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PubMed1999

Genomic structure, chromosomal mapping, and muscle-specific expression of a PH domain-associated intronless gene, cded/lior.

The aim of our study was to isolate novel gene(s) involved in cell differentiation and embryonic liver development. Mouse cded/lior was identified from subtraction hybridization of embryonic liver cDNA libraries as well as an adult mouse liver genomic DNA library. The full open reading frame of cded/lior encodes a 131-amino acid protein with 71.88% overall similarity to the PH domain of rat PLC-gamma1. A gapped search with the C-terminal region of CDED/LIOR revealed a 36-41% similarity to several proteins related to signal transduction and cell replication, such as ORC1 and KSR. Northern blot analysis of adult mouse tissues shows a strong 2.6-kb transcript restricted to heart and skeletal muscle. RT-PCR utilizing cded/lior-specific primers demonstrates cded/lior mRNAs in heart, brain, and liver tissue throughout mid-embryonic mouse gestation. cded/lior maps to the distal end of mouse Chromosome (Chr) 2. Analysis of the genomic structure for cded/lior demonstrated a single exon gene that is not an alternatively spliced isoform of PLC-gamma1. Analysis of the cded/lior promoter region revealed a high GC-content, high ratio of CpG/GpC, multiple GC-boxes, the lack of a TATA box, CTF/NFI element, and two MyoD-MCK binding sites. These characteristics are also found in several genes important in the regulation of cell growth or DNA synthesis, such as transforming growth factor-beta1, c-Ha-ras, nerve growth factor, epidermal growth factor receptor, and DNA polymerase beta. These results suggest that cded/lior is a mesoderm/muscle-specific transcript that may be involved in the mesodermal inductive and regulatory interactions required for liver formation and embryonic development.

Amino Acid Sequence↗
PubMed1992

Multiple cis-acting elements of the proximal promoter region are required for basal level transcription of the H1(0) histone gene.

Basal level transcription of the mouse histone H1(0) gene is mediated by 531 base pairs of the promoter region. Deletion of the most distal upstream 80 bp of this fragment reduces transcription to very low values. By in vitro footprinting we demonstrate now that multiple factors bind to the DNA fragment localized between the 80 bp and the cap nucleotide. In addition to the presence of motifs for the binding of SP1, H1-box, H4TF-2 and TATA-box-factors, other not yet described protein-binding elements were identified. Internal deletions in the wild type promoter enclosing these motifs strongly restrict transcription. Furthermore, when one of these motifs was modified by site-directed mutagenesis a strong impairment of transcription followed. Thus for basal level transcription, in addition to the 80 bp distal fragment, cis-acting elements localized in the 450 bp proximal promoter region are required.

Animals↗
PubMed1996

Cloning the 5' flanking region of neuron-specific Hel-N1: evidence for positive regulatory elements governing cell-specific transcription.

A 5.4 kilobase-pair segment of DNA flanking the 5' end of Hel-N1 was isolated and characterized. Primer extension studies with normal human brain and neuroblastoma cells revealed a major and minor transcription-initiation site. Sequence analysis of the initial 536 bp upstream to the major start site revealed a core promoter (-1 to -181) which contained two CCAAT boxes, a weakly-conserved TATA box, and an SP1 site. This region was also moderately GC-rich (62%). Using a transient luciferase-reporter-gene assay, the core promoter was found to be essential for basal transcription both in neural (PC12) and non-neural (HeLa and glial) cell types. Two positive regulatory elements, however, were identified in the initial 536 bp (-1 to -181 and -182 to -350) which produced a five- to six-fold increase in transcriptional activity in PC12 cells vs. HeLa or glial cells. These elements, therefore, were sufficient to confer cell-specific enhanced transcription and likely contribute to the neuronal specificity of Hel-N1 mRNA expression.

Animals↗
PubMed1989

Schizosaccharomyces pombe U4 small nuclear RNA closely resembles vertebrate U4 and is required for growth.

The single-copy gene snu4, which encodes the small nuclear RNA (snRNA) U4, has been cloned and sequenced. Schizosaccharomyces pombe U4 is 128 nucleotides in length, similar in size to vertebrate U4 and shows substantial primary and secondary structure homology. The gene lacks sequences closely resembling vertebrate snRNA transcription signals, but has a TATA box at -33 to -30; TATA sequences flanked by several additional conserved nucleotides are found in the same position in the 5' regions of other snRNA genes from Schiz. pombe. The cloned snu4 gene was disrupted by transposon mutagenesis and used to replace one chromosomal copy of snu4 in a diploid strain. On sporulation snu4- haploid strains could not be recovered, demonstrating that U4 is required, at least for spore germination. Haploid snu4- strains are viable if they also carry snu4+ on a replicating plasmid but are unable to loose the plasmid under non-selective growth, demonstrating a continuous requirement for U4 for viability.

