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Different Sp1 family members differentially affect transcription from the human elongation factor 1 A-1 gene promoter.

The GC box is an important transcriptional regulatory element present in the promoters of many mammalian genes. In the present study we examine the effect of known GC-box-binding proteins on the promoter of the human elongation factor 1 A-1 (hEF1A-1) gene in human HeLa cells and Drosophila SL2 cells. In HeLa cells co-transfection with the GC-box-binding protein BTEB resulted in a 4-10-fold increase in hEF1A-1 promoter activity. This stimulation was dependent on a single GC box located between positions -69 and -50 of the promoter. Little or no effect was observed of other GC-box-binding proteins including Sp1, Sp3, Sp4 and BTEB2. In SL2 cells stimulation by Sp1 and Sp3 through the single GC box of the proximal promoter led to 13-fold and 21-fold increases respectively in promoter activity. Inclusion of further upstream sequences resulted in high levels of expression when Sp1 or Sp3 was co-transfected with the reporter plasmid. In this setting Sp1 stimulated transcription by 750-fold, whereas Sp3 was even more potent, yielding a 1150-fold stimulation. Mobility-shift assays performed with the promoter-proximal GC box demonstrated the binding of Sp1, Sp3 and Sp4 to this sequence. To our knowledge, the present study represents the first comparison of all known GC-box-binding proteins on a natural promoter.

Animals↗

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.

We developed a new DNA microarray-based technology, called protein binding microarrays (PBMs), that allows rapid, high-throughput characterization of the in vitro DNA binding-site sequence specificities of transcription factors in a single day. Using PBMs, we identified the DNA binding-site sequence specificities of the yeast transcription factors Abf1, Rap1 and Mig1. Comparison of these proteins' in vitro binding sites with their in vivo binding sites indicates that PBM-derived sequence specificities can accurately reflect in vivo DNA sequence specificities. In addition to previously identified targets, Abf1, Rap1 and Mig1 bound to 107, 90 and 75 putative new target intergenic regions, respectively, many of which were upstream of previously uncharacterized open reading frames. Comparative sequence analysis indicated that many of these newly identified sites are highly conserved across five sequenced sensu stricto yeast species and, therefore, are probably functional in vivo binding sites that may be used in a condition-specific manner. Similar PBM experiments should be useful in identifying new cis regulatory elements and transcriptional regulatory networks in various genomes.

Base Sequence↗

Identification of a nuclear factor that binds to a conserved sequence of the I-A beta gene.

Human and murine class II genes of the MHC show a striking homology 50 to 120 bp upstream of the transcription start site. This area is composed of two conserved sequences (a 13-mer and an 8-mer separated by 19 to 20 bp). Recently, these conserved sequences have been identified as cis-acting transcriptional regulatory elements. We have sought nuclear factors that bind specifically to an upstream fragment (-245 to +75 bp) of the murine I-A beta chain gene that contains the conserved sequences by application of a modified gel electrophoresis DNA binding assay. We report here the identification of a nuclear factor whose binding site overlaps the 8-mer conserved sequence. This factor is present in murine B and T lymphocytes, macrophages, mastocytes, fibroblasts, and human B lymphocytes and macrophages. The binding site was defined by using DNase I and dimethylsulfate protection assays. The putative binding sequence is closely related to the sequence, CCAAT, which is often found associated with the promoter of a gene and is recognized by the transcriptional factors CCAAT-binding transcription factor and nuclear factor I. Oligonucleotides that contain the binding site sequences for nuclear factor I and the alpha-globin CCAAT element, however, do not compete for binding of the nuclear factor to the sequence identified here, suggesting that, in spite of the similarity of the binding sequence, the nuclear factor identified in this report may be different. This nuclear protein may be one of the trans-acting factors that mediate transcription of class II genes.

Animals↗

Molecular cloning and functional analysis of the adenovirus E1A-associated 300-kD protein (p300) reveals a protein with properties of a transcriptional adaptor.

