Minimal Promoter Activity Research Articles

Genomic Structure and Promoter Activity of the Mouse Polysialic Acid Synthase Gene (mST8Sia II): BRAIN-SPECIFIC EXPRESSION FROM A TATA-LESS GC-RICH SEQUENCE

The mouse ST8Sia II (mST8Sia II/STX) gene encodes a neural cell adhesion molecule-specific polysialic acid synthase whose expression is regulated during the developmental stages of mouse brain. To elucidate the molecular mechanism by which the expression is tissue-specifically and developmentally regulated, we isolated the complete genomic DNA and characterized the promoter of the gene for mST8Sia II. The gene encoding mST8Sia II was found to span about 80 kilobases and to be composed of six exons. Primer extension and S1 nuclease protection analyses revealed that the transcription started from 167 nucleotides upstream of the translational initiation site. Promoter analyses of the 5'-flanking region of the mST8Sia II gene using a luciferase gene reporter system revealed strong promoter activity in retinoic acid-induced differentiated P19 cells, which highly express the mST8Sia II gene. Deletion analyses demonstrated that the minimal promoter activity detected for the proximal region 325 base pairs upstream from the translational initiation codon (-158 to +167) could be modulated by various sequences within the 9. 5-kilobase 5'-flanking region. The minimal promoter was embedded in a GC-rich domain (74%, GC content), in which two Sp1 binding motifs as well as a long purine-rich region were found, but it lacked TATA and CAAT boxes. The positive regulatory region located between -159 and -659 contained two additional Sp1 binding motifs and a long pyrimidine-rich region. We also found that the minimal promoter region of the mST8Sia II gene was sufficient for expression of a reporter gene in mST8Sia II gene-expressing neural differentiated P19 cells but not in nonexpressing ones. Thus the TATA-less GC-rich minimal promoter region of mST8Sia II probably controls the cell type-specific expression of the mST8Sia II gene.

Multiple Factors Regulate the Rat Liver Basolateral Sodium-dependent Bile Acid Cotransporter Gene Promoter

The hepatic uptake of bile acids from the portal circulation is primarily dependent upon a sodium-dependent basolateral membrane transporter. In order to begin to investigate the factors controlling rat liver sodium-dependent bile acid cotransporter (ntcp) gene expression, we isolated approximately 30 kilobase pairs of rat genomic DNA in three overlapping lambdaphage clones. The rat ntcp gene is distributed over 16.5 kilobase pairs as five exons. Primer extension analysis revealed two closely spaced transcription initiation sites, 27 and 41 nucleotides downstream of a TATA sequence. Regulation of transcription was investigated first by transfection of primary rat hepatocytes by a series of 5'-deleted rat ntcp promoter-driven luciferase constructs (from approximately -6 kilobase pairs to -59 base pairs of upstream sequences, terminating at nucleotide +47), identifying a minimal promoter element: nucleotide -158 to +47. This minimal promoter was active in transfected HepG2, but inactive in NIH3T3, Caco-2, and Madin-Darby canine kidney cells, indicating that the determinants of hepatocyte-specific expression reside within this region. The individual elements within the minimal promoter were investigated via transfection of HepG2 cells by a series of 20 mutant plasmids, each containing a 10-base pair sequential block mutation. Eight mutant constructs profoundly suppressed promoter activity; encompassing sequences from -66 to +4 nt, and +15 to +24 nucleotides, while no other 10-base pair mutation significantly interfered with minimal promoter activity. Deoxyribonuclease I footprint analysis of the minimal promoter revealed three bound regions; -92 to -74 (footprint C), -50 to -37 (footprint B), and -17 to +12 (footprint A). Gel mobility shift assays provided evidence for hepatocyte nuclear factor 1 binding within footprint A and a liver-enriched factor(s) that binds within a novel palindrome in footprint B. These studies indicate that three elements direct the basal and tissue-restricted expression of the rat ntcp promoter; a TATA element, the liver-enriched transcription factor hepatocyte nuclear factor 1, and an unknown liver-enriched factor that binds within a novel palindrome in footprint B.

CAMP motifs regulating transcription in the aquaporin 2 gene.

