Compilation and analysis of eukaryotic POL II promoter sequences

Cloning and functional analysis of the promoter for KDR/flk-1, a receptor for vascular endothelial growth factor

KDR/flk-1 is one of two receptors for vascular endothelial growth factor, a potent angiogenic peptide. KDR/flk-1 is an early marker for endothelial cell progenitors, and its expression is restricted to endothelial cells in vivo. To investigate the molecular mechanisms regulating expression of KDR/flk-1, we cloned and characterized the promoter of the human KDR/flk-1 gene. The transcription start site was localized by primer extension and ribonuclease protection to a nucleotide 303 base pairs (bp) 5' of the initiation methionine codon. The 5'-flanking sequence is rich in G and C residues and contains five Sp1 elements but no TATA consensus sequence. By reporter gene transfection experiments, we found that approximately 4 kilobases of KDR/flk-1 5'-flanking sequence directed high level luciferase activity in bovine aortic endothelial cells; further deletion analysis revealed positive regulatory elements between bp -225 to -164, -95 to -77, -77 to -60, and +105 to +127. Mutation of an atypical GATA sequence between bp +105 and +127 did not affect promoter activity, suggesting that GATA elements are not essential for the high level promoter activity of this gene. Consistent with endothelial cell-restricted expression of KDR/flk-1 mRNA, we found that the 4-kilobase flanking sequence directed high level promoter activity in endothelial cells but not in other cell types. To our knowledge this is the first report characterizing the KDR/flk-1 promoter. Understanding the KDR/flk-1 promoter will allow us to investigate endothelial cell-specific gene regulation and to uncover methods for targeting gene delivery specifically to endothelial cells.

Isolation and characterization of the androgen-dependent mouse cysteine-rich secretory protein-3 (CRISP-3) gene

The mRNA for cysteine-rich secretory protein-3 (CRISP-3) was originally identified in the mouse salivary gland as an androgen-dependent transcript, and is closely related to CRISP-1 and CRISP-2 which are abundantly expressed in the epididymis and testis respectively. Overlapping phage clones encompassing the entire length of the CRISP-3 gene were isolated from a lambda EMBL3 genomic library and analysed. DNA sequencing revealed that the gene consisted of eight exons ranging between 55 and 740 bp in size, and seven introns. All exon-intron junctions conformed to the GT/AG rule established for eukaryotic genes. The length of the introns was determined by PCR and was found to vary between 1.0 and 3.7 kb, indicating that the gene spans over 20 kb of the mouse genome. Primer extension allowed the mapping of the major transcription initiation site to an adenine located at the appropriate position downstream of a bona fide TATA box, in a region corresponding well to the eukaryotic consensus sequence. Over 800 bp of CRISP-3 promoter region were determined and two regions almost exactly matching the androgen-responsive element consensus RGWACANNNTGTWCY detected. In addition, sequences described in the Drosophila melanogaster Sgs-3 gene as being involved in its salivary gland-specific expression as well as two putative OTF- and GATA-binding elements were also found.

NAD-dependent methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase is targeted to the cytoplasm in insect cell lines

Cytosolic NADP-dependent methylenetetrahydrofolate dehydrogenase-cyclohydrolase synthetase and the mitochondrial NAD-dependent methylenetetrahydrofolate dehydrogenase-cyclohydrolase (NMDMC) are differentially expressed during insect development although both enzymes are detectable at all stages. In contrast, cell lines derived from a variety of insect species express high levels of NMDMC but undetectable levels of the NADP-dependent enzyme. Northern analysis indicates the NMDMC message is expressed at levels 50-100 times higher in a Drosophila cell line compared to adult flies. RNase protection showed the predominance of shortened transcripts that require initiation at a downstream AUG producing a truncated protein that lacks a mitochondrial targeting sequence. These changes in expression effectively exchange the cytosolic NADP-dependent dehydrogenase for one with NAD specificity.

The DNA sequence of a 7941 bp fragment of the left arm of chromosome VII of Saccharomyces cerevisiae contains four open reading frames including the multicopy suppressor gene of the pop2 mutation and a putative serine/threonine protein kinase gene

We report the sequence of a 7941 bp DNA fragment from the left arm of chromosome VII of Saccharomyces cerevisiae which contains four open reading frames (ORFs) of greater than 100 amino acid residues. ORF biC834 shows 100% bp identity with the recently identified multicopy suppressor gene of the pop2 mutation (MPT5); its deduced protein product carries an eight-repeat domain region, homologous to that found in the hypothetical regulatory YGL023 protein of S. cerevisiae and the Pumilio protein of Drosophila. ORF biE560 protein exhibits patterns typical of serine/threonine protein kinases, with which it shares high degrees of homology.

Molecular cloning of LSIRF, a lymphoid-specific member of the interferon regulatory factor family that binds the interferon-stimulated response element (ISRE)

Interferon regulatory factor (IRF) genes encode a family of DNA-binding proteins that are involved in the transcriptional regulation of type-I interferon and/or interferon-inducible genes. We report here the characterization of LSIRF, a new member of the IRF gene family cloned from mouse spleen by the polymerase chain reaction using degenerate primers. LSIRF was found to encode a 51 kDa protein that shares a high degree of amino acid sequence homology in the DNA-binding domain with other IRF family members. LSIRF expression was detectable only in lymphoid cells. In contrast to other IRF genes, LSIRF expression was not induced by interferons, but rather by antigen-receptor mediated stimuli such as plant lectins, CD3 or IgM crosslinking. In in vitro DNA binding studies, LSIRF was able to bind to the interferon-stimulated response element (ISRE) of the MHC class I promoter. The expression pattern and DNA binding activities suggest that LSIRF plays a role in ISRE-targeted signal transduction mechanisms specific to lymphoid cells.

Cloning and analysis of the nuclear gene MRP-S9 encoding mitochondrial ribosomal protein S9 of Saccharomyces cerevisiae

The Saccharomyces cerevisiae nuclear gene MRP-S9 was identified as part of the European effort in sequencing chromosome II. MRP-S9 encodes for a hydrophilic and basic protein of 278 amino acids with a molecular mass of 32 kDa. The C-terminal part (aa 153-278) of the MRP-S9 protein exhibits significant sequence similarity to members of the eubacterial and chloroplast S9 ribosomal-protein family. Cells disrupted in the chromosomal copy of MRP-S9 were unable to respire and displayed a characteristic phenotype of mutants with defects in mitochondrial protein synthesis as indicated by a loss of cytochrome c oxidase activity. Additionally, no activities of the gluconeogenetic enzymes, fructose-1,6-bisphosphatase and phosphoenolpyruvate carboxykinase, could be observed under conditions of glucose de-repression. The respiration-deficient phenotype could not be restored by transformation of the disruption strain with a wild-type copy of MRP-S9, indicating that MRP-S9 disruption led to rho- or rho0 cells. Sequence similarities of MRP-S9 to other members of the ribosomal S9-protein family and the phenotype of disrupted cells are consistent with an essential role of MRP-S9 is assembly and/or function of the 30s subunit of yeast mitochondrial ribosomes.