The growth-controlling functions of the adenovirus E1A oncoprotein depend on its ability ot interact with a set of cellular proteins. Among these are the retinoblastoma protein, p107, p130, and p300. We have isolated a cDNA encoding full-length human p300 and mapped the chromosomal location of the gene to chromosome 22q13. p300 contains three cysteine- and histidine-rich regions of which the most carboxy-terminal region interacts specifically with E1A. In its center, p300 contains a bromodomain, a hallmark of certain transcriptional coactivators. We have examined the ability of p300 to overcome the repressive effect of E1A on the SV40 enhancer. We show that p300 molecules lacking an intact E1A-binding site can bypass E1A repression and restore to a significant extent the activity of the SV40 enhancer, even in the presence of high levels of E1A protein. These results imply that p300 may function as a transcriptional adaptor protein for certain complex transcriptional regulatory elements.

Adenovirus E1A Proteins↗

Genomic organization and characterization of promoter function of the human CDK9 gene.

CDK9 is the catalytic subunit of a general RNA polymerase II (RNAP II) elongation factor termed p-TEFb which is targeted by the human immunodeficiency virus (HIV) Tat protein to activate elongation of the integrated proviral genome. CDK9 mRNA and protein levels have been observed to be induced in activated peripheral blood lymphocytes, a cell type relevant to HIV infection. To investigate mechanisms that regulate CDK9 RNA expression, we isolated genomic sequences containing the human CDK9 gene and found that CDK9 coding sequences are interrupted by six introns. There is a major transcriptional start site located 79 nucleotides upstream of the ATG initiator codon at nucleotide +1. Nucleotides -352 to -1 contain all the transcriptional regulatory elements needed for full promoter activity in transient expression assays. The CDK9 promoter contains features characteristic of a housekeeping gene, including GC-rich sequences and absence of a functional TATA element. The CDK9 promoter possesses high constitutive activity and may therefore have utility in expression vectors or gene therapy vectors.

Base Sequence↗

Transcriptional regulation of smooth muscle contractile apparatus expression.

The transcriptional regulatory mechanisms that control gene expression during differentiation and contractile protein accumulation are becoming well understood in skeletal and cardiac muscle lineages. Current understanding of smooth muscle-specific gene transcription is much more limited, though recent studies have begun to shed light on this topic. In this review, we summarize some of the themes emerging from these studies and identify transcriptional regulatory elements common to several smooth muscle genes. These include potential binding sites for serum response factor, Sp1, AP2, Mhox, and YY1, as well as a potential transforming growth factor-beta control element. We speculate that it may be possible to manipulate smooth muscle-specific gene expression in asthma or pulmonary arterial hypertension as an eventual therapy.

Asthma↗

Cloning and sequence analysis of the human beta 1-adrenergic receptor 5'-flanking promoter region.

We present 3.1 kb of the nucleotide sequence from the 5'-flanking region of the human beta 1-adrenergic receptor gene. The first 1.0 kb upstream from the translational start site is composed of 72% G + C residues. The sequence was analyzed for the presence of transcriptional regulatory elements and contains putative thyroid hormone, glucocorticoid hormone and cAMP response elements. These putative hormone response elements support physiological evidence that thyroid and glucocorticoid hormones regulate beta 1AR function by affecting receptor expression in tissues such as heart and adipose, where beta 1-adrenergic receptors are important regulators of heart rate and lipolysis, respectively.

Base Sequence↗

Transient expression system to measure the efficiency of vaccinia promoter regions.

A transient expression system has been developed to compare the relative efficiency of expression of various vaccinia virus DNA sequences containing transcriptional regulatory elements. A plasmid vector was constructed containing both the Escherichia coli galactokinase gene (galK) and the guanine phosphoribosyltransferase gene (gpt). To direct the expression of gpt within this vector, a vaccinia virus promoter region was isolated from the HindIII-F fragment of the genome and inserted 5' to gpt coding sequence. Four unique cloning sites in front of galK allow simple and precise fusion of various vaccinia virus DNA fragments that contain the regulatory site of interest to galK. Sequences containing promoter regions were ligated to the coding segment of the galK to create four recombinant plasmids, which were introduced into vaccinia virus-infected cells by transfection. Both galK and gpt were thus expressed under the control of vaccinia virus transcriptional units, and the enzymatic activities were measured in the same cell extract with a filter-binding assay. The major advantage of this transient expression system is that the variations in galK expression are always measured relative to the internal gpt standard. Changes in the galK/gpt ratio resulting from different vaccinia promoters of galK are thus a quantitative measurement of promoter strength.