Genomic clones including the 5' flanking regions of the AQP2 (aquaporin 2) gene were isolated, and the promoter region was examined by transiently transfecting a promoter-luciferase reporter fusion gene into renal cultured epithelial cells. An orientation specific promoter for the AQP2 gene was found within the proximal 3 kb of 5'-flanking region. Minimal basal promoter activity of the AQP2 gene was found within 198 bp upstream from the transcription start site by deletion analysis. Sequencing the transcriptionally active region revealed a typical TATA box, adenosine 3',5'-cyclic monophosphate (cAMP) responsive element (CRE) and three putative CCAAT boxes in the proximal 1.2-kb region. Significantly, a GATA motif, AP1, AP2, and SP1 transcriptional factor consensus sites were also found in this region. Exposure to cAMP-enhancing agents (1 nM vasopressin or 20 mM forskolin and 250 mM 3-isobutyl-1-methylxanthine) showed that these agents increased luciferase activity in a parallel fashion, suggesting that vasopressin-induced AQP2 gene transcription is mediated through increases in intracellular cAMP in at least one renal cell type, the LLC-PK1 cells. The mechanism of cAMP responsiveness of AQP2 gene transcription was further studied using a series of deletion mutants in renal epithelial cells and other cell types. The cAMP regulatory motifs were shown to exist in a 50-bp sequence between -340 and -290 (containing CRE) and a 65-bp sequence (containing an AP2 site) between -150 and the ATG start site in LLC-PK1 cells. In rat inner medullary collecting duct (IMCD) cells, the cAMP regulatory motifs also exist in a 50-bp sequence between -340 and -290 (containing CRE) and in a 10-bp sequence between -160 and -150 (containing an SP1 site). These separate regions may cooperate to confer full cAMP inducibility to the AQP2 gene in a cell-specific manner.

Regulation of function of the murine luteinizing hormone receptor promoter by cis- and trans-acting elements in mouse Leydig tumor cells

The transcriptional activity of various lengths of the 5′-untranslated region (UTR) of the murine LH receptor (R) gene were studied using the luciferase reporter gene in transiently transfected mouse Leydig tumor cells (mLTC-1). Chinese hamster ovarian (CHO) and HeLa cells were used as controls. The basal transcriptional promoter activity in mLTC-1 cells resided within the first 173 base pairs (bp) of the 5′-UTR. Placing and LHR promoter fragment (bases −715 −56 ) in front of the Herpes simplex virus thymidine kinase (TK) minimal promoter resulted in a 7-fold increase in luciferase activity. Deletion of bases −56 to −173 of the above construct totally abolished the increased luciferase activity, brought about by the LHR promoter sequences. Basically similar results on LHR promoter function were observed using CHO cells. In contrast, no LHR promoter activity was detected in HeLa cells, indicating a cell specific nature of its function. The first 173 bp promoter domain is GC-rich, with several SP-1 binding domains, and it bound specifically nuclear proteins isolated from mLTC-1 and HeLa cells. RNAse protection assays reconfirmed the presence of several transcription initiation sites within the first 310 bp of the 5′-UTR, also in the absence of the cognate LHR coding sequences. The most distal site at bp −310 did not function in the absence of the first 173 bp of the 5′-UTR. Other transcription initiation sites were identified closer to the translation initiation site. hCG (50 μg/l), 8-bromo (Br)-cAMP (100 μmol/l) and cholera toxin (100 μg/l) displayed qualitatively similar negative effects on the LHR promoter activity in the transfected mLTC-1 cells when the constructs containing at least the first 565 bp of the LHR 5′-UTR were used, but the inhibitory effects were greatly decreased in constructs containing ≤304 bp of the promoter region. Hence, the hCG cAMP associated inhibitory effects interact with region(s) located mainly between bp −565 and −305 of the LHR promoter. The inhibitory role of cAMP on LHR gene expression was also confirmed at the level of hCO-binding and hCG stimulated cAMP production of mLTC-1 cells. In conclusion, the current results elucidate the cis- and trans-acting elements in the regulation of expression of the murine LHR gene in cultured mouse Leydig cells. The minimal basal promoter activity is within the first 173 nucleotides of the 5′-UTR and the structural elements of the negative LHR regulation by the cognate hormone and elevated cAMP levels are mainly located within nucleotides −305 to −565 of the 5′-UTR. The function of the murine LHR promoter is similar to, though not identical with that of the rat, but at variance with that of the human LHR gene.