Southern hybridization analyses of somatic cell hybrids reveal that human BB1 is a member of a multigene family dispersed throughout the human genome and appears to be linked to the human G25K genes

The hBB1 RNA (2.3 kb in length) encodes a 57-amino-acid protein whose production is essential for cellular transit of G1 phase of the cell cycle (Moats-Staats et al., 1994). Homology searches of GenBank and EMBL revealed that bases 1-234 of the hBB1 cDNA were 97% homologous to the 3' terminal 234 bases of the g25K cDNA (bases 940-1,175, Shinjo et al., 1990) the human homolog of the yeast cdc42 cDNA. We have used the techniques of the long-range polymerase chain reaction (PCR) (Barnes, 1994) and Southern hybridization analyses of a somatic cell hybrid panel to investigate hBB1 gene structure and to determine whether the hBB1 gene(s) overlaps the g25K gene. These studies have demonstrated that the hBB1 RNA is encoded by a gene family composed of eight members that is dispersed throughout the human genome localizing under high-stringency conditions to chromosomes 1, 4, 7, 8, and 20. We have also determined that two hBB1 gene(s) and two g25K gene(s) map to similar-size Bam HI restriction fragments on chromosomes 4 and 7.

Inverse PCR-mediated cloning of the promoter for the rat vasopressin V2 receptor gene

The adenylyl cyclase-coupled vasopressin V2 receptor has been cloned recently and shown, in rats, to be produced from the predominant form of two alternate spliced variants. To begin to unravel the transcriptional regulation of this receptor, we have isolated the 5' flanking region of the rat vasopressin V2 receptor gene and characterized its promoter sequence. The method of inverse polymerase chain reaction (PCR), which allows the amplification of DNA fragments adjacent to a segment of known sequence, was used as an alternative approach to genomic DNA library screening. Using a probe encompassing part of the coding region, first we identified by Southern blot analysis, a single BstX I hybridizing fragment of 2.3 kilobases (kb). This size predicted a BstX I restriction site 1.5 kb upstream to the gene coding region. Cloning of this fragment was accomplished through circularization of BstX I restriction digests and inverse PCR-mediated amplification. Sequence analysis of the gene 5' flanking domain enabled the design of oligonucleotide primers with the usual forward/reverse orientation, and additional clones were generated from native genomic DNA using a high fidelity thermoresistant DNA polymerase. Reverse transcription-PCR (RT-PCR) and primer extension analysis mapped the major transcription start site 422 nucleotides upstream to the translation initiation codon. The promoter region lacks a TATA box but contains a CAAT box and a consensus binding site for transcription factor Sp1. Multiple potential binding sites for the transcription factor PEA3 are clustered in two DNA portions located 0.6 kb and 1 kb upstream to the coding region. In addition, sequences homologous to glucocorticoid response elements are present and might be responsible for the regulation by adrenal steroids of vasopressin-dependent adenylyl cyclase activity in the kidney.

Isolation of a differentially regulated splicing isoform of human NF-E2

The transcription factor NF-E2 (nuclear factor erythroid 2), interacting via DNA motifs within regulatory regions of several hematopoietic genes, is thought to mediate the enhancer activity of the globin locus control regions. By screening a human fetal liver cDNA library with probes derived from mouse NF-E2, we have isolated a splicing variant of the NF-E2 gene (fNF-E2) that differs in the 5' untranslated region from the previously reported cDNA (aNF-E2). The fNF-E2 isoform is transcribed from an alternative promoter located in the 3' end of the first intron and joined by alternative splicing to the second and third exons, which are shared by both RNA isoforms. Although the two forms produce the same protein, they are expressed in different ratios during development. fNF-E2 is more abundant in the fetal liver and less abundant in the adult bone marrow compared to the previously described form. Their distribution apparently follows the differential expression of fetal and adult hemoglobins.

Molecular characterization of a developmentally regulated porcine skeletal myosin heavy chain gene and its 5′ regulatory region

Members of the myosin heavy chain (MyHC) gene family show developmental stage- and spatial-specificity of expression. We report on the characterization and identification of a porcine skeletal fast MyHC gene, including its corresponding 5′ end cDNA and 5′ regulatory region. This MyHC isoform was found exclusively in skeletal muscles from about the last quarter of gestation through to adulthood. Expression of this isoform was higher postnatally and its spatial distribution resembled a rosette cluster; each with a ring of fast fibres surrounding a central slow fibre. This rosette pattern was absent in the adult diaphragm but about 20% of the fibres continued to express this MyHC isoform. Further in vivo expression studies, in a variety of morphologically and functionally diverse muscles, showed that this particular skeletal MyHC isoform was expressed in fast oxidative-glycolytic fibres, suggesting that it was the equivalent of the fast IIA isoform. Two domains in the upstream regulatory region were found to confer differentiation-specific expression on C2 myotubes (−1007 to -828 and -455 to -101), based on in vitro transient expression assays using the chloramphenicol acetyltransferase (CAT) reporter gene. Interestingly, for high levels of CAT expression to occur, a 3′ region, extending from the transcriptional start site to part. of intron 2, must be present in all the DNA constructs used.

Structural and functional characterization and cloning of Xenopus FOSP-1 (frog oviduct-specific protein-1) genes

As a model for tissue-specific gene expression, our laboratory has been studying the expression of vitellogenin and FOSP-1 (frog oviduct-specific protein-1) genes in Xenopus laevis which are expressed exclusively in the liver and oviduct, respectively, both strictly regulated by estrogen. Whereas the structure and function of Xenopus vitellogenin mRNAs and the upstream regulatory sequences (URS) of their genes are well established, little or no similar information is available for FOSP-1 genes. In this study, using a combination of 5' rapid amplification of cDNA ends (RACE) and reverse-transcriptase PCR, we have identified two gene copies of FOSP-1, termed FOSP-1A and FOSP-1B. Comparison of the sequences of full-length FOSP-1A and partial FOSP-1B cDNAs revealed a high degree of similarity at the 5' end. We next isolated FOSP-1A and FOSP-1B genomic clones. Dot-plot comparison of their URS showed both similarities and differences. Two estrogen-responsive elements (EREs), termed proximal (pERE) and distal (dERE), were identified at -1070/-1082 and -1167/-1179, respectively, in FOSP-1B, but not FOSP-1A, URS. Quantitative electrophoretic mobility shift assay (EMSA) and DNA footprinting with recombinant Xenopus estrogen receptor (xER) expressed in insect Sf9 cells, showed that xER interacted with a higher affinity with dERE than pERE in a hormone-independent manner, and that the two EREs do not act cooperatively. Functional studies involving transient transfection of human MCF-7 cells with a FOSP-1B URS-tkCAT construct confirmed that both EREs act as hormone-inducible cis-acting elements. These studies now pave the way for analysis of tissue specificity of estrogen-inducible gene expression in Xenopus liver and oviduct.