Animals↗
PubMed1986

Heat shock regulatory elements function as an inducible enhancer in the Xenopus hsp70 gene and when linked to a heterologous promoter.

The Xenopus hsp70 promoter contains three copies of the consensus heat shock element (HSE) between positions -260 and -100. When the gene is transfected into mammalian cells, maximal heat-induced expression requires two HSEs in addition to a CCAAT box located next to the TATA box. The HSE-containing region can be separated from the CCAAT/TATA region without affecting expression of the gene, and it can enhance transcription of a linked beta-globin gene upon heat shock. It thus has the properties of a heat-inducible enhancer. Such an enhancer can also be generated by duplication of HSE sequences from the Drosophila hsp70 promoter, which were previously identified as an upstream promoter element and are known to bind a purified heat shock transcription factor in vitro.

Animals↗
PubMed1998

Structure and organization of the genes encoding mouse small proline-rich proteins, mSPRR1A and 1B.

Two genomic clones comprising the entire coding sequence of mouse SPRR1A and 1B genes were isolated and sequenced. Sequence analysis of the 1A and 1B genomic clones indicated that both genes contain two exons separated by an intron slightly larger than 1.1kb in size (1147 and 1152nt, respectively). This type of genomic structure is identical to the counterpart of human SPRR1 gene and other genes encoding for cornified envelope proteins. Primer extension analysis using 1A and 1B gene-specific primers indicates that 1A gene is expressed in squamous tissues such as skin and esophagus, whereas 1B gene is expressed in papilloma tumors but not in squamous tissues. The first 300nt of 5'-flanking region of the mouse SPRR 1A and 1B genes reveal an overall approximately 50% identity to the human counterpart. However, there is a high degree of identity (?75%) at the promoter region containing a TATA box and TRE/TRE-like motifs. Both TATA and TRE/TRE-like motifs are almost identical in sequence and positions to those found in the counterpart of human promoter. Using transient transfection for the analysis of promoter activity, we observed that both 1A and 1B 5'-flanking regions contain the promoter activity to direct the expression of the reporter gene, chloramphenicol acetyltransferase, in airway epithelial cells in a fashion similar to that observed in the human counterpart. These results indicate a conserved nature of genetic structure and regulation of SPRR1 gene expression between human and mouse.

Amino Acid Sequence↗
PubMed1999

cDNA cloning of mouse tumor necrosis factor-alpha converting enzyme (TACE) and partial analysis of its promoter.

Tumor necrosis factor-alpha (TNFalpha) is a cytokine that induces pleiotropic inflammatory reactions. Soluble TNFalpha is released from its membrane-bound precursor by TNFalpha converting enzyme (TACE)/a disintegrin and metalloproteinase 17 (ADAM17). We have recently cloned the mouse TACE complete cDNA and the 5' flanking promoter region of the gene. Two versions of the mouse TACE cDNA having a coding region of 2541bp were obtained: one was about 4.1kb and the other was 4.4kb in length, in which only the length of the 3' UTR was different. Rapid amplification of 5' cDNA ends suggested that there were multiple transcriptional start sites. From the coding sequence, 827 amino acids were deduced which were 91.9 % identical to those of human TACE. Northern blot analysis indicated that the major transcript was approx. 4.4kb product in the mouse. The mouse TACE mRNA was ubiquitously expressed, and was particularly high in the lung. The proximal promoter contained multiple AP2 and Sp1 transcription factor binding sites and included a GC box and a CCAAT box, but lacked a consensus TATA box. Reporter gene analysis using RAW264.7 cells showed that the fragment at nt -290 to -1 from the translation start site has a strong promoter activity, and appeared to be essential for transcription of the mouse TACE mRNA. Finally, we found that the mouse TACE promoter at nt -2304 to -1 also worked in NIH3T3, 3T3L1 and C6 cell lines.

3' Untranslated Regions↗
PubMed2002

Sequencing of the putative promoter region of the cocaine- and amphetamine-regulated-transcript gene and identification of polymorphic sites associated with obesity.