The Promoter and 5' Flanking Sequences Controlling Human B29 Gene Expression

The product of the B-cell-specific B29 gene (B29, Ig beta, CD79b) is essential for Ig-mediated B-cell activation via the B-cell antigen receptor complex (BCR) on human and murine B lymphocytes. To better understand the regulation of this pivotal gene, we have analyzed the human genomic DNA sequence upstream of the B29 ATG start codon for transcriptional control activity. The human B29 gene lacks either a TATA or a CAAT box and transcription is initiated at multiple sites. The minimal promoter of the human B29 gene is contained within a 193-bp region 5' of these multiple start sites. This minimal promoter exhibits B-cell-specific activity and contains SP1, ETS, OCT, and IKAROS/LYF-1 transcription factor motifs. All these motifs are strikingly conserved in sequence and placement relative to the previously characterized murine B29 promoter. Additional upstream gene segments dramatically affected B29 minimal promoter activity. A newly identified motif called the B29 conserved sequence (BCS), found upstream of both human and murine B29 promoters, appears to stimulate B29 transcription through a novel mechanism. A single BCS had little effect either on the minimal B29 promoter or on a heterologous promoter. Instead, the BCS stimulated transcription by counteracting 5' negative regulatory DNA sequences that block the activity of the B29 minimal promoter in its absence. These findings indicate that B29 gene expression is controlled by the complex interplay of positive and negative regulatory elements.

Unique genomic structure and expression of the mouse alpha 2,8-sialyltransferase (ST8Sia III) gene.

The mouse Sia alpha 2,3Gal beta 1, 4GalNAc alpha 2,8-sialyltransferase (ST8Sia III) genomic gene, whose transcripts are only expressed in fetal and newborn brain and testis, was isolated and its 5'-flanking region was analyzed. The gene was found to span about 8 kb and to be composed of only four exons. The genomic ST8Sia III gene is much smaller and its organization much simpler than other sialyltransferase genes so far reported, which span more than 25 kb and comprise seven or more exons. In particular, the sialyl motif L of ST8Sia III, which is a highly conserved region in all cloned sialyltransferases, was in one exon. In contrast, this motif is encoded by discrete exons in the other sialyltransferases. The ST8Sia III gene was highly expressed in the mouse brain and gave rise to at least three transcripts (2.1 kb, 2.4 kb, and 6.5 kb), which differed in the length of their 3'-untranslated regions through the alternative use of different polyadenylation sites. Primer extension and S1 nuclease protection analyses of mRNA prepared from newborn brain revealed that ST8Sia III gene expression started from a unique site at 382 nt upstream of ATG. Although the promoter region lacked an apparent TATA or CCAAT box and potential regulatory motifs, a transfection experiment involving neuroblastoma cells expressing ST8Sia III demonstrated the minimal promoter activity exhibited by the proximal region 418 bp upstream from the ATG codon, which suggests the presence of tissue-specific enhancer elements.

Structural and functional analysis of the promoter of the murine V gamma 1.1 T cell receptor gene.

The expression of the germ-line gene V gamma 1.1-C gamma 4 of the T cell receptor (TcR) gamma chain depends on interleukin (IL)-3 induction in hematopoietic cells, while in T cells, the rearranged gene is expressed constitutively. To understand the mechanism that controls TcR gamma gene expression, we cloned and characterized the structure and function of the V gamma 1.1-C gamma 4 TcR promoter. IL-3-dependent cell lines and T cell lines utilized the same transcriptional start sites. In chloramphenicol acetyltransferase (CAT) assays, the minimal 70-bp promoter confers strong transcriptional activity which is 50-60% of the Moloney long terminal repeat promoter activity. The 500-bp promoter region linked to the CAT gene exhibits IL-3 dependency similar to the endogenous TcR gamma gene. The immediate 3' and 5' flanking sequences inhibit the promoter activity two- to fourfold. The promoter lacks an obvious TATA box or CAAT box sequences, but contains a GC box in the untranslated region 3' to the promoter. The GC box is the core sequence of the element which binds Sp1-like proteins. Cloning of this Sp1 binding element in front of the thymidine kinase (TK) promoter and mutations generated in this site demonstrate its function as a silencer. Ultraviolet cross-linking analysis with the Sp1 binding site from the TcR gamma promoter revealed binding of a 90-100-kDa protein in a T cell line (EL-4) and 40-50 and 90-100-kDa proteins in FDC-P1 cells. The possible function of the Sp1-like protein in silencing the minimal promoter activity is discussed.