Characterization of the 5' and promoter regions of the gene encoding the mouse neuronal cell adhesion molecule F3

F3 is a 135 kDa neuronal cell surface adhesive glycoprotein belonging to the immunoglobulin supergene family (IgSF) which mediates heterophilic contact formation among neural cells and is involved in the control of neurite growth. F3 expression is regulated, during critical developmental periods, on neuronal subpopulations thus suggesting that control of F3 gene expression could be of morphogenetic relevance. To shed light on the mechanism involved in the control of F3 gene expression we isolated clones covering about 50 kilobases of the F3 gene which also included the promoter region. The study of F3 gene exon/intron organization revealed that, like other neural IgSF molecules, each of the first two F3 C2 domains is encoded by two exons while the N-terminus, the signal peptide and the 5' untranslated region are each encoded by distinct exons. A single transcription start site was identified, surrounded by a short 114 bp sequence able to direct reporter gene expression in both F3-expressing and -non-expressing cells. In addition, a cell type-specific enhancer, only active in F3-expressing cells, was found immediately upstream to it. Structural analysis of the promoter region revealed consensus sequences for binding transcription factors involved in cell type-specific and/or developmental regulations. Most of them are homeobox containing transcription factors thus suggesting that regulation of F3 gene expression could be part of a large developmental program.

In vivo definition of an archaeal promoter

We have used a plasmid-based transcriptional reporter system to examine the transcriptional effects of 33 single point mutations in the box A region (TATA-like sequence) of the Haloferax volcanii tRNA(Lys) promoter. The most pronounced effects on transcriptional efficiency were found when the nucleotides corresponding to the TATA-like region were altered. Promoters with wild-type or higher levels of transcriptional activity conformed to the general archaeal box A consensus, 5'-T/CTTAT/AA-3'. The preference for a pyrimidine residue in the 5' position of this region and the exclusion of guanine and cytosine in the next four positions in the 3' direction are defining characteristics shared by all efficient archaeal promoters. We have also observed that replacement of a 10-nucleotide purine-rich sequence, located 5' of the H. volcanii tRNA(Lys) box A element, completely abolished transcription from this promoter. These data show that the H. volcanii tRNA(Lys) promoter is dependent on two separate, and essential, sequence elements. The possible functions of these sequences, in view of the recent descriptions of eucaryal-like transcription factors for Archaea, are discussed.

Characterization of the human inosine-5'-monophosphate dehydrogenase type II gene

Inosine-5'-monophosphate dehydrogenase (IMPDH) activity and mRNA levels are induced up to 15-fold upon mitogenic or antigenic stimulation of human peripheral blood T lymphocytes. This increase in IMPDH activity is required for cellular proliferation and has been associated with malignant transformation. We have cloned the human IMPDH type II gene and show that it contains 14 exons and is approximately 5.8 kilobases in length. Exons vary in size from 49 to 207 base pairs and introns from 73 to 1065 base pairs. The transcription start site was mapped to a position 50 nucleotides upstream of the translation initiation site. The 5'-flanking region consisting of 463 base pairs upstream of the translation initiation site confers induced transcription and differential regulation upon a chloramphenicol acetyltransferase reporter gene when transfected into Jurkat T cells and human peripheral blood T lymphocytes, respectively. DNase I footprinting analysis using Jurkat T cell nuclear extract identified four protected regions in the promoter which coincide with consensus transcription factor binding sites for the nuclear factors AP2, ATF, CREB, Egr-1, Nm23, and Sp1. These findings suggest that several of these nuclear factors may play a critical role in the regulation of IMPDH type II gene expression during T lymphocyte activation.

Promoter elements in Drosophila melanogaster revealed by sequence analysis

A Drosophila Promoter Database containing 252 independent Drosophila melanogaster promoter entries has been compiled. The database and its subsets have been searched for overrepresented sequences. The analysis reveals that the proximal promoter region displays the most dramatic nucleotide sequence irregularities and exhibits a tripartite structure, consisting of TATA at -25/-30 bp, initiator (Inr) at +/- 5 bp and a novel class of downstream elements at +20/+30 bp from the RNA start site. These latter elements are also strand-specific. However, they differ from TATA and Inr in several aspects: (1) they are represented not by a single, but by multiple sequences, (2) they are shorter, (3) their position is less strictly fixed with respect to the RNA start site, (4) they emerge as a characteristic feature of Drosophila promoters and (5) some of them are strongly overrepresented in the TATA-less, but not TATA-containing, subset. About one-half of known Drosophila promoters can be classified as TATA-less. The overall sequence organization of the promoter region is characterized by an extended region with an increase in GC-content and a decrease in A, which contains a number of binding sites for Drosophila transcription factors.

Human eosinophil major basic protein, a mediator of allergic inflammation, is expressed by alternative splicing from two promoters

Human eosinophil major basic protein (MBP) is one of the principal mediators of injury to parasites and tissues in allergic inflammation. MBP is stored in eosinophil crystalloid granules and released with other granule constituents during eosinophil action. Previous studies have identified an MBP gene promoter that generates a 1.0 kb mRNA transcript encoding MBP preproprotein which undergoes processing to the mature storage form. To investigate how the MBP gene is regulated, we have examined the identity and levels of the MBP transcripts both in precursor cells and in blood eosinophils. It was found that the gene was expressed from two upstream promoters, a distal promoter P1 in addition to the previously described promoter P2. Evidence for the second promoter was initially provided by isolation from a human HL-60 leukaemic cell cDNA library of a novel 1.6 kb MBP cDNA that was distinct from the known 1.0 kb cDNA. The complete nucleotide sequence of the 1.6 kb cDNA was determined, and showed that the two cDNAs had identical coding and 3' untranslated regions but differed in their 5' sequences. By isolating and sequencing MBP genomic clones from an arrayed chromosome 11 library, it was demonstrated that the MBP gene is composed of nine upstream exons and five coding exons. The 1.6 and 1.0 kb cDNAs arise by differential splicing of alternate MBP transcripts from promoters P1 and P2 respectively, located 32 kb apart in the genomic DNA. Primer extension analysis identified two transcription start sites at P1, neither associated with a typical TATA box motif. Northern blotting and reverse-transcription PCR analysis showed that the 1.0 kb mRNA was present at higher levels than the 1.6 kb species in immature cells including HL-60 and bone-marrow cells. By contrast, low levels of 1.6 kb mRNA transcripts predominated in differentiated blood eosinophils. The results are compatible with differential use of P1 and P2 promoters as a mechanism for regulation of MBP expression during eosinophil maturation.