OBJECTIVE: We tested the hypothesis that polymorphisms in the cocaine- and amphetamine-regulated-transcript (CART) gene is associated with the development of obesity. SUBJECTS: Five-hundred and twenty-eight subjects (325 men and 203 women) aged 49.6+/-11.0 y with body mass index (BMI) of 26.9+/-5.1. MEASUREMENTS: The 5(')-flanking region of the CART gene was cloned using adaptor-ligated genomic DNA fragments. The CART gene including the 5(')-flanking region was screened for mutation by PCR-single strand conformation polymorphism and direct sequencing. Associations between polymorphisms and obesity were investigated by PCR-restriction fragment length polymorphism analysis and direct sequencing. RESULTS: The 5(')-flanking region of the CART gene up to -1072 bp from the transcription initiation site was sequenced. The region contained a putative cyclic AMP-responsive element and four E-box motifs upstream of a TATA box. Six polymorphic sites were identified in the upstream region; A-->G at -156, T-->C at -390, T-->G at -484, G-->T at -915, G-->C at -929 and C-->T at -962. The nucleotide substitution at -156 was significantly associated with greater BMI (P=0.036). The allele frequency of the -156 variant was significantly higher in obese subjects with BMI > or = 30 than in non-obese subject (0.41 vs 0.32, P=0.0076). The -929 variant allele in linkage disequilibrium with the -156 variant was also more common in obese subjects. No mutation was found in the coding regions. A single nucleotide insertion/deletion polymorphism at +1355 in the 3(') untranslated region was not associated with obesity. CONCLUSION: The 5(')-flanking region of the CART gene was highly polymorphic. The -156 polymorphism or polymorphisms in linkage disequilibrium with the site may be associated with genetic predisposition to obesity.

Base Sequence↗
PubMed2002

Characterization of the promoter for the mouse alpha 3 integrin gene.

The alpha 3 beta 1 integrin is an adhesion receptor for extracellular matrix proteins including isoforms of laminin, and the changes of its expression level in various cancer cells are thought to cause their malignant phenotypes. We have cloned an approximately 4 kb DNA fragment of the 5'-flanking region of the murine alpha 3 integrin gene and analyzed its promoter activity. Transfection of MKN1 gastric carcinoma cells with serially truncated segments of the 5'-flanking region linked to a luciferase gene indicated that a 537-bp SalI/SacI fragment upstream of exon 1 was sufficient to promote high level gene expression. By 5'-rapid amplification of cDNA ends (5'-RACE) using a cap site-labeled cDNA library, we determined one major and one minor transcription start sites in this region. The murine alpha 3 integrin gene was found to contain a CCAAT box, but to lack a TATA box. Luciferase assay following transfection with a series of deletion constructs of the SalI/SacI fragment revealed that the sequence between positions -260 and -119 bp (relative to the major transcription start site) is required for efficient transcription in gastric carcinoma cells. The sequence analysis of this segment showed the presence of several consensus sequences for transcription factors including Ets, GATA and MyoD/E-box binding factors. The introduction of mutation in one of the Ets-binding sequences greatly decreased its promoter activity, suggesting that the transcription of the alpha 3 integrin gene in these cells is regulated by the Ets-family of transcription factors.

5' Flanking Region↗
PubMed2000

p300 collaborates with Sp1 and Sp3 in p21(waf1/cip1) promoter activation induced by histone deacetylase inhibitor.

We have reported that histone acetylation induced by trichostatin A (TSA) promotes p21(waf1/cip1) (p21) expression, the GC-box located just upstream of TATA box was responsible for TSA-induced promoter activation, and both Sp1 and Sp3 were the working activator of this GC-box. To understand the molecular pathway from histone acetylation to this Sp1 family factors-mediated promoter activation, we investigated the function of p300, one of the histone acetyltransferase, in the present work. The evidence supporting the linkage between p300 and TSA-induced p21 promoter activation were realized from the following findings: 1) cotransfection of p300 elevated p21 promoter activity, and this elevation was dependent on TSA-responsive GC-box; 2) TSA-induced promoter activation was blocked by the introduction of p300 dominant-negative mutant into cells; and 3) Sp1- or Sp3-mediated activation was also suppressed by this p300 dominant-negative mutant. Our data also suggested that p300 collaborates with Sp1 in a way which is different from that when p300 collaborates with p53 in p21 transcription.

Animals↗
PubMed2004

Glucocorticoid-inducible gene expression vectors for use in Drosophila melanogaster Schneider 2 cells.