Constitutive human steroid 21-hydroxylase promoter gene and pseudogene activity in steroidogenic and nonsteroidogenic cells with the luciferase gene as a reporter.

This study was directed toward initial comparison and characterization of the activities of the human steroid 21-hydroxylase gene (CYP21) and pseudogene (CYP21P) promoters. DNA fragments containing the promoter regions of CYP21 and CYP21P were amplified and cloned into promoterless luciferase reporter plasmids either containing or lacking an enhancer element. Cells of the nonsteroidogenic COS-1 cell line, and the steroidogenic Y-1 cell line were transiently transfected with these recombinant plasmids and a beta-galactosidase cotransfection control plasmid. Cellular lysates were analyzed for luciferase and beta-galactosidase activities. In the nonsteroidogenic system, transfectants with either the CYP21 or CYP21P upstream sequence in enhancer containing plasmids showed a 2.3 fold increase (p < .001) in light production over controls. In the steroidogenic Y-1 cell system, these same CYp21 and CYP21P transfectants showed a 14.3 (+/- 0.8) and 5.2 (+/- 0.6) fold increase in luciferase activity respectively (p < .001) Transfections with recombinant reporter plasmids lacking an enhancer produced light emission which was not significantly different than controls. These observations indicate that 1.) one or more of the 35 nucleotide differences between the CYP21 and CYP21P upstream regions alters a DNA recognition site important for transcriptional activation of this gene in steroidogenic cells, 2.) the steroidogenic milieu has a stimulatory effect on both CYP21 and CYP21P promoter activities, and 3.) based on the minimal promoter activity observed in either cell type transfected with constructs lacking an enhancer element, both of these promoter sequences are enhancer dependent under constitutive conditions in both steroidogenic and nonsteroidogenic cells.

Thyroid-specific expression and cyclic adenosine 3',5'-monophosphate autoregulation of the thyrotropin receptor gene involves thyroid transcription factor-1.

The chimeric chloramphenicol acetyltransferase (CAT) construct, pTRCAT5'-199, containing the TSH receptor (TSHR) minimal promoter, -199 to -39 base pairs (bp), exhibits the thyroid specificity and TSH/cAMP autoregulation evident in TSHR gene expression. The present report shows that a cis-acting element between -189 and -175 bp, which binds thyroid transcription factor-1 (TTF-1), is involved in both activities. The 22 bp between -199 and -178 contains a positive element important for expression of the TSHR minimal promoter in rat FRTL-5 thyroid cells. DNAase I footprinting shows that extracts from functioning FRTL-5, but not non-functioning FRT thyroid or Buffalo rat liver (BRL) cells, protect a region between -189 and -175 bp. The protection is duplicated by TTF-1, and the protected element has only a two-base mismatch from the consensus TTF-1 element identified in the thyroglobulin (TG) and thyroid peroxidase minimal promoters. Gel mobility shift analyses reveal that FRTL-5 thyroid cell nuclear extracts form a specific protein/DNA complex with this region, which is prevented by the TTF-1 binding element from the TG promoter; FRT and BRL cell nuclear extracts do not have TTF-1 and do not form this complex. A role for the TSHR/TTF-1 binding element in thyroid-specific expression of the TSHR gene is evidenced as follows. Overexpression of TTF-1 in FRT or BRL cells, which have no TTF-1, increased the activity of pTRCAT5'-199, but not pTRCAT5'-177, which has no TTF-1 binding element. A nonsense mutation of the TTF-1 binding element eliminated TTF-1-induced activation of TSHR promoter activity in FRT or BRL cells and reduced TSHR promoter activity in FRTL-5 thyroid cells. In contrast, mutation of this element to the TTF-1 consensus sequence of the TG or thyroid peroxidase promoter had no significant influence on TSHR promoter activity. The activity of the TSHR/TTF-1 binding element requires a functioning cAMP response element (CRE). Thus, TTF-1 activity is lost when the CRE site is mutated to a nonfunctional, nonpalindromic sequence; it is, in contrast, maximized when CRE activity is maximized by its mutation to a consensus AP1 element. TTF-1 phosphorylation is important for binding and activity. Thus, binding of TTF-1 to the TSHR/TTF-1 element is phosphatase-sensitive and is increased by treating nuclear extracts with the catalytic subunit of protein kinase A. Overexpression of the catalytic subunit of PKA enhances TTF-1-increased activity of the TSHR minimal promoter.(ABSTRACT TRUNCATED AT 400 WORDS)

