S1 Nuclease Protection Analysis Research Articles

Transcriptional activation signals found in the Epstein-Barr virus (EBV) latency C promoter are conserved in the latency C promoter sequences from baboon and Rhesus monkey EBV-like lymphocryptoviruses (cercopithicine herpesviruses 12 and 15).

The Epstein-Barr virus (EBV) EBNA2 protein is a transcriptional activator that controls viral latent gene expression and is essential for EBV-driven B-cell immortalization. EBNA2 is expressed from the viral C promoter (Cp) and regulates its own expression by activating Cp through interaction with the cellular DNA binding protein CBF1. Through regulation of Cp and EBNA2 expression, EBV controls the pattern of latent protein expression and the type of latency established. To gain further insight into the important regulatory elements that modulate Cp usage, we isolated and sequenced the Cp regions corresponding to nucleotides 10251 to 11479 of the EBV genome (-1079 to +144 relative to the transcription initiation site) from the EBV-like lymphocryptoviruses found in baboons (herpesvirus papio; HVP) and Rhesus macaques (RhEBV). Sequence comparison of the approximately 1,230-bp Cp regions from these primate viruses revealed that EBV and HVP Cp sequences are 64% conserved, EBV and RhEBV Cp sequences are 66% conserved, and HVP and RhEBV Cp sequences are 65% conserved relative to each other. Approximately 50% of the residues are conserved among all three sequences, yet all three viruses have retained response elements for glucocorticoids, two positionally conserved CCAAT boxes, and positionally conserved TATA boxes. The putative EBNA2 100-bp enhancers within these promoters contain 54 conserved residues, and the binding sites for CBF1 and CBF2 are well conserved. Cp usage in the HVP- and RhEBV-transformed cell lines was detected by S1 nuclease protection analysis. Transient-transfection analysis showed that promoters of both HVP and RhEBV are responsive to EBNA2 and that they bind CBF1 and CBF2 in gel mobility shift assays. These results suggest that similar mechanisms for regulation of latent gene expression are conserved among the EBV-related lymphocryptoviruses found in nonhuman primates.

Cloning, characterization and tissue-specific expression of the gene encoding bovine keratocan, a corneal keratan sulfate proteoglycan.

Keratocan is one of three major keratan sulfate proteoglycans characteristically expressed in cornea. We reported previously the sequence of bovine Kera cDNA. In this study, the complete bovine Kera gene was cloned and sequenced, and its expression pattern was determined. The Kera gene is composed of three exons and two introns that span 8.830kb of the bovine genome. The first exon contains 287 nucleotides of 5'-UTR sequence. Both of the two large introns of 1322 and 4178bp contain (CA)n repeats. The bovine Kera gene has a TATA box that is located 28bp upstream from tsp. Primer extension and S1 nuclease protection analyses were used to determine the major tsp. RPA indicate that cornea and sclera are the two tissues with the highest expression of Ktcn mRNA. This restricted expression in eye tissues, as well as the unique modification of keratocan with long keratan sulfate chains in cornea, suggests that this molecule may be important in developing and maintaining corneal transparency.

Cloning and Functional Characterization of the 5′-Flanking Region of Human Methionine Adenosyltransferase 2A Gene

Methionine adenosyltransferase (MAT) is a critical cellular enzyme which catalyzes the formation ofS-adenosylmethionine, the principal methyl donor. In mammals, two different genes, MAT1A and MAT2A, encode for liver-specific and non-liver-specific MAT, respectively. We have cloned and characterized a 1.4-kb 5′-flanking region of the human MAT2A (GenBank Accession No. AF039088). Two major transcriptional start sites were identified by primer extension and S1 nuclease protection analysis; one was within 10 nucleotides downstream and the other was located at 158 nucleotides upstream from the consensus TATA box, respectively. The promoter is highly GC rich (75%) in the first 300 base pairs and contains several Sp-1 binding sites, a C/EBP, a HSF2, a STATx, a c-Myb, several v-Myb, and numerous GATA consensus binding sites. The human MAT2A promoter was able to efficiently drive luciferase expression in both Jurkat and 293 cells, but sequential deletion analysis of the promoter revealed that different regions of the promoter are important for cell-specific MAT2A expression.