Inducible, vector-based, expression systems that allow fine control of transgene expression are gaining more and more use in fundamental research as well as in therapeutic applications. In an effort to develop a tightly regulated heterologous expression system for Drosophila Schneider 2 cells, three different inducible reporter constructs were compared. These comprised six copies of the glucocorticoid response element fused to one of three distinct types of Drosophila gene promoters: (1) a TATA-box containing, (2) a TATA-less and (3) a bidirectional core sequence. These were fused to a luciferase reporter gene. The promoter constructs displayed different basal as well as agonist-induced activities. The implications of the observations made are discussed in the context of promoter properties and of induction of genes that may be studied in Drosophila.

Animals↗
PubMed1998

Isolation and characterization of kidney-specific ClC-K1 chloride channel gene promoter.

The rat ClC-K1 chloride channel is a kidney-specific member of the ClC chloride channel family found exclusively in the thin ascending limb of Henle's loop in the kidney. To gain insight into the mechanism(s) of kidney-specific expression of ClC-K1, a genomic clone that contains the 5'-flanking region of the rat ClC-K1 gene was isolated. A single transcription start site was located 84 bp upstream of the start codon. The sequence of the proximal 5'-flanking region contained an activator protein (AP)-3 site, a glucocorticoid-responsive element, several AP-2 sites, and several E-boxes, but it lacked a TATA box. To functionally express the promoter, the approximately 2.5-kb pair 5'-flanking region was ligated to a luciferase reporter gene and transfected into inner medullary (IM) cells, a stable ClC-K1-expressing cell line derived from the inner medulla of simian virus 40 transgenic mouse, and ClC-K1-nonexpressing cell lines. Luciferase activity was 7-to 24-fold greater in IM cells than those in nonexpressing cell lines, suggesting that the approximately 2.5-kb fragment contained cis-acting regulatory elements for cell-specific expression of the ClC-K1 gene. Deletion analysis revealed that this cell-specific promoter activity in IM cells was still present in the construct containing 51 bp of the 5'-flanking region but was lost in the -29 construct, clearly demonstrating that the 22 bp from -51 to -30 have a major role in the cell-specific activity of the ClC-K1 promoter. These 22 bp consist of purine-rich sequence (GGGGAGGGG-GAGGGGAG), and gel-retardation analysis demonstrated the existence of a specific protein(s) binding to this element in IM cells. These results suggest that the novel purine-rich element may play a key role in the activity of the ClC-K1 gene promoter.

Animals↗
PubMed2000

Purification and cloning of type A/B hnRNP proteins involved in transcriptional activation from the Rat spi 2 gene GAGA box.

The GAGA box of the rat serine protease inhibitor 2 (spi 2) genes not only acts as a basal promoter element, but also mediates transcriptional activation by growth hormone and interleukin-6. The GAGA box is separated from the TATA box by only 12 bp, and this close association is required for efficient transcription. Hence, the GAGA box may influence transcription efficiency through interactions between GAGA box binding proteins and some components of the RNA polymerase II complex. Here we report the cloning of two GAGA box-binding proteins termed p38 and p40, that belong to the type A/B heterogeneous nuclear ribonucleoprotein subgroup. GAGA box mutations that diminish the affinity for p38 and p40 decrease basal and GH-induced reporter gene expression. Furthermore, nuclear extracts depleted of p38 and p40 can no longer support GAGA box-dependent in vitro transcription. Therefore, two polypeptides previously assigned to a family of RNA processing proteins also act as DNA-binding, promoter-specific transcription factors.

Amino Acid Sequence↗
PubMed2000

Transcription factor Sp3 activates the liver/bone/kidney-type alkaline phosphatase promoter in hematopoietic cells.

The promoter region of the liver/bone/ kidney-type alkaline phosphatase gene was examined to define the cis-acting regulatory sequences and transcription factors responsible for its expression in hematopoietic cells. Transient transfection experiments revealed that regions deleted up to -154 base pairs upstream from the transcription initiation site had significant activities to induce bacterial chloramphenicol acetyltransferase gene. The shortest DNA fragment was found to contain three GC boxes in addition to a TATA box. Electrophoretic mobility shift assay and Southwestern analysis showed that Sp3 could bind to the fragment. Western blot analysis also detected Sp3 protein in eluate from the DNA probe mixed with the nuclear extracts. Through the use of Drosophila Schneider cells that lack the Sp1 family of transcription factors, Sp3 was shown to activate the basal promoter in a dose-dependent manner. When the amount of Sp3 was limited, the most proximal GC box was found to be critical for the basal promoter activity.

Alkaline Phosphatase↗
PubMed1988

A bidirectional promoter is regulating the Drosophila ras2 gene.