The promoter of the Xwnt-5C gene contains octamer and AP-2 motifs functional in Xenopus embryos.

The Xwnt-5C gene is expressed in Xenopus embryos from the early gastrula stage onwards. The transcription of Xwnt-5C is regulated differentially with respect to transcript size, timing and localization. To gain insight into the generation of the Xwnt-5C expression pattern, we started to analyze the transcriptional regulation of this gene. We isolated Xwnt-5C genomic DNA sequences. By microinjection of chimaeric reporter constructs into Xenopus embryos we demonstrate that the upstream region contains a promoter functional in vivo. Of the several putative binding sites for trans-acting factors, present in a minimal promoter fragment, some have been studied in more detail. Mutations in an octamer motif and in an AP-2 consensus sequence interfere with the activity of the Xwnt-5C minimal promoter. In vitro binding assays with extracts from gastrula stage Xenopus embryos show that the octamer motif of the Xwnt-5C promoter can bind several Octamer binding factors, one of which is Oct1.

The minimal self-sufficient element in a murine G+C-rich promoter is a large element with imperfect dyad symmetry.

The murine adenosine deaminase gene has a structurally archetypal TATAA-box-deficient G+C-rich promoter. The three Sp1 binding sites of the promoter are neither necessary nor sufficient for promoter function. Minimal basal promoter activity resides within a 48-bp element downstream of the Sp1 binding sites. This element shows an imperfect dyad symmetry around the promoter's major transcriptional initiation site and contains at least two nuclear protein binding sites. The distinctive sequence characteristics and nuclear protein binding locations of this element led us to propose a model for how such promoters may function.

Modified binding of proteins from calcitonin-negative tumor cells to the neuroendocrine-specific CANNTG motif of the calcitonin gene.

Transcription of the calcitonin (CT) gene in the medullary thyroid carcinoma (MTC) cell line TT is modulated by a neuroendocrine-specific enhancer fragment (nucleotides -965 to -905) containing two CANNTG motifs (E2 and E3) and an ETs-like response element. To determine the cell-specific component of this fragment, oligonucleotides containing the individual elements were inserted in front of a minimal CT promoter and tested for reporter protein production in CT-positive (TT) and -negative (RO-D81 and HeLa) cells. In TT cells, using two copies of E2 or four copies of Ets increased minimal promoter activity a 20-40 fold. Using two copies of E3 had no effect on minimal promoter activity. In CT-negative MTC cells (RO-D81), the Ets response element was active but the two copies of E2 were not. Similar results were obtained with the non-neuroendocrine cell-line HeLa. I therefore concluded that E2 was the cell-type-specific component of the enhancer. An E2-specific binding protein was detected in both MTC cell lines but not in HeLa. This protein had different mobility and DNA-binding specificity in CT-positive TT cells and CT-negative RO-D81 cells. In conclusion, the CAGCTG motif of E2 modulated the cell-specific transcription of the CT gene, and its inactivation in CT-negative MTC cells correlated with modifications in its binding proteins.

Site-directed mutagenesis of hepatocyte nuclear factor (HNF) binding sites in the mouse transthyretin (TTR) promoter reveal synergistic interactions with its enhancer region