Animals↗

A novel trans-spliced mRNA from Onchocerca volvulus encodes a functional S-adenosylmethionine decarboxylase.

Complete cDNA and genomic sequences encoding the Onchocerca volvulus S-adenosylmethionine decarboxylase (SAMDC), a key enzyme in polyamine biosynthesis, have been isolated and characterized. The deduced amino acid sequence encodes a 42 kDa proenzyme with a moderate level of sequence homology to eukaryotic SAMDCs. Enzymically active O. volvulus SAMDC was expressed at a high level in an Escherichia coli mutant strain lacking endogenous SAMDC. The recombinant enzyme was purified to homogeneity using DEAE-cellulose, methylglyoxal bis(guanylhydrazone)-Sepharose and Superdex S-200 chromatography. It was determined that the recombinant proenzyme is cleaved to produce 32 and 10 kDa subunits. The sequence of the N-terminal portion of the large subunit was determined and comparison with the sequence of the proenzyme revealed that the precise cleavage site lies between Glu86 and Ser87. Gel-filtration experiments demonstrated that these two subunits combine to form an active heterotetramer. Comparison of the cDNA and genomic sequences revealed that the SAMDC mRNA undergoes both cis- and trans-splicing in its 5'-untranslated region (UTR). Anchored PCR on O. volvulus mRNA confirmed the cDNA sequence and identified two distinct trans-spliced products, a 22-nucleotide spliced-leader sequence and a 138 bp sequence containing the 22 nucleotide spliced-leader sequence. Genomic Southern-blot analysis suggests that the O. volvulus SAMDC is encoded by a single-copy gene. This gene spans 5.3 kb and is comprised of nine exons and eight introns. The first intron is located in the 5'-UTR and processing of this intron has a potential regulatory function. The 5'-flanking region of the gene contains potential transcriptional regulatory elements such as a TATA box, two CAAT boxes and AP-1-, C/EBP-, ELP-, H-APF-1-, HNF-5- and PEA3-binding sites.

Adenosylmethionine Decarboxylase↗

Transcriptional control of the platelet-derived growth factor subunit genes.

Platelet-derived growth factor (PDGF) is a potent mitogen consisting of heterodimers of two distinct but homologous polypeptide chains, denoted A and B. PDGF-like homodimers of the A- and B-chains have been isolated, as well as two distinct receptor types (alpha and beta), which discriminate among the PDGF isoforms. The PDGF A- and B-chains are encoded by distinct genes located on human chromosomes 7 and 22, respectively. Although PDGF has been implicated as an important participant in development, tissue repair, and numerous pathologic states including tumorigenesis, atherosclerosis and inflammation, the mechanisms which determine the rate of its synthesis are only beginning to be understood. Basal expression of the PDGF A- and B-chain genes has been characterized in a number of cell types and is directed in part by elements in the respective proximal promoter-regulatory regions of the two genes. In addition, the first intron of PDGF-B has been shown to contain both positive and negative regulatory elements. Transcription of the PDGF subunit genes is inducible by a wide variety of mitogenic growth factors, cytokines and other agonists. These agents produce a rapid increase in steady-state concentrations of PDGF A- and B-chain mRNAs, peaking within 4-8 h of stimulation. The inductive effects of protein kinase C-activating phorbol 12-myristate 13-acetate (PMA), thrombin and transforming growth factor-beta (TGF-beta) are mediated through increases in the transcription rates of both genes. In addition, cAMP blocks the increases in transcription of the B-chain gene induced by thrombin and TGF-beta. Studies have demonstrated the importance of sequences immediately upstream of the B-chain transcription start site for induction in response to PMA-initiated megakaryocyte differentiation, an effect which is dependent on protein synthesis. However, cis-acting elements which mediate more rapid transcriptional induction seen in endothelial cells and astrocytes have yet to be identified in the proximal 5'-flanking sequences of either the A- or B-chain genes, suggesting that such events may be mediated by elements located outside of this region.

Base Sequence↗

Sp1 binding activity increases in activated Ito cells.