Characterization of the murine mitochondrial glycerol-3-phosphate acyltransferase promoter

Glycerol-3-phosphate acyltransferase (GPAT) catalyzes the acylation of sn-glycerol 3-phosphate to form 1-acyl-sn-glycerol 3-phosphate, a committed step in triacylglycerol and phospholipid biosynthesis. We have previously reported the cDNA cloning and transcriptional regulation of the murine mitochondrial GPAT (mGPAT). We now report the cloning of the 5'-flanking region of the murine mitochondrial GPAT. The transcription start site was identified by primer extension and RNase protection assays. A TATA box-like motif (TTATTAT) was located between -34 and -29 and a reverse CCAAT box (ATTGG) was located between -78 and -74, relative to the transcription start site. To begin studying mechanisms underlying transcriptional regulation of the mGPAT gene, chimeric luciferase (LUC) plasmids containing serial deletions, from -1447 to -38, of the 5'-flanking region of the murine mGPAT gene were prepared and transfected into 3T3-L1 cells. The fusion construct -1447 GPAT.LUC showed high promoter activity and deletions to -1353, -747, -322, and -86 did not markedly change the promoter activity. With all constructs, luciferase activity was 2-fold higher when plasmids were transfected into 3T3-L1 adipocytes. However, deletion of sequences between -86 and -55 resulted in a 9-fold decrease in LUC activity in both preadipocytes and adipocytes. Deletion of sequences between -55 and -38 did not alter promoter activity. DNase I footprint analysis revealed a protected region between -95 and -65 which included the putative CTF/NF1 binding site. Electrophoretic mobility shift assays demonstrated a single protein-DNA complex formation. Oligonucleotides synthesized according to the CTF/NF1 consensus sequence or the adenovirus NF-1 site showed a different and more complex pattern of protein-DNA interaction and were not able to compete away the mGPAT promoter-protein complex, indicating that a distinct protein was bound to -86/-55, a region important for the basal promoter activity in 3T3-L1 cells. Luciferase activity was increased 2.8- and 8-fold when adipocytes stably transfected with -322 GPAT.LUC were treated with 5 and 25 mM glucose, respectively, in the presence of 10 nM insulin. These results indicate that carbohydrate-responsive sequences are located within -322 base pairs of the mGPAT promoter.

Identification and characterization of a functional promoter region in the human eosinophil IL-5 receptor alpha subunit gene

The molecular basis for the commitment of multipotential myeloid progenitors to the eosinophil lineage, and the transcriptional mechanisms by which eosinophil-specific genes are subsequently expressed and regulated during eosinophil development are currently unknown. Interleukin-5 (IL-5) is a T cell and mast cell-derived cytokine with actions restricted to the eosinophil and closely related basophil lineages in humans. The high affinity receptor for IL-5 (IL-5R) is composed of an alpha subunit (IL-5R alpha) expressed by the eosinophil lineage, that associates with a beta c subunit shared with the receptors for IL-3 and granulocyte-macrophage colony stimulating factor (GM-CSF). As a prerequisite to studies of the transcriptional regulation of the IL-5R alpha subunit gene, we used three different methods, including primer extension, RNase protection, and 5'-RACE to precisely map the transcriptional start site to a position 15 base pairs (bp) upstream of the 5' end of the published sequence of IL-5R alpha exon 1. To initially identify the IL-5R alpha promoter, 3.5 kilobases (kb) and 561 bp of the 5' sequence flanking the transcriptional start site were subcloned into the promoterless pXP2-luciferase vector. Transient transfection of these constructs into an eosinophil-committed HL-60 subline, clone HL-60-C15, induced the expression of approximately 240-fold greater luciferase activity than the promoterless vector, identifying a strong functionally active promoter region within the 561 bp of sequence proximal to the transcriptional start site and with activity equivalent to pXP2 constructs containing the entire 3.5 kb of upstream sequence. To more precisely localize the cis-acting regulatory elements in this region important for promoter activity, a series of 5' deletion mutants of the 561-bp region were generated in the pXP2-luciferase vector. Deletion of the region between bp -432 and -398 reduced promoter activity by more than 80% in the HL-60-C15 cell line. Further analyses of the activity of the IL-5R alpha promoter constructs in various other eosinophil, myeloid, and non-myeloid cell lines indicated that the promoter was relatively myeloid and eosinophil lineage-specific in its expression. Consensus sequences for known transcription factor binding sites were not present in the 34-bp region of the promoter required for maximal activity, suggesting unique myeloid- and possibly eosinophil-specific regulatory elements.(ABSTRACT TRUNCATED AT 400 WORDS)

Glucocorticoid activation of chromogranin A gene expression. Identification and characterization of a novel glucocorticoid response element

Glucocorticoids regulate catecholamine biosynthesis and storage at several sites. Chromogranin A, an abundant protein complexed with catecholamines in secretory vesicles of chromaffin cells and sympathetic axons, is also augmented by glucocorticoids. This study reports isolation of the rat chromogranin A promoter to elucidate transcriptional regulation of chromogranin A biosynthesis by glucocorticoids in neuroendocrine cells. Endogenous chromogranin A gene expression was activated up to 3.5-fold in chromaffin cells by glucocorticoid, in time-dependent fashion. Inhibition of new protein synthesis by cycloheximide did not alter the rise in chromogranin A mRNA, suggesting that glucocorticoids directly activate the chromogranin A promoter; nuclear runoff assays confirmed a 3.3-fold increased rate of initiation of new chromogranin A transcripts after glucocorticoid. Transfected rat chromogranin A promoter/luciferase reporter constructs were activated 2.6-3.1-fold by glucocorticoid, and selective agonist/antagonist studies determined that dexamethasone effects were mediated by glucocorticoid receptors. Both rat and mouse chromogranin A promoter/luciferase reporter constructs were activated by glucocorticoid. A series of promoter deletions narrowed the region of glucocorticoid action to a 93-bp section of the promoter, from position -526 to -619 bp upstream of the cap site. A 15-bp sequence ([-583 bp] 5'-ACATGAGTGTGTCCT-3' [-597 bp]) within this region showed partial homology to a glucocorticoid response element (GRE; half-site in italics) consensus sequence, and several lines of experimental evidence confirmed its function as a GRE: (a) site-directed mutation of this GRE prevented glucocorticoid activation of a chromogranin A promoter/reporter; (b) transfer of this GRE to a heterologous (thymidine kinase) promoter/reporter conferred activation by glucocorticoid, in copy number-dependent and orientation-independent fashion; and (c) electrophoretic gel mobility shifts demonstrated binding of this GRE by ligand-activated glucocorticoid receptor, though at 2.75-fold lower affinity than the glucocorticoid receptor interaction with a consensus GRE. The rat chromogranin A GRE showed functional and structural similarities to GREs in other genes proportionally regulated by glucocorticoids. We conclude that a discrete domain of the chromogranin A promoter is both necessary and sufficient to confer glucocorticoid regulation onto the gene, and that the activity of this region also explains the degree of activation of the endogenous gene by glucocorticoid.