Analysis of the in vivo decay of the Escherichia coli dicistronic pyrF-orfF transcript: evidence for multiple degradation pathways

Messenger RNA decay in Escherichia coli is slowed in pnp-7 (PNPase) rnb-500 (RNase II) rne-1(RNase E) multiple mutants. We have used Northern blots, S1 nuclease protection and primer extension analysis to map 18 endonucleolytic cleavage sites within the pyrF-orfF dicistronic transcript. Although examination of a total of 27 cleavage sites including those determined for the monocistronic trxA transcript revealed a complex pattern, the central four nucleotides within a cluster of 12 residues encompassing the cleavage sites showed a definite A/U preference. Also of interest was the processing of the dicistronic transcript to remove the downstream orfF sequence as a stable but untranslated RNA fragment. The data provide further support for the hypothesis that multiple decay pathways are involved in the decay of a single transcript. In particular, the pyrF-orfF transcript apparently can be degraded either in the 5′ to 3′ or the 3′ to 5′ direction. Our results are discussed in light of current models of mRNA decay involving polyadenylation and multiprotein decay complexes.

Recharacterization of the start sites for the major human transforming growth factor-β1 mRNA

The start sites for the major human TGF-β1 transcripts have been reexamined. A comparison of ribonuclease and S1 nuclease protection analyses on native TGF-β1 mRNA and in vitro transcribed human TGF-β1 transcripts of defined sizes places the most 5′ start site for the native TGF-β1 message approx. 50 nucleotides upstream from the previously published start site at base +1. Furthermore, the same techniques indicate that the apparent downstream start site at base +271 is an artefact due to the presence of an A+T-rich island in the middle of an otherwise highly G+C-rich sequence. This is not apparent if S1 nuclease protection is used alone, which emphasizes the importance of using the two techniques in combination for this type of analysis. Thus the major 2.5 kb TGF-β1 band seen on Northern blots comprises only mRNA transcribed from the more upstream of the two previously characterized promoters. This has important implications both for the transcriptional and translational regulation of this growth factor.

Interactions of OxyR with the promoter region of the oxyR and ahpC genes from Mycobacterium leprae and Mycobacterium tuberculosis.

In contrast to the intact oxyR gene (a homolog of the central regulator of peroxide stress response in enteric bacteria) in Mycobacterium leprae, this gene is inactive in all strains of M. tuberculosis. In both species, oxyR is divergently transcribed from ahpC, which encodes a homolog of alkyl hydroperoxide reductase. To initiate investigations of the regulation of oxidative stress in mycobacteria and consequences of the elimination of oxyR in M. tuberculosis, in this work we tested the hypothesis that mycobacterial OxyR acts as a DNA binding protein and analyzed its interactions with the oxyR and ahpC promoters. M. leprae OxyR was overproduced and purified, and its binding to the oxyR-ahpC intergenic region of M. leprae was demonstrated. By using a sequential series of overlapping DNA fragments, the minimal OxyR binding site was delimited to a 30-bp DNA segment which included a palindromic sequence conforming with the established rules for the LysR family of regulators. A consensus sequence for the mycobacterial OxyR recognition site (cTTATCggc-N3-gccGATAAg) was deduced based on its conservation in different mycobacteria. A variance in two potentially critical nucleotides within this site was observed in M. tuberculosis, in keeping with its reduced affinity for OxyR. Transcription of plasmid-borne M. leprae oxyR and ahpC was investigated in M. smegmatis and M. bovis BCG by S1 nuclease protection and transcriptional fusion analyses. Two mRNA 5' ends were detected in each direction: (i) P1oxyR and P2oxyR and (ii) P1ahpC and P2ahpC. The binding site for OxyR overlapped P1oxyR, reminiscent of the autoregulatory loops controlling expression of oxyR in enteric bacteria and characteristic of the LysR superfamily in general. This site was also centered 65 bp upstream of P1ahpC, matching the usual position of LysR-type recognition sequences in relationship to positively controlled promoters. Superimposed on these features was the less orthodox presence of multiple transcripts and their unique arrangement, including a region of complementarity at the 5' ends of the P2ahpC and P2oxyR mRNAs, suggesting the existence of complex regulatory relationships controlling oxyR and ahpC expression in mycobacteria.