Ito cells are the primary cell type in the liver responsible for increased type I collagen production observed during fibrogenesis. After a fibrogenic stimulus, Ito cells change from their normal quiescent state to an activated state. In this study, we examined the expression of the alpha 1(I) collagen gene in Ito cells that were freshly isolated from normal rat liver (quiescent) and Ito cells that were activated by culture on plastic. Northern blots showed that alpha 1(I) collagen messenger RNA levels were low in freshly isolated Ito cells and Ito cells cultured on plastic for up to 4 days, but were induced after 7 days in culture. To determine the location of important transcriptional regulatory elements within the 5'-flanking region of the alpha 1(I) collagen gene, transient transfections using various portions of the alpha 1(I) collagen gene promoter linked to the luciferase gene were performed in cultured Ito cells. As in fibroblast cells, only 220 base pairs (bp) of immediate 5'-flanking sequence of the collagen alpha 1(I) gene was necessary for efficient expression of the reporter gene. Deoxyribonuclease I footprinting analysis and mobility shift assays showed dramatic differences in the DNA binding proteins that interact with the 220 base pair promoter region of the alpha 1(I) collagen gene between freshly isolated and activated Ito cells. Sp1 binding activity was greatly increased in activated Ito cells, as was binding activity for CCAAT binding factor (CBF), a transcription factor previously shown to interact with the alpha 2(I) collagen gene promoter. The increased Sp1 binding activity to the alpha 1(I) collagen gene promoter involves a posttranscriptional event, as shown by Northern and Western blots. Therefore, we show that activated Ito cells have a different pattern of transcription factor binding activity interacting with the alpha 1(I) collagen gene promoter compared with quiescent Ito cells, including increased Sp1 binding activity, and that this may contribute to the increase in alpha 1(I) collagen gene expression during fibrosis.

Animals↗

Simian virus 40 large T-antigen, but not small T-antigen, trans-activates the human cytomegalovirus major immediate early promoter.

Cytomegalovirus infection is a major cause of morbidity in immunocompromised patients. The major immediate early promoter/enhancer (MIEP) of the human cytomegalovirus controls the expression of the immediate early genes 1 and 2 which play a central role both in primary and reactivated human cytomegalovirus (HCMV)-infections. Our previous studies have shown that co-infection of A549 cells with human cytomegalovirus and human polyomavirus BK resulted in enhanced expression of the immediate early genes 1 and 2 and that the early gene products of BK virus trans-activated the MIEP. However, neither the MIEP sequences required for mediating this trans-activation, nor the contribution of the individual BK virus early gene products were examined. The MIEP contains multiple binding sites for the transcription factors CREB, AP1, Sp1 and NFkappaB, which may mediate polyomavirus large T- or small t-antigens-induced promoter activation. Transient transfection studies in A549 cells demonstrated that SV40 large T-antigen, but not small t-antigen, trans-activated MIEP activity approximately 9-fold. Mutations in individual binding motifs in the context of the complete MIEP did not impair traits-activation by large T-antigen. The level of induction of a truncated MIEP consisting of a single set of CRE/AP1, NFkappaB, and Sp1 binding motifs by large T-antigen was reduced 2-fold compared to the full length MIEP. Extended truncations diminished trans-activation by large T-antigen. To determine the contribution of a single binding motif in the trans-activation by large T-antigen, a CRE/AP1, an NFkappaB, an Sp1, or a non-consensus Sp1-motif, respectively, was linked to the MIEP TATA-sequence respecting the natural spacing between the two transcription regulatory elements. Only the MIEP TATA-box with the correctly spaced non-consensus Sp1 binding site (GT-motif) was stimulated by large T-antigen. These results suggest that an isolated non-consensus Sp1-motif is important for trans-activation of the MIEP by large T-antigen, but that other cis-acting elements can compensate for this element in the context of the whole MIEP.

Antigens, Polyomavirus Transforming↗

The characterisation and functional analysis of the human glyoxalase-1 gene using methods of bioinformatics.