Transcriptional regulation of tubulin gene expression in differentiating trochoblasts during early development of Patella vulgata

The expression of alpha- and beta-tubulin genes during the early development of the marine mollusk Patella vulgata has been investigated. From the 32-cell stage onwards, an enhanced expression of both alpha- and beta-tubulin mRNAs was detected in the primary trochoblasts. After one additional cleavage, these cells become cleavage-arrested and then form cilia. They are the first cells to differentiate during Patella development. Later, alpha- and beta-tubulin mRNA is also found in the accessory and secondary trochoblasts. Together these three cell-lines form the prototroch, the ciliated locomotory organ of the trochophore larva. The early and abundant expression of tubulin genes precede and accompany cilia formation in the trochoblasts and provides us with an excellent molecular differentiation marker for these cells. Apart from the trochoblasts, tubulin gene expression was also found in other cells at some stages. At the 88-cell stage, elevated tubulin mRNA levels were found around the large nucleus of the mesodermal stem cell 4d. In later stages, tubulin gene expression was detected in the cells that form the flagella of the apical tuft and in the refractive bodies. An alpha-tubulin gene was isolated and characterized. A lacZ fusion gene under control of the 5′ upstream region of this tubulin gene was microinjected into embryos at the two-cell stage. The reporter gene product was only detected in the three trochoblast cell-lines at the same time as tubulin genes were expressed in these cells. Reporter gene product was not detected in any other cells. Thus, this 5′ upstream region of this alpha-tubulin gene contains all the elements required for the correct spatiotemporal pattern of expression.

Gene structure and cell type-specific expression of the human ATP synthase alpha subunit

The gene structure of the human ATP synthase alpha subunit (hATP1) was determined by cloning and sequencing. This gene is approximately 14 kbp in length and contains 12 exons interrupted by 11 introns. Mapping of the clones of hATP1 and Southern blot analysis of the genomic gene showed that there were a single copy of bona fide hATP1 gene and two pseudogenes. Primer extension and S1 mapping analysis showed the presence of multiple transcription initiation sites of the hATP1 gene. No TATA box or CAAT box was found near the transcription initiation sites. Comparison with the bovine gene showed that the 5'-flanking region of the hATP1 gene has an unconserved guanine-cytosine (GC) rich region, including several binding motifs of transcriptional factors, such as Sp1, AP-2, and GCF. By functional assay of gene expression, the basal promoter activity was located near the GC rich region. Comparison of the 5'-upstream region of the hATP1 gene with those of the genes for bovine ATP synthase alpha, human beta, and human gamma subunits indicated three common sequences, suggesting that putative cis-elements coordinate the expressions of the three subunit genes for the ATP synthase. The enhancer activities derived from the 5'-deletion mutants of a hATP1-CAT chimeric gene were different in cell lines from four different human tissues, suggesting the existence of cell type-specific gene regulation.

The European Bioinformatics Institute (EBI) databases

This paper describes the databases and services of the European Bioinformatics Institute (EBI). In collaboration with DDBJ and GenBank/NCBI, the EBI maintains and distributes the EMBL Nucleotide Sequence Database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence Database, in collaboration with Amos Bairoch of the University of Geneva. Over thirty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists, are also available. The EBI network services include database searching, entry retrieval, and sequence similarity searching facilities.

Structural characterization and alternate splicing of the gene encoding the preadipocyte EGF-like protein pref-1

Preadipocyte factor 1 (pref-1), a member of the EGF-like protein family, is a transmembrane protein with six tandem EGF-like repeats in the putative extracellular domain. Expression of pref-1 is abolished during the in vitro differentiation of 3T3-L1 preadipocytes to adipocytes, and constitutive expression of pref-1 in preadipocytes inhibits their differentiation [Smas, C.M., & Sul, H.S. (1993) Cell 73, 725-734]. In the present studies, we have isolated and characterized genomic clones for pref-1 and have identified multiple pref-1 transcripts generated by alternate splicing. The pref-1 gene consists of five exons and four introns spanning approximately 7.3 kb. By primer extension analysis, the transcription start site was determined to be 169 bp upstream from the translation initiation codon. We have identified functional promoter sequences by transient transfection using a 2.1 kb fragment of the pref-1 5' flanking region linked to a luciferase gene; the pref-1-luciferase fusion gene construct gave 20-fold higher promoter activity as compared to the promoterless vector. Analysis of exon-intron junctions reveals that unlike the majority of the mammalian EGF-like genes, EGF-like repeats of pref-1 are not encoded by discrete exons. Through RT-PCR and the isolation and analysis of multiple pref-1 cDNA clones, we have identified, in addition to full-length pref-1, five alternately spliced forms with various in-frame deletions of all or a part of the sixth EGF-like repeat, juxta-membrane, and predicted transmembrane domains.(ABSTRACT TRUNCATED AT 250 WORDS)

A deductive database system for analyzing human nucleotide sequence data

The analysis of the human genome is one of the most significant topics in both biology and medical science. There is a growing need for a well-designed database system for searching and analyzing the human genome data. We developed a deductive database system to search and analyze nucleotide sequence data derived from the GenBank primates data. A deductive database system is a next generation one and it contains an inference mechanism that can handle problems beyond the capabilities of classical database systems. Database queries are described in logical rules. These rules are simple even for molecular biologists who are not experts in computer programs because they are declarative and do not require the procedural commands that are usually used in computer programs. Furthermore, queries based on logical rules are powerful enough to express complicated biological problems. Particularly, recursive rules are suitable for examining secondary structures of nucleotide sequences. In our analysis of TfR's IRE, we noted five stem-and-loop structures.