The transthyretin (TTR) gene is regulated by two DNA regions which elicit hepatocyte-specific expression: a proximal promoter and distal enhancer. The TTR promoter and enhancer are composed of at least eight DNA binding sites for three different hepatocyte nuclear factors (HNF), CCAAT/enhancer binding protein (C/EBP), and AP-1/cJun. Site directed mutations within each of the HNF binding sites in the TTR promoter were introduced to evaluate their contribution to transcriptional activity in hepatoma cells. The data indicate that the strong affinity HNF-3-S binding site (-106 to -94) is absolutely required for TTR promoter activity since several mutations in this site eliminate TTR expression in the context of its enhancer. Conversion of a second weak affinity HNF3-W site (-140 to -131) in the TTR promoter to a high affinity site resulted in higher levels of expression. TTR mutations that disrupted several weak affinity sites (HNF1, HNF3-W, and HNF4) only slightly diminished expression levels in the presence of the TTR enhancer. In contrast, when we deleted the TTR enhancer from these HNF mutant constructs, TTR expression decreased to undetectable levels. This result suggests cooperation between the factors binding to the TTR promoter and enhancer regions. These results also demonstrate that the HNF3-S site alone is not sufficient to activate TTR transcription, but rather requires the participation of three cell-specific factors to elicit minimal promoter activity. The complexity of this promoter design and the requirement for a minimal number of cell-specific factors to achieve transcription allows us to propose a model which may explain the maintenance of tissue-specific expression of TTR.

Identification and characterization of the promoter for the cytotactin gene.

The extracellular glycoprotein cytotactin is expressed in a characteristic and complex spatiotemporal sequence during development of the chicken embryo. To identify the various control elements underlying its expression, the promoter region of the cytotactin gene has been isolated and characterized. Clones were isolated from genomic libraries by using a fragment near the 5' end of the cDNA sequence. The sequence of this cDNA fragment was found to be distributed over two exons separated by a large first intron. The site of transcription initiation was determined by S1 nuclease and primer-extension mapping. Sequencing of a 4.3-kilobase (kb) genomic DNA clone that contains 3986 base pairs (bp) upstream of the RNA start site, the first exon, and part of the first intron revealed a number of sequence motifs implicated in the regulation and expression of eukaryotic genes. These included CCAAT boxes, phorbol ester-responsive elements, enhancer elements, and a consensus TATA sequence located 24 bp upstream of the major RNA cap site. The flanking sequence also contained a number of regions of dyad symmetry and direct repeats unique to cytotactin, as well as an array of A + T-rich sequences that resemble engrailed elements. Constructs containing fragments of the upstream region of the cytotactin gene fused to a promoterless gene for chloramphenicol acetyltransferase were transiently transfected into chicken embryo fibroblasts to define functional promoter sequences. Although sequences from -721 to +121 exhibited minimal promoter activity, the entire region between -3986 to +374 was required to yield maximal expression in chicken embryo fibroblasts. Transfection of the -3986/+374 chloramphenicol acetyltransferase plasmid into the human U251MG astrocytoma cells but not HT1080 fibrosarcoma cells resulted in chloramphenicol acetyltransferase expression, consistent with the observed synthesis of cytotactin protein only by the U251MG cell line. These data indicate that the chicken cytotactin promoter can control expression in a cell type-specific fashion within cells of another species. These studies provide a basis for the dissection of cis elements and trans factors that govern the developmental expression of the cytotactin gene.

Identification of Positive and Negative Regulatory Regions Controlling Expression of the Cartilage Matrix Protein Gene

A complex pattern of regulation of the cartilage matrix protein gene was revealed by transient expression experiments. A minimal promoter from positions -15 to +64 functioned in chondrocytes and fibroblasts. An enhancer located in the first intron exerted chondrocyte-specific stimulation on the minimal promoter activity. The same fragment, however, had a negative effect in fibroblasts. Between -334 and -15, a silencer was found which inhibited the gene expression driven from its homologous as well as heterologous promoters both in chondrocytes and fibroblasts. Additional positive and negative control regions were mapped further upstream of the promoter.

Identification of positive and negative regulatory regions controlling expression of the cartilage matrix protein gene.

A complex pattern of regulation of the cartilage matrix protein gene was revealed by transient expression experiments. A minimal promoter from positions -15 to +64 functioned in chondrocytes and fibroblasts. An enhancer located in the first intron exerted chondrocyte-specific stimulation on the minimal promoter activity. The same fragment, however, had a negative effect in fibroblasts. Between -334 and -15, a silencer was found which inhibited the gene expression driven from its homologous as well as heterologous promoters both in chondrocytes and fibroblasts. Additional positive and negative control regions were mapped further upstream of the promoter.