Methylglyoxal (MG), which forms MG-derived AGE, is elevated in diabetic subjects with vascular disease. Detoxification of MG occurs through the glyoxalase system incorporating glyoxalase-1 (GLO1) and glyoxalase-2. Perturbations of the glyoxalase-1 gene (GLO1) may result in vulnerability to vascular complications through alterations in AGE interactions. We used bioinformatics to predict the structure, function and genetic variation of GLO1. We identified a previously unreported exon. Seventy single nucleotide polymorphisms (SNPs) were identified bioinformatically. The amino acid substitution Ala 111 Glu was confirmed and predicted to be tolerant. Though no alternative splice variants were identified, novel multiple alternative transcription start sites and alternative 3' UTRs were demonstrated. Ubiquitous expression of GLO1 was confirmed. Conserved regulatory regions were predicted 5' to the transcription start site and in the distal promoter, and several predicted conserved transcription regulatory elements were suggested in the 5' UTR. This study of GLO1 demonstrates multiple sequence variants at DNA and mRNA levels, areas of sequence conservation and SNPs that are predicted to affect function. A differential ability of glyoxalase-1 to reduce the formation and subsequent interaction of AGEs may have a role in the structural and functional manifestations of diabetic vascular disease.

Amino Acid Sequence↗

Adenovirus type 12-induced fragility of the human RNU2 locus requires p53 function.

Adenovirus type 12 (Ad12) infection of human cells induces four chromosomal fragile sites corresponding to the U1 small nuclear RNA (snRNA) genes (the RNU1 locus), the U2 snRNA genes (RNU2), the U1 snRNA pseudogenes (PSU1), and the 5S rRNA genes (RN5S). Ad12-induced fragility of the RNU2 locus requires U2 snRNA transcriptional regulatory elements and viral early functions but not viral replication or integration, or chromosomal sequences flanking the RNU2 locus. We now show that Ad12 cannot induce the RNU1, RNU2, or PSU1 fragile sites in Saos-2 cells lacking the p53 and retinoblastoma (Rb) proteins but that viral induction of fragility is rescued in these cells when the expression of wild-type p53 or selected hot-spot mutants (i.e., V143A, R175H, R248W, and R273H) is restored by transient expression or stable retroviral transduction. We also observed weak constitutive fragility of the RNU1 and RNU2 loci in cells belonging to xeroderma pigmentosum complementation groups B and D (XPB and XPD) which are partially defective in the ERCC2 (XPD) and ERCC3 (XPB) helicase activities shared between the repairosome and the RNA polymerase H basal transcription factor TFIIH. We propose a model for Ad12-induced chromosome fragility in which interaction of p53 with the Ad12 E1B 55-kDa transforming protein (and possibly E4orf6) induces a p53 gain of function which ultimately perturbs the RNA polymerase II basal transcription apparatus. The p53 gain of function could interfere with chromatin condensation either by blocking mitotic shutdown of U1 and U2 snRNA transcription or by phenocopying global or local DNA damage. Specific fragilization of the RNU1, RNU2, and PSU1 loci could reflect the unusually high local concentration of strong transcription units or the specialized nature of the U1 and U2 snRNA transcription apparatus.

Adenoviruses, Human↗

Developmental origins of hematopoietic stem cells.

Hematopoietic stem cells (HSCs) are at the foundation of the hematopoietic hierarchy and give rise to all blood lineages in the adult organism. A thorough understanding of the molecular, cellular, and developmental biology of HSCs is of fundamental importance, but is also clinically relevant for the advancement of cell replacement therapies and transplantation protocols in blood-related genetic disease and leukemias. While the major anatomical sites of hematopoiesis change during ontogeny, it was long believed that the developmental origin of the adult mammalian hematopoietic system was the yolk sac. However, current studies have shown that the first adult-type HSCs are autonomously generated in the intrabody portion of the mouse embryo, the aorta-gonads-mesonephros (AGM) region, and sublocalize to the dorsal aorta. HSCs are also found in the other large embryonic vessels, the vitelline and umbilical arteries. The intraluminal hematopoietic clusters along these vessels, together with the role of the Runx1 transcription factor in cluster and HSC formation and the HSC/endothelial/mesenchymal Runxl expression pattern, strongly suggest a vascular endothelial/mesenchymal origin for the first HSCs. Moreover, a transgenic mouse line expressing the GFP marker under the control of the Sca-1 transcriptional regulatory elements (GFP expression marks all HSCs) shows a clear localization of GFP-expressing cells to the endothelial cell layer of the dorsal aorta. Thus, highly enriched GFP-positive AGM HSCs will serve as a basis for the future examination of the cellular and molecular factors involved in the induction and expansion of adult HSCs.