Comparing nucleotide and protein sequences by linguistic methods

Nucleotide and amino acid sequences can be analyzed and compared by their oligomer compositions. Such methods are fundamentally different from comparison methods based on sequence alignment. They are analogous to the linguistic analysis of human texts. The methods have a wide range of sensitivity and can identify homologous as well as functionally and taxonomically related sequences. Significant sequence dissimilarity can also be identified enabling detection of foreign DNA sequences in genomes, genetic libraries and databases. The simplicity and speed of linguistic methods make them very suitable for database searching and maintenance and as a preliminary step to more specific and time-consuming analysis methods.

Identification of two initiator elements in the bidirectional promoter of the human dihydrofolate reductase and mismatch repair protein 1 genes

The human dihydrofolate reductase (DHFR) gene and mismatch repair protein 1 (MRP1) genes are organized in a head-to-head configuration separated by an 90 base pair sequence. We have previously shown that as small as a 114 bp promoter sequences is sufficient for accurate and efficient initiation of divergent transcription. In this study, the mechanism of accurate transcription initiation in vivo from this short bidirectional promoter was analyzed by a newly developed highly sensitive primer extension assay. The GC boxes in the middle of this sequence were essential for bidirectional promoter activity, but not sufficient for accurate initiation. The sequences overlapping the transcription initiation sites of the DHFR and MRP1 genes were shown to function as the initiator, which directs transcription from an internal site. These initiators were strictly position dependent and were active only when located from 40 to 50 base pairs downstream from the GC box. Although there is no apparent sequence homology between two initiators, a common nuclear factor bound to these elements. Existence of two initiators located on both sides of the middle GC box seems to be the molecular basis of bidirectional activity of this short DNA sequence.

TBP-DNA interactions in the minor groove discriminate between A:T and T:A base pairs

In this report, we test the hypothesis that TBP binds DNA promiscuously due to its manner of recognition of the DNA minor groove. The experiment performed was to select TBP-binding sequences from a pool of random double stranded oligonucleotides. Sixty two clones from this pool were sequenced. Surprisingly, the results show that TBP has a marked preference for stably binding one sequence (TATATAA) over all others, yet only four classes of TATA box were selected. The features of the selected sequences allow definition of a binding consensus for TBP. The DNA binding properties of TBP to the four TATA variants was examined, the results being in accord with the observed selection frequencies. However, the nature of TBP-DNA binding is strongly affected by ionic strength. We infer that recognition of DNA via the minor groove can be highly selective even where A:T and T:A discrimination is required. Models for how this might be accomplished are discussed.

Identification of two promoter regions in the rat B-50/GAP-43 gene

To determine cis-acting elements controlling the rat B-50/GAP-43 gene expression, the genomic DNA encoding exon 1 and the 5' flanking sequence was isolated. Sequence analysis of 1 kb 5' untranslated region (UTR) revealed the presence of a (GA)-repeat and a (GT)-repeat. The size of the (GA)-repeat varied due to both an instability of phage lambda lambda DNA in E. coli and genomic variation between rats. Transcription initiation sites were mapped in 8-day-old rat brain poly(A)+ mRNA. Primer extension indicated multiple transcription start sites at -159 and -339/-342 nt upstream of the translation start site; reverse transcriptase coupled PCR showed that the most 5' transcription start site is located between -465 and -440. Northern blotting demonstrated that approximately 90% of the B-50 mRNAs initiates at approximately -50. Promoter analysis by transient transfection assays in undifferentiated and retinoic acid-differentiated P19-EC cells revealed that the rat B-50 gene contains two promoters. P1 (located between -750 and -407) contains commonly observed promoter elements such as a TATA box and CCAAT boxes. P2 (located between -233 and -1) neither contains TATA boxes, CCAAT boxes nor consensus sequences of house-keeping gene promoters like GC-boxes. The activity of P1 is inhibited at neuroectodermal differentiation of P19-EC cells whereas the activity of P2 is stimulated. In 8 day old rat brain the majority of the B-50 mRNA transcripts are derived from P2. It is concluded that at this developmental stage P2 is the most important promoter.

Second-site long terminal repeat (LTR) revertants of replication-defective human immunodeficiency virus: effects of revertant TATA box motifs on virus infectivity, LTR-directed expression, in vitro RNA synthesis, and binding of basal transcription factors TFIID and TFIIA

Second-site revertants from replication-incompetent molecular clones of human immunodeficiency virus (HIV) contain base substitutions adjacent to the TATA motif. The altered TATA box motifs were analyzed for their effect(s) on virus infectivity, long terminal repeat (LTR)-directed expression in transient transfection assays, in vitro RNA synthesis, and assembly of the TFIID-TFIIA preinitiation complex. The revertant TATA boxes accelerated the kinetics of HIV replication when present in the context of an LTR containing a Sp1 mutation (deletion or site specific); no effect was observed on the infectivity of wild-type HIV. In chloramphenicol acetyltransferase assays and in vitro transcription systems, the altered TATA box motifs led to elevated basal levels of RNA synthesis from NF-kappa B- and Sp1-mutagenized and wild-type templates, respectively, but did not increase responsiveness to Tat transactivation. The revertant TATA boxes accelerated the binding of TFIID and TFIIA to the LTR and stabilized their association with the promoter. The revertants did not assemble a more-processive elongation complex. These results suggest that in the context of an impaired enhancer/promoter (viz., three mutated Sp1 elements), a series of HIV revertants emerge which contain LTR alterations that significantly augment basal RNA synthesis. The TATA motif revertants are capable of rescuing the enhancer/promoter defect and sustain virus infectivity.

