CpG binding protein is crucial for early embryonic development.

Epigenetic modification of DNA via CpG methylation is essential for the proper regulation of gene expression during embryonic development. Methylation of CpG motifs results in gene repression, while CpG island-containing genes are maintained in an unmethylated state and are transcriptionally active. The molecular mechanisms involved in maintaining the hypomethylation of CpG islands remain unclear. The transcriptional activator CpG binding protein (CGBP) exhibits a unique binding specificity for DNA elements that contain unmethylated CpG motifs, which makes it a potential candidate for the regulation of CpG island-containing genes. In order to assess the global function of this protein, mice lacking CGBP were generated via homologous recombination. No viable mutant mice were identified, indicating that CGBP is required for murine development. Mutant embryos were also absent between 6.5 and 12.5 days postcoitum (dpc). Approximately, one-fourth of all implantation sites at 6.5 dpc appeared empty with no intact embryos present. However, histological examination of 6.5-dpc implantation sites revealed the presence of embryo remnants, indicating that CGBP mutant embryos die very early in development. In vitro blastocyst outgrowth assays revealed that CGBP-null blastocysts are viable and capable of hatching and forming both an inner cell mass and a trophectoderm. Therefore, CGBP plays a crucial role in embryo viability and peri-implantation development.

The matrix attachment region-binding protein SATB1 interacts with multiple elements within the gp91phox promoter and is down-regulated during myeloid differentiation.

The gp91(phox) gene encodes a component of the respiratory burst NADPH oxidase complex and is highly expressed in mature myeloid cells. The transcriptional repressor CCAAT displacement protein binds to at least five sites within the proximal gp91(phox) promoter and represses expression prior to terminal phagocyte differentiation. The DNA binding activity of CCAAT displacement protein decreases during terminal phagocyte differentiation, thus permitting the binding of transcriptional activators and induction of gp91(phox) expression. We report here that the matrix attachment region-binding protein SATB1 interacts with at least seven sites within the -1542 to +12-base pair gp91(phox) promoter. Four additional binding sites for CCAAT displacement protein were also identified. Furthermore, the most proximal SATB1-binding site within the gp91(phox) promoter binds specifically to the nuclear matrix fraction in vitro. SATB1 expression is down-regulated during terminal myeloid cell differentiation, coincident with induction of gp91(phox) expression. Transient transfection assays demonstrate that a SATB1-binding site derived from the gp91(phox) promoter represses promoter activity in cells expressing SATB1. These findings underscore the importance of transcriptional repression in the regulation of gp91(phox) expression and reveal a candidate myeloid cell target gene for SATB1, a factor previously found to be essential for T cell development.

Identification and characterization of the DNA binding domain of CpG-binding protein.

CpG-binding protein is a transcriptional activator that exhibits a unique DNA binding specificity for unmethylated CpG motifs. CpG-binding protein contains a cysteine-rich CXXC domain that is conserved in DNA methyltransferase 1, methyl binding domain protein 1, and human trithorax. In vitro DNA binding assays reveal that CpG-binding protein contains a single DNA binding domain comprised of the CXXC domain and a short carboxyl extension. Specific mutation to alanine of individual conserved cysteine residues within the CXXC domain abolishes DNA binding activity. Denaturation/renaturation experiments in the presence of various metal cations demonstrate that the CXXC domain requires zinc for efficient DNA binding activity. Ligand selection of high affinity binding sites from a pool of degenerate oligonucleotides reveals that CpG-binding protein interacts with a variety of sequences that contains the CpG dinucleotide with a consensus binding site of (A/C)CpG(A/C). Mutation of the CpG motif(s) present within ligand-selected oligonucleotides ablates the interaction with CpG-binding protein, and mutation to thymine of the nucleotides flanking the CpG motifs reduces the affinity of CpG-binding protein. Hence, a CpG motif is necessary and sufficient to comprise a binding site for CpG-binding protein, although the immediate flanking sequence affects binding affinity.