Animals↗

p67 isoform of mouse disabled 2 protein acts as a transcriptional activator during the differentiation of F9 cells.

The mouse disabled 2 (mDab2) gene is a mouse homologue of the Drosophila disabled gene and is alternatively spliced to form two isoforms, p96 and p67. Although p96 has been known to regulate the Ras-Sos G-protein signal transduction pathway by interacting with Grb2, little is known about the biological function of p67. Recent studies have shown that the expression of mDab2 is markedly up-regulated during the retinoic acid (RA)-induced differentiation of F9 cells, suggesting another role for mDab2 in cell differentiation [Cho, Lee and Park (1999) Mol. Cells 9, 179-184). In the present study, we first elucidated the biological function of p67 isoform of mDab2 and identified its binding partner. Unlike p96, p67 largely resides in RA-treated F9 cell nuclei. In this system, p67 interacts with mouse androgen-receptor interacting protein 3, termed the mDab2 interacting protein, which acts as a transcriptional co-regulator. By using a fusion protein with a heterologous DNA-binding domain (GAL4), we showed that p67 had an intrinsic transcriptional activation function. These results suggest that mDab2 p67 may function as a transcriptional co-factor for certain complexes of transcriptional regulatory elements involved in the RA-induced differentiation of F9 cells.

3T3 Cells↗

USF1 and dyslipidemias: converging evidence for a functional intronic variant.

Upstream transcription factor 1 (USF1), the first gene associated with familial combined hyperlipidemia (FCHL), regulates numerous genes of glucose and lipid metabolism. Phenotypic overlap between FCHL, type 2 diabetes and the metabolic syndrome makes this gene an intriguing candidate in the disease process of these traits as well. As no disease-associated mutations in the coding region of USF1 have been identified, we addressed the functional role of intronic single nucleotide polymorphisms (SNPs) which define the FCHL-risk alleles of USF1, and identified that a 20 bp DNA sequence, containing the critical intronic SNP, binds nuclear protein(s), representing a likely transcriptional regulatory element. This functional role is further supported by the differential expression of USF1-regulated genes in fat biopsy between individuals carrying different allelic variants of USF1. Importantly, apolipoprotein E (APOE) is the most downregulated gene in the risk individuals, linking the potential risk alleles of USF1 with the impaired APOE-dependent catabolism of atherogenic lipoprotein particles.

Animals↗

Structure and expression of the mouse Oct2a and Oct2b, two differentially spliced products of the same gene.

A large family of tissue-specific nuclear proteins interact with the octamer motif ATTTGCAT, a transcriptional regulatory element found in the promoter and enhancer sequences of many genes. As a step towards elucidating the mechanism of this regulation, cDNA clones of the mouse Oct2 protein were isolated. One, called here Oct2b, encodes a larger variant of the previously described Oct2a proteins. The Oct2b cDNA has an insertion of 74 bp close to the 3' end which creates an open reading frame distinct from Oct2a. As a result, the Oct2b protein has a carboxy end which is similar to that of the ubiquitous octamer-binding protein Oct1. Analysis of the Oct2 gene shows that Oct2a and Oct2b are differentially spliced products of the same gene. The insertion in the Oct2b cDNA results from the inclusion of an additional exon in the mRNA which would otherwise reside in an intron sequence of the Oct2a transcript. RNA analysis demonstrates that both Oct2a and 2b mRNAs are most abundant in B-cells but they are also expressed in a variety of tissues including brain, intestine, testis, kidney, as well as in embryos. Interestingly, the ratio of Oct2a and 2b varies among tissues. In situ hybridization studies during mouse embryogenesis show that the Oct2 gene is widely expressed in the developing nervous system. In contrast, expression in the adult brain is confined to very specific areas which include the suprachiasmatic and medial mammillary nuclei, hippocampus, olfactory tract and the olfactory bulb. Oct2 proteins are present in both neuronal and oligodendroglial cells, although they are more abundant in glial cells.

Amino Acid Sequence↗