Structural organization of the human tyrosinase gene and sequence analysis and characterization of its promoter region

Tyrosinase is the principal enzyme in the biosynthesis of melanin. The expression of tyrosinase is tissue-specific and appears to be regulated by various hormonal and environmental factors. Elucidation of the genomic structure and molecular basis of control of tyrosinase gene expression will greatly enhance our understanding of the regulation of human pigmentation. To this end, we have isolated and performed restriction mapping of recombinant cosmid and lambda phage clones containing the human tyrosinase gene, sequenced a 2.2-kilobase (kb) region of its promoter, and determined the potential regions regulating the tyrosinase gene expression in transient-expression system. The human tyrosinase gene is comprised of five exons and four introns. Based on our restriction mapping studies, the gene spans a distance of over 65-kb on chromosome 11 (q14-->q21). We constructed a series of plasmids (pHTY-CAT) that contain 5' sequential deletions of the human tyrosinase 5' flanking sequence fused to the reporter gene, chloramphenicol acetyltransferase (CAT). The plasmids were used to locate promoter regions that are potential regulators of tyrosinase gene expression in a transient expression system using melanoma cell lines. In human melanoma cells, the plasmid construct with a -2020 base pair (bp) promoter yielded the highest CAT activity. When the deletions reached -1739 bp, the CAT activity was dramatically reduced, indicating that important enhancer elements for transcription control are present between -1739 and -2020 bp. Further deletions up to -550 bp also resulted in dramatic decreases of CAT activity. However, when the deletion included -550 bp of the 5' flanking sequence, there was 26 percent of the CAT activity compared to that of the -2020 bp promoter. Deletions beyond -550 bp also showed markedly decreased CAT activity. Based on our data, we suggest that human tyrosinase gene expression is governed by both tissue-specific and multiple regulatory elements.

Structure and sequence of the Arabidopsis thaliana lipoxygenase 1 gene

We have isolated and sequenced the Arabidopsis thaliana LOX1 gene which encodes a lipoxygenase. The 5255 bp sequence includes 763 bp upstream from the start codon, 4345 bp spanning the coding region and 147 bp downstream from the stop codon. The coding region of the LOX1 gene consists of 8 exons separated by 7 introns. The introns in the LOX1 gene are located in sites predicted by the closely related soybean seed LOX3 gene sequence. With the exception of intron 1, the LOX1 introns are smaller in size than the LOX3 introns. Furthermore the Arabidopsis gene contains 7 introns, while the soybean gene contains 8. Four putative TATA box elements were identified in the 763 bp sequence upstream from the coding region, however only one is followed by a cap site which is located in a position appropriate for it to act as the initiation site for transcription.

Expression of the carboxypeptidase E gene: characterization of the initiator-binding proteins

Several of the genes for enzymes involved in peptide hormone processing, such as carboxypeptidase E (CPE), do not contain a TATA box. The region surrounding the major transcription initiation site of the CPE gene has sequence homology with the 'initiator' (Inr) elements of the TATA-less terminal deoxynucleotidyltransferase (TdT) gene, and the adenovirus major late (AdML) and other promoters. To investigate the promoter region of the CPE gene, GH4C1 cells were transiently transfected with constructs containing the luciferase reporter gene attached to various portions of the rat CPE gene (-395 to +45). Positive regulator elements were detected in positions -84 to -12 and +30 to +47. However, the Inr-like element of the CPE gene (-12 to +20) produced detectable luciferase activity in the absence of upstream and downstream sequences. This region of the CPE gene was much more active when expressed in the normal (sense) orientation than when expressed in the antisense orientation. A mutation within the consensus sequence between CPE and other Inr elements was much less active than the wild-type sequence. Interestingly, deletion of the Inr and surrounding sequences produced a large increase in the transcription from upstream sites, suggesting that proteins which bind at, or near, the Inr sequence suppress transcription from other sites. To characterize GH4C1 nuclear proteins which bind to the CPE gene, Southwestern blotting, UV cross-linking, and gel shift analyses were performed. The Southwestern analysis showed that the CPE and AdML Inr sequences labeled several proteins of similar sizes which are distinct from the transcription factor USF; this factor has been previously reported to bind to the AdML Inr sequence. A CPE Inr-binding protein co-purifies with an AdML Inr-binding protein on a CPE Inr affinity column. Gel shift assays showed that with some binding conditions, the proteins that bind to the CPE sequence also bind to the TdT and AdML Inr elements. Taken together, these results indicate that the -12 to +20 region of the CPE gene has the properties of an Inr element which binds some, but not all, of the factors which bind to other Inr elements.

Nucleotide sequence of human adenovirus type 12 DNA: comparative functional analysis

A fresh inoculum of human adenovirus type 12 (Ad12) was obtained from the American Type Culture Collection and passaged once on human embryonic kidney cells, and Ad12 DNA was prepared from the first-passage yield to avoid higher passages which might have generated host-virus DNA recombinants. The 18 PstI fragments of Ad12 DNA were cloned into the pBluescript KS vector, and the entire nucleotide sequence of both strands from all 18 fragments was determined by using successive oligodeoxyribonucleotide primers. Ad12 DNA extends over 34,125 nucleotide pairs, and its molecular weight is calculated to be about 22 x 10(6). The nucleotide sequence of Ad12 DNA was subjected to computer analyses that determined possible open reading of frames on the two strands, the leader sequences, the position of the virus-associated RNA coding region, possible TATA, and polyadenylation signals. The distribution of the Ad12 open reading frames was similar to that in the previously sequenced Ad2 DNA, but there were also distinct differences. Ad12 DNA has an inverted terminal redundancy of 161 nucleotides, compared with 102 nucleotides in Ad2 DNA. There were stretches of sequence identity between Ad2 and Ad12 DNAs at both termini; the overall sequence similarity between the two viral genomes ranged between 59% (polypeptide IX) and 77% (in the E2 region), with high homology also in the sequences for the adenovirus DNA polymerase.

Comparative analysis of the sequence and structure of two Drosophila melanogaster genes encoding vitelline membrane proteins

Two Drosophila melanogaster vitelline membrane protein-encoding genes (VM), located at polytene band positions 26A and 34C, have been cloned and comparatively characterized at the nucleotide level. Sequence analysis of genomic and cDNA clones for the two genes, VM26A.1 and VM34C.1, indicates that both are similarly organized with a central highly conserved domain [Scherer et al., Dev. Biol. 130 (1988) 786-788] which is flanked by unrelated regions, and that both genes lack introns. Comparison of the upstream regions reveals that both VM genes contain a hepatmeric element identical to one associated with the D. melanogaster yolk protein-encoding genes (YP). This heptamer occurs in the specific 5' flanking region responsible for ovarian temporal- and tissue-specific control in both VM and YP genes. A putative chorion transcription factor 2 site is also associated with an upstream control element of VM26A.1, but not with any sequenced portion of VM34C.1.

DNA sequence requirement of a TATA element-binding protein from Arabidopsis for transcription in vitro

We have analyzed the DNA sequence requirements for the functioning of TATA elements by examining the transcriptional activities associated with 24 promoters, including representatives of each of the 21 point mutations in the consensus sequence from plants, TATATATA, in a HeLa in vitro system and in a chimeric in vitro system in which human TATA-binding protein (hTBP) was replaced by purified TBP of Arabidopsis (aTBP-1). Although the relative transcriptional activities varied among these promoters, both systems gave virtually identical results. Among the mutant TATA elements, those with the sequences TAGAGATA and GAGAGAGA had undetectable activity. The rest had activities that ranged from 7% to 130% of the activity associated with the consensus element. These results suggest the functional conservation of TBP between plants and animals.