We isolated and delimitated the Drosophila ras2 promoter region, determined its sequence and mapped the transcription units expressed in this region. The results showed that the Drosophila ras2 gene is flanked by another transcription unit, which codes for two larger transcripts, 2.5 and 2.9 kb long. Orientation experiments, in which sense and antisense RNA probes were used, revealed that both these and the ras2 transcripts are synthesized from different DNA strands. Thus, the flanking transcription unit is in the opposite polarity relative to the ras2 gene. The transcription start sites of the ras2 gene and the flanking transcription unit were determined by external primer extension with T4 DNA polymerase and by RNAase-protection assay and were found to be only 94 nucleotides apart. Apparently, the Drosophila ras2 promoter is a bidirectional promoter. Nucleotide sequence analysis revealed that the 5'-end of the ras2 transcript is within an inverted repeat of the insect cap box. TATA- and GC-like boxes were also found. Analysis of direct and inverted repeats in the promoter region suggested that it is asymmetrical. To demonstrate promoter activity, each side of the ras2 bidirectional promoter was fused to the bacterial chloramphenicol acetyltransferase (CAT) gene and tested by transfecting Drosophila Schneider 2 culture cells. Significant CAT activity was obtained with both transcription fusions.

Animals↗
PubMed1998

Analysis of selective gene activation in yeast by differential display.

TATA box binding protein-associated factors (TAF(II)s) are dispensable for transcription of most genes in yeast. To further investigate the in vivo functions of TAF(II)s, differential display was used to identify a small subset of yeast genes whose transcription is dependent on yeast TAF(II)145, the core TAF(II) component that contacts TATA box-binding protein (TBP). Messenger RNA profiles derived from a wild-type TAF(II)145 strain and a temperature-sensitive taf(II)1145 strain were analyzed. Those genes whose messenger RNA level was greatly reduced in the temperature-sensitive taf(II)145 strain were cloned and further characterized. The procedure for performing differential display described here is modified from protocols provided by the manufacturer (Display Systems) and optimized for the yeast system.

Binding Sites↗
PubMed1993

A new factor related to TATA-binding protein has highly restricted expression patterns in Drosophila.

The TATA-binding protein TBP is necessary for the transcription of eukaryotic genes. Multi-protein complexes formed by TBP and different TBP-associated factors are involved in the initiation of transcription by polymerases I and II, and probably III as well. During the formation of an active initiation complex, TBP makes specific contacts with other proteins, for example TFIIB and RNA polymerase II (refs 2-4). Here we describe the cloning and characterization of a Drosophila gene product with considerable sequence similarity to TBP and a highly restricted expression pattern in the embryo. This TBP-related factor is a DNA-binding protein but is not likely to be a basal transcription factor. Our results suggest that TBP-related factor is a sequence-specific transcription factor that shares the DNA-binding properties of TBP.

Animals↗
PubMed1998

Transcription factor IIA derepresses TATA-binding protein (TBP)-associated factor inhibition of TBP-DNA binding.

The interaction of the general transcription factor (TF) IIA with TFIID is required for transcription activation in vitro. TFIID consists of the TATA-binding protein (TBP) and TBP associated factors (TAFIIs). TFIIA binds directly to TBP and stabilizes its interaction with TATA-containing DNA. In this work, we present evidence that TAFIIs inhibit TBP-DNA and TBP-TFIIA binding, and that TFIIA stimulates transcription, in part, by overcoming this TAFII-mediated inhibition of TBP-DNA binding. TFIIA mutants modestly compromised for interaction with TBP were found to be significantly more defective in forming complexes with TFIID. Subtle changes in the stability or conformation of the TFIIA-TBP complex resulted in a failure of TFIIA to overcome TAFII-mediated inhibition of TBP-DNA binding and transcription function. Inhibition of TBP-DNA binding by TAFIIs could be partially relieved by limited proteolysis of TFIID. Proteolysis significantly stimulated TFIIA-TFIID-TATA binding in both electrophoresis mobility shift assay and DNase I footprinting but had little effect on complexes formed with TBP. Recombinant TAFII250 inhibits TBP-DNA binding, whereas preincubation of TFIIA with TBP prevents this inhibition. Thus, TFIIA competes with TAFII250 for access to TBP and alters the TATA binding properties of the resulting complex. Transcriptional activation by Zta was enhanced by temperature shift inactivation of TAFII250 in the ts13 cell line, suggesting that TAFII250 has transcriptional inhibitory activity in vivo. Together, these results suggest that TAFIIs may regulate transcription initiation by inhibiting TBP-TFIIA and TBP-DNA complex formation.

DNA↗