B site in the bidirectional promoter of the TAP1 and LMP2 genes has been found to depend on the flanking Sp1 site for TNF{alpha}-induced transcription by NF-{kappa}B (49, 50). The other HLA class I loci were not found to be regulated by NF-{kappa}B, which is in accordance with the lack of NF-{kappa}B binding to the {kappa}B1 site (HLA-C, HLA-E) or to the {kappa}B2 site (HLA-F), as explained above. Finally, the lack of NF-{kappa}B-induced transactivation of HLA-G can simply be explained by a lack of transactivating activity by the p50-p50 homodimer (this study and Refs. 29 and 43).

In this study, it is shown that two classical, but none of the nonclassical, HLA class I genes are transactivated by NF-{kappa}B. Transactivation was most important in the HLA-A locus, which contains two NF-{kappa}B binding sites in the enhancer A region. Although the enhancer A of HLA-B contains only one NF-{kappa}B binding site ({kappa}B1), there was still a moderate transactivation by NF-{kappa}B. Binding of Sp1 to the upstream {kappa}B2 site seems to contribute to this transactivation through the {kappa}B1 motif in HLA-B, because HLA-F, which also has one NF-{kappa}B binding site but lacks an NF-{kappa}B or Sp1 binding site flanking the {kappa}B1 site, was not transactivated by NF-{kappa}B. Thus, NF-{kappa}B-mediated transactivation of the HLA class I genes seems to require the binding not only of the {kappa}B1 site by NF-{kappa}B, but also of the {kappa}B2 by either NF-{kappa}B or Sp1. Since transcriptional regulation of HLA class I genes by NF-{kappa}B is restricted to HLA-A and HLA-B genes, the expression and activation of NF-{kappa}B contribute only to the developmental and tissue-specific expression patterns of these classical HLA class I genes.


    Acknowledgments
 
We thank Drs. C. S. Bigland, F. H. J. Claas, M. J. Giphart, A. Peijnenburg, and C. Verweij for critically reading the manuscript; and Drs. J. Arts, L. Struyk, and D. Thanos for the kind gift of the anti-Sp1 Ab, NF-{kappa}B expression vectors, and anti-HMG I(Y) antiserum, respectively.


    Footnotes
 
1 This work was supported in part by the Netherlands Organisation for Research (NWO Grant 901-09-200) and the Netherlands Foundation for the Support of Multiple Sclerosis Research (96-248 MS). Back

2 Address correspondence and reprint requests to Dr. S. J. P. Gobin, Department of Immunohematology and Blood Bank, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands. Back

3 Abbreviations used in this paper: HMG I(Y), high mobility group I(Y); IRF-1, IFN regulatory factor-1; EMSA, electrophoretic mobility gel shift assay; Sp1, specificity protein 1; AEBSF, 4-(2-aminoethyl)-benzenesulfonylfluoride. Back

Received for publication October 24, 1997. Accepted for publication April 30, 1998.


    References
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
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