Evidence for erosion of mouse CpG islands during mammalian evolution

In housekeeping and many tissue-specific genes, the promoter is embedded in a so-called CpG island. We have compared the available human and mouse DNA sequences with respect to their CpG island properties. While mouse sequences showed a simple gradient distribution of G + C content and CpG densities, man had a distinct peak of sequences with typical CpG island characteristics. Pairwise comparison of 23 orthologous genes revealed that mouse almost always had a less pronounced CpG island than man, or none at all. In both species the requirements for a functional CpG island may be similar in that most DNA regions with a density of six or more CpG per 100 bp remain unmethylated. However, the mouse has apparently experienced more accidental CpG island methylation, suggested by local TpG and CpA excess. We propose that: (1) in mouse the CpG islands do not represent the ancestral state but have been eroded during evolution, and (2) this erosion may be related to the mouse's small body mass and short life-span, allowing for a more relaxed control of gene activity.

In vivo expression and molecular characterization of the porcine slow-myosin heavy chain

We report on the molecular characterization of the porcine slow-myosin heavy chain (HC) beta gene and the isolation of its 5′ end cDNA. In vivo expression study, by in situ hybridization and histochemistry, revealed a highly regular rosette pattern of fiber arrangement, with a slow fiber occupying the central core, in all the skeletal muscles examined. This feature can be advantageous in the distinction of primary and secondary fibers in myogenic lineage studies. In the neonatal heart, beta isoform expression is diffuse, with higher expression occurring in the ventricle than in the atrium. Transient transfection assays showed the porcine promoter functions in a muscle- and differentiation stage-specific manner. In the 5′ regulatory region are several putative positive and negative regulatory elements, including a positive and a negative element in close proximity to each other in intron 1.

The frequency of two-base tracts in eukaryotic genomes

The frequency of two-base tracts is surveyed in a wide range of eukaryotic genomes using the special program TRACTS. All three two-base families are surveyed: R.Y (A,G.C,T), K.M (A,C.G,T), and S;W (A.T and G.C). Data for the human beta-globin complex, for the tobacco chloroplast, and for 247 nt mammalian promoter regions are presented. All two-base tracts longer than three or four bases are overrepresented to an extent surpassing by far their occurrence in a randomized DNA population in the majority of the genomic regions analyzed; 20-30 long tracts are quite frequent, against the statistical odds. R.Y tracts are found at the largest excess, K.M tract to a slightly lesser extent, while S.W tracts are found at a moderate yet significant excess. The majority of the tracts manifest only a limited extent of tandem repeat structures. The idea that the two base tracts serve as unwinding elements is considered.

BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.)

Retroviruses and retrotransposons make up the broad class of retroelements replicating and transposing via reverse transcriptase. Retroelements have recently been found to be ubiquitous in the plants. We report here the isolation, sequence and analysis of a retroelement from barley (Hordeum vulgare L.) with all the features of a copia-like retrotransposon. This is named BARE-1 (for BArley RetroElement 1), the first such element described for barley. BARE-1 is 12,088 bp, with long terminal repeats (LTRs) of 1829 bp containing perfect 6 bp inverted repeats at their ends and flanked by 4 bp direct repeats in the host DNA. Between the long terminal repeats is an internal domain with a derived amino acid sequence of 1285 residues, bearing homology to the gag, pro, int and rt domains of retroviruses and both plant and non-plant copia-like retrotransposons. Cultivated barley contains about 5000 elements in the genome similar to the BARE-1 putative gag domain, but ten-fold more hybridizing to rt or LTR probes. The particular BARE-1 element reported here appears to be inactive, as the putative protein-coding domain is interrupted by four stop codons and a frameshift. In addition, the 3' LTR is 4% divergent from the 5' LTR and contains a 3135 bp insertion. Nevertheless, we have recently detected transcripts hybridizing to BARE-1 on northern blots, presumably from active copies. Analysis of BARE-1 expression and function in barley is currently underway.

Structural organization of the bovine gene for the heart/muscle isoform of cytochrome c oxidase subunit VIa

The bovine gene for the nuclear-encoded heart/muscle isoform of cytochrome c oxidase subunit VIa (COX6A1) was isolated from a library of bovine genomic DNA in lambda EMBL3 and sequenced. The gene spans 760 bp and comprises three exons and two small introns. Exon 1 encodes a 193 bp 5' untranslated region, a 12 amino acid presequence, and the first 12 amino acids of the mature COX VIa protein. Exon 2 encodes amino acids 13 to 58, and exon 3 amino acids 59 to 85 plus the 35 bp 3' untranslated region. Exons 2 and 3 are separated by a small intron of only 96 bp. All exon-intron boundaries matched the consensus splice junction sequences. COX6A1 transcripts are present in RNA from bovine heart but not brain. Primer extension and ribonuclease protection assays were used to map the 5' ends of COX6A1 transcripts in heart; both methods identified several clusters of transcription initiation sites, indicating that COX6A1 mRNA is heterogeneous at the 5' end. The proximal 5' flanking region is AT-rich and contains potential basal promoter elements, such as TATA and CCAAT boxes, associated with tissue-specific genes. A single consensus binding site for the muscle-specific transcription factor, MyoD1, was also located within this AT-rich region. The distal promoter region contained a perfect AP4 site plus potential binding sites for enhancer elements (NRF-1, Mt1, Mt3, and Mt4) proposed to regulate expression of genes for mitochondrial proteins.

Vectors for the expression of PCR-amplified immunoglobulin variable domains with human constant regions

Cassette vectors have been constructed for mammalian expression of complete immunoglobulin heavy and light chain genes whose variable regions are produced by the polymerase chain reaction (PCR). The light and heavy chain vectors have promoter, leader, partial intron, enhancer and constant region segments within modified pSV2-gpt and pSV2-neo plasmids, respectively. Variable (V) regions are obtained by PCR using a two step process: 1) the V gene is amplified from genomic or cDNA, cloned into an intermediate vector and sequenced; 2) the first PCR product serves as the template for a second amplification in which restriction enzyme recognition sites and limited flanking intron sequence are added. The second PCR product is inserted into the expression vector, which is then transfected into mouse myeloma cells. These vectors contain human constant regions and may be used to express chimeric, humanized or human Ig genes. This report describes the design of these vectors and their application for the expression of chimeric 60.3, an anti-CD18 antibody.