Cloning of a mammalian transcriptional activator that binds unmethylated CpG motifs and shares a CXXC domain with DNA methyltransferase, human trithorax, and methyl-CpG binding domain protein 1.

Ligand screening was utilized to isolate a human cDNA that encodes a novel CpG binding protein, human CpG binding protein (hCGBP). This factor contains three cysteine-rich domains, two of which exhibit homology to the plant homeodomain finger domain. A third cysteine-rich domain conforms to the CXXC motif identified in DNA methyltransferase, human trithorax, and methyl-CpG binding domain protein 1. A fragment of hCGBP that contains the CXXC domain binds to an oligonucleotide probe containing a single CpG site, and this complex is disrupted by distinct oligonucleotide competitors that also contain a CpG motif(s). However, hCGBP fails to bind oligonucleotides in which the CpG motif is either mutated or methylated, and it does not bind to single-stranded DNA or RNA probes. Furthermore, the introduction of a CpG dinucleotide into an unrelated oligonucleotide sequence is sufficient to produce a binding site for hCGBP. Native hCGBP is detected as an 88-kDa protein by Western analysis and is ubiquitously expressed. The DNA-binding activity of native hCGBP is apparent in electrophoretic mobility shift assays, and hCGBP trans-activates promoters that contain CpG motifs but not promoters in which the CpG is ablated. These data indicate that hCGBP is a transcriptional activator that recognizes unmethylated CpG dinucleotides, suggesting a role in modulating the expression of genes located within CpG islands.

Overexpression of CCAAT displacement protein represses the promiscuously active proximal gp91(phox) promoter.

CCAAT displacement protein (CDP) is a transcriptional repressor that restricts expression of the gp91(phox) gene to mature myeloid cells. CDP interacts with multiple sites within the -450 to +12 bp human gp91(phox) promoter, and down-regulation of CDP DNA-binding activity is required for induction of gp91(phox) transcription in mature phagocytes. Truncation of the gp91(phox) promoter to -102 to +12 bp removes 4 CDP-binding sites and reveals a promiscuous promoter activity that is active in some nonphagocytic cells. A cis-element at -90 bp is required for derepressed transcription and serves as a binding site for multiple transcriptional activators. We now report that this element also serves as a binding site for CDP. The affinity of CDP for this element is relatively weak compared with upstream CDP-binding sites within the promoter, consistent with the promiscuous transcriptional activity exhibited by the -102 to +12 bp gp91(phox) promoter fragment. Further analysis of the proximal promoter reveals an additional weak-affinity CDP-binding site centered at approximately -20 bp. Overexpression of cloned CDP represses the -102 to +12 bp gp91(phox) promoter, indicating that these proximal CDP-binding sites are functionally significant. The constellation of transcriptional activators and a repressor that interacts with the -90 bp cis-element is identical to that observed for a promoter element at -220 bp, reflecting the highly modular organization of the gp91(phox) promoter. These studies illustrate the complex interplay between transcriptional activators and a repressor that contribute to the myeloid-restricted expression of the gp91(phox) gene.

YY1 binds five cis-elements and trans-activates the myeloid cell-restricted gp91(phox) promoter.

Four transcriptional activating cis-elements within the gp91(phox) promoter bind a protein complex of similar mobility and binding specificity, denoted BID (binding increased during differentiation). The intensity of BID complexes increases upon myeloid cell differentiation, coincident with induction of gp91(phox) expression, and BID competes with the transcriptional repressor CDP for binding to each of these promoter elements. To determine the identity of BID, an expression library was ligand screened with the BID-binding site that surrounds the -145-base pair (bp) region of the gp91(phox) promoter. One recovered factor that exhibits the expected binding specificity is YY1, a ubiquitous multifunctional transcription factor. BID complexes that form with the four binding sites within the gp91(phox) promoter are disrupted by YY1 antiserum, and a fifth YY1-binding site was detected in the -412-bp promoter region. Overexpression of YY1 in transient co-transfection assays trans-activates a minimal promoter containing two copies of the -145-bp binding site from the gp91(phox) promoter. Neither the level of YY1 protein nor DNA binding activity increases during myeloid cell differentiation. These studies identify a target gene of YY1 function in mature myeloid cells, and demonstrate that YY1 function can be controlled during myeloid development by the modulation of a competing DNA-binding factor.

Elf-1 and PU.1 induce expression of gp91(phox) via a promoter element mutated in a subset of chronic granulomatous disease patients.

The cytochrome b heavy chain (gp91(phox)) is the redox center of the NADPH-oxidase and is highly expressed in mature myeloid cells. Point mutations at -57, -55, -53, and -52 bp of the gp91(phox) promoter have been detected in patients with chronic granulomatous disease (CGD; Newburger et al, J Clin Invest 94:1205, 1994; and Suzuki et al, Proc Natl Acad Sci USA 95:6085, 1998). We report that Elf-1 and PU. 1, ets family members highly expressed in myeloid cells, bind to this promoter element. Either factor trans-activates the -102 to +12 bp gp91(phox) promoter when overexpressed in nonhematopoietic HeLa cells or the PLB985 myeloid cell line. However, no synergy of gp91(phox) promoter activation occurs when both Elf-1 and PU.1 are overexpressed. Introduction of the -57 bp or -55 bp CGD mutations into the gp91(phox) promoter significantly reduces the binding affinity of Elf-1 and PU.1 and also reduces the ability of these factors to trans-activate the promoter. These results indicate that Elf-1 and PU.1 contribute to directing the lineage-restricted expression of the gp91(phox) gene in phagocytes and that failure of these factors to effectively interact with this promoter results in CGD.

Identification and functional characterization of the murine Rac2 gene promoter.

Rac2, a member of the Rho family of GTPases, is highly expressed in myeloid cells and is a regulator of the NADPH-oxidase complex. A murine genomic clone was isolated that contains the 5' end and putative promoter region of the Rac2 gene. Ribonuclease protection experiments detected 13 transcription initiation sites scattered 50 to 130 bp upstream of the translation initiation site. Transient transfection studies revealed that -7 kb to +31 bp (relative to the strongest transcription initiation site) of the Rac2 gene 5'-flanking region exhibited strong promoter activity in both RAW 264.7 macrophage cells that express the endogenous Rac2 gene and NIH-3T3 fibroblast cells that do not express the endogenous gene. Truncated Rac2 promoter fragments containing as little as the -74 to +31 bp sequence produced full transcriptional activity. However, a -57 to +31 promoter fragment directed significantly less transcription, and a -39 to +31 promoter fragment was transcriptionally inactive. In vitro binding assays revealed sequence-specific and widely expressed DNA-binding activities that interacted within the -74 to -58 Rac2 promoter cis element. Oligonucleotide competition and antibody disruption studies indicated that these complexes contained the transcription factors Spl and Sp3. Specific ablation of the Sp1/Sp3 binding site significantly decreased Rac2 promoter activity in both RAW 264.7 and NIH-3T3 cells. Additional cis elements may be required to restrict Rac2 promoter activity to hematopoietic cells expressing the endogenous gene.

CCAAT displacement protein (CDP/cut) binds a negative regulatory element in the human tryptophan hydroxylase gene.

Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in the biosynthesis of serotonin, a neurotransmitter that has been implicated in many psychiatric illnesses. The mechanism of transcriptional regulation of the human TPH gene is largely unknown. We have identified a negative regulatory element located between nucleotides -310 and -220 in the human TPH (hTPH) gene. Electromobility shift analyses performed with the -310/-220 hTPH probe and nuclear extract from P815-HTR (a TPH-expressing cell line) revealed two slow migrating protein-DNA complexes, designated I and II. CCAAT displacement protein (CDP/Cut) is involved in complex I formation as shown in electromobility shift analysis, using consensus oligonucleotide competitor and antibody. Mutations in the CDP/Cut binding site not only disrupted the CDP-DNA complex but also disrupted the second complex, suggesting that the core binding sequences of the two proteins are overlapping. The functional importance of these protein-DNA interactions was assessed by transiently transfecting wild-type and mutant pTPH/luciferase reporter constructs into P815-HTR cells. Mutations in the core CDP/Cut site resulted in an approximately fourfold increase in relative luciferase activities. Because CDP/Cut has been shown to repress transcription of many target genes, we speculate that disruption of the CDP/Cut binding was responsible, at least in part, for the activation of hTPH gene.

DNA-binding properties of CCAAT displacement protein cut repeats.

CCAAT displacement protein (CDP) is a transcriptional repressor that contains four distinct DNA-binding domains; a homeodomain and three cut repeats. Each DNA-binding domain of CDP was expressed as a glutathione S-transferase (GST)-fusion protein and analyzed for relative binding affinity to five CDP-binding sites within the gp91phox promoter. Each cut repeat exhibits a unique pattern of DNA-binding affinities for the five binding sites in the gp91phox promoter, suggesting that each may make a distinct contribution to the DNA-binding behavior of native CDP. Although measurement of DNA/protein complex mass indicates that an isolated cut repeat can bind DNA as a monomer, mixing of GST-cut repeat and GST-homeodomain fusion proteins enhances DNA-binding activity. Far-Western blot and two-hybrid analyses indicate, however, that the CDP domains do not directly interact. We hypothesize that GST-mediated dimerization leads to spatial juxtaposition of these DNA-binding domains, and that the resulting enhanced DNA-binding activity mimics cooperative interactions that occur between these domains in native CDP.

CCAAT displacement protein, a regulator of differentiation-specific gene expression, binds a negative regulatory element within the 5' end of the human papillomavirus type 6 long control region.

We have reported previously that a 636-bp fragment spanning the 5' two-thirds of the human papillomavirus type 6 (HPV6)-W50 long control region (LCR) functions as a transcriptional silencer (A. Farr, S. Pattison, B.-S. Youn, and A. Roman, J. Gen. Virol. 76:827-835, 1995). We have utilized nested deletion analyses to implicate a 66-bp sequence which appears to be critical for this activity. A comparison of the transcriptional regulatory activities of the LCRs of HPV6-W50 and HPV6b (which has a 94-bp deletion, resulting in the elimination of the 66-bp sequence) indicates that sequences within the 94-bp region negatively regulate the activity of the intact HPV6 LCR. Two sequence-specific DNA-protein interactions were visualized via electrophoretic mobility shift assays. One of the binding events is mediated by the transcriptional repressor CCAAT displacement protein (CDP), a factor which is active in undifferentiated cells but inactive in terminally differentiated cells. This conclusion is based on the following three lines of evidence: (i) a consensus CDP binding site oligonucleotide serves as a competitor in band shift assays, (ii) the band shift complex is not seen when a CDP-negative nuclear extract is used, and (iii) anti-CDP antiserum specifically inhibits the binding. These studies identify a DNA-protein interaction occurring within the 5' end of the LCR which may be important in maintaining the tight link between keratinocyte differentiation and HPV gene expression.

Interferon regulatory factor-2 directs transcription from the gp91phox promoter.

Repressor elements in the gp91(phox) promoter are necessary to restrict tissue-specific transcription to mature phagocytes. Deletion of these elements leads to significant promoter activity in cell lines such as HEL and K562 that do not normally express gp91(phox). The -100 to +12 base pair gp91(phox) promoter region is sufficient to direct maximal de-repressed transcription in these cells. However, promoter activity is dramatically decreased following a 16-base pair truncation that deletes an interferon-stimulated response element. This element interacts with IRF-1 and IRF-2, members of the interferon regulatory factor family of transcription factors. In addition, this promoter region is bound by a factor with properties similar to BID, a DNA-binding protein that also interacts with three upstream sites within the gp91(phox) promoter. Transient transfection studies using mutated promoters indicate that both the IRF and BID binding sites are required for maximal gp91(phox) promoter activity. Overexpression of IRF-1 or IRF-2 in K562 cells leads to transactivation of gp91(phox) promoter constructs, which is dependent on the presence of an intact IRF binding site. IRF-2 predominates in macrophages that express the gp91(phox) gene as well as in HEL and K562 cells. We conclude that IRF-2 and BID activate gp91(phox) promoter activity in the absence of transcriptional repression.

Characterization of three promoter elements and cognate DNA binding protein(s) necessary for IFN-gamma induction of gp91-phox transcription.

The cytochrome b558 heavy chain (gp9l-phox) is expressed in terminally differentiated myelomonocytic cells. Three cis-elements located between -450 and -100 bp of the gp91-phox promoter are required for IFN-gamma induced transcription. Mutations that disrupt individual cis-elements incrementally decrease gp9l-phox promoter activity, and one of the two proximal elements must be present for an IFN-gamma response. The DNA-binding activities that interact with each of the cis-elements exhibit similar gel mobility and binding site specificity, although a consensus binding site common to the three elements is not apparent. An increased level of each DNA/protein complex is observed in myeloid cells following treatment with PMA, retinoic acid/dimethylformamide, or IFN-gamma, but not in similarly treated HeLa cells. The myeloid-specific increase in the intensity of each complex is delayed 12 to 24 h following IFN-gamma treatment, and the complexes are not immunoreactive with antisera directed against IFN-responsive factors such as IRF-1, IRF-2, IFN consensus sequence binding protein, Stat1, and IFN-stimulated gene factor-3 gamma, although IRF-2 is additionally detected as binding to the middle cis-element. These results reveal cis-elements and a DNA-binding factor(s) that participate in a common pathway in response to various stimuli that induce gp9l-phox transcription.

CCAAT displacement protein competes with multiple transcriptional activators for binding to four sites in the proximal gp91phox promoter.

CCAAT displacement protein (CDP) competes with transcriptional activating proteins for binding to each of four elements within the myeloid-specific gp91(phox) promoter. CDP exhibits the strongest affinity for a site centered at -110 base pairs (bp) of the promoter and progressively weaker affinities for three more distal binding sites. CDP binding to each site is down-regulated during terminal phagocytic differentiation, coincident with induction of gp91(phox) expression. Deletion of the high affinity CDP-binding site at -110 bp leads to inappropriate gp91(phox) promoter activity in HeLa, K562, and HEL cells. An overlapping binding site for the CCAAT box-binding factor CP1 is required for derepressed promoter activity in HeLa and K562 cells, but is dispensable in HEL cells, indicating that different cell types require distinct cis-elements for gp91(phox) promoter activity. Derepressed gp91(phox) promoter activity is further increased upon removal of a second CDP-binding site centered at -150 bp, revealing that CDP represses gp91(phox) expression via multiple cis-elements. We present a model in which restriction of gp91(phox) expression to mature myeloid cells involves competition between transcriptional activators and repressors for binding to multiple sites within the promoter.

Characterization of a gp91-phox promoter element that is required for interferon gamma-induced transcription.

The cytochrome b558 heavy chain (gp91-phox) is expressed nearly exclusively in terminally differentiating myelomonocytic cells, thereby providing a model to study the events of late myeloid differentiation. We describe a tissue culture assay for studying interferon gamma induction of gp91-phox expression and a cis-element in the gp91-phox promoter that is necessary but not sufficient for this activity. In vitro assays reveal two DNA-binding proteins that interact with this cis-element. One factor is restricted to hematopoietic cells, is required for an interferon gamma response, and binds to an element similar to the Ets protein family consensus, although it does not correspond to known family members. The second factor is the ubiquitous CCAAT-binding protein CP1, which is dispensable for an interferon gamma response. Single base pair mutations in the gp91-phox promoter that specifically abolish the binding of the hematopoietic-associated factor have previously been identified in chronic granulomatous disease patients (Newburger, P. E., Skalnik, D. G., Hopkins, P. J., Eklund, E. A., and Curnutte, J. T. (1994) J. Clin. Invest. 94, 1205-1211). The data reported here directly demonstrate the functional significance of the hematopoietic-associated factor for gp91-phox promoter activity and reveal the binding properties and tissue distribution of this novel DNA-binding protein.

Cloning of a cDNA encoding a human DNA-binding protein similar to ribosomal protein S1.

We report the cloning of a human complementary DNA that encodes a protein which exhibits 36% identity and 62% similarity to Escherichia coli ribosomal protein S1 (rpS1), including conservation of four copies of an RNA-binding domain. This clone was obtained by ligand-screening a lambda gt11 expression library with a DNA probe derived from the CYBB gene promoter. Electrophoretic mobility shift and Southwestern blot assays confirm DNA binding activity of the protein, which exhibits preferential binding to single-stranded and double-stranded DNA and a low binding affinity for RNA. Hence, the rpS1 protein domain previously identified as an RNA-binding motif can also serve as a DNA-binding domain.

Mutations in the promoter region of the gene for gp91-phox in X-linked chronic granulomatous disease with decreased expression of cytochrome b558.

We examined the molecular defect in two kindreds with "variant" X-linked chronic granulomatous disease (CGD). Western blots of neutrophil extracts showed decreased immunoreactive cytochrome b558 components gp91-phox and p22-phox. Analysis of mRNA demonstrated reduced gp91-phox transcripts, with relative preservation of an alternative mRNA species created by transcription initiation in the third exon of the gene. Single strand conformation polymorphism analysis of the 5' flanking region of the patients' gp91-phox genes revealed an electrophoretic abnormality not detected in 40 other gp91-phox genes. Genomic sequencing demonstrated a single base change associated with CGD in each kindred: in one, adenine to cytosine at base pair-57 and in the other, thymidine to cytosine at -55. These mutations are located between the "CCAAT" and "TATA" box consensus sequences involved in eukaryotic gene transcription. Gel shift assays revealed two specific DNA-protein complexes formed between phagocyte nuclear extracts and an oligonucleotide probe representing bases -31 to -68 of the gp91-phox promoter region; the faster-migrating complex could not be formed with oligonucleotides containing either of the promoter mutations. Thus, these promoter region mutations appear to be causally related to the loss of association of a DNA-binding protein and lead to diminished gp91-phox expression, abnormal transcription initiation, and the development of CGD.

Sequence-specific binding of HMG-I(Y) to the proximal promoter of the gp91-phox gene.

Screening of a cDNA expression library with a CCAAT-box element derived from the myelomonocyte-specific gp91-phox promoter resulted in the isolation of three independent HMG-I(Y) cDNA clones. Filter binding competition studies reveal that HMG-Y binds to this promoter element in a sequence-specific manner and exhibits a gradient of binding affinities for various A/T-rich sequences. Two adjacent A/T-rich regions within the gp91-phox promoter CCAAT-box element are required for maximal binding. In addition, competition experiments demonstrate that the binding affinity of HMG-Y is influenced by sequences that flank A/T-rich core binding sites.

Human CCAAT displacement protein is homologous to the Drosophila homeoprotein, cut.

Human CCAAT displacement protein (CDP), a putative repressor of developmentally regulated gene expression, was purified from HeLa cells by DNA binding-site affinity chromatography. cDNA encoding CDP was obtained by immunoscreening a lambda gt11 library with antibody raised against purified protein. The deduced primary amino acid sequence of CDP reveals remarkable homology to Drosophila cut with respect to the presence of a unique homeodomain and "cut repeats". As cut participates in determination of cell fate in several tissues in Drosophila, the similarity predicts a broad role for CDP in mammalian development.