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.

Zonal distribution of 11 beta-hydroxysteroid dehydrogenase types 1 and 2 messenger ribonucleic acid expression in the rat placenta and decidua during late pregnancy.

Glucocorticoid action in several target tissues is dependent on expression of 11 beta-hydroxysteroid dehydrogenase (11 beta-HSD), and in the placenta 11 beta-HSD is thought to regulate transfer of active glucocorticoid to the fetus. This study compared expression of the two recognized 11 beta-HSD enzymes, types 1 and 2, in the rat placenta and decidua on Days 16 and 22 of gestation (term = Day 23). According to S1 nuclease protection analysis, although mRNA for 11 beta-HSD-1 was only just detectable in the labyrinth zone on Day 16, by Day 22 this expression had increased almost 20-fold. There was also an increase (approximately 2-fold) in 11 beta-HSD-1 mRNA in the basal zone between Days 16 and 22. In Day 16 decidua, 11 beta-HSD-1 mRNA was also highly expressed, but insufficient tissue was available for analysis on Day 22. Western blot analysis showed that immunoreactive 11 beta-HSD-1 (molecular mass 34 kDa) was present in those tissues with the highest 11 beta-HSD-1 mRNA expression (Day 16 decidua and Day 22 labyrinth zone). With respect to mRNA for 11 beta-HSD-2, high expression was observed in the decidua and labyrinth zone at Day 16, but in the latter this expression then declined 90% by Day 22. In contrast, expression of mRNA for 11 beta-HSD-2 increased more than 3-fold in the basal zone over the same period. Consistent with coexpression of the two 11 beta-HSD enzymes, both 11-oxoreductase and 11 beta-dehydrogenase bioactivity were clearly evident in all tissues, and each varied with stage of gestation. Specifically, 11 beta-dehydrogenase activity in the basal zone increased from 38 +/- 2% (mean +/- SEM) on Day 16 to 56 +/- 2% on Day 22, while 11-oxoreductase activity fell from 55 +/- 3% to 43 +/- 2% over the same period. In contrast, 11 beta-dehydrogenase activity in the labyrinth zone fell with advancing pregnancy (Day 16: 63 +/- 2%; Day 22: 48 +/- 2%). Both 11-oxoreductase (58 +/- 3%) and 11 beta-dehydrogenase (38 +/- 4%) activities were also evident in decidua at Day 16. In conclusion, this study shows that expression of 11 beta-HSD-1 and -2 is zone-specific in the placenta and maternal decidua. Moreover, opposite changes in the expression of the two enzymes occur in the basal and labyrinth zones of the placenta over the last days of pregnancy, indicative of distinct regulatory mechanisms and functional significance for the enzymes in the two placental zones.

Isolation and analysis of inducibility of the rat N-methylpurine-DNA glycosylase promoter.

Alkylations at base nitrogens in DNA are removed by excision repair, the first step of which is catalyzed by the repair enzyme N-methylpurine-DNA glycosylase (MPG). To study regulation of MPG expression, we have cloned the rat MPG promoter. A cosmid clone containing the rat MPG gene was isolated from a library using rat MPG cDNA as a probe. The 5' part of the MPG gene and the nontranscribed 5'-flanking region were isolated and characterized. Transcription start sites of the rat MPG gene were identified by primer extension and S1 nuclease protection analysis of RNA from primary rat hepatocytes. Promoter activity of the 5'-flanking noncoding region was shown by transfection in H4IIE rat hepatoma cells of various genomic MPG fragments cloned in front of the reporter gene chloramphenicol acetyltransferase. The rat MPG promoter does not contain a TATA box, but has a CCAAT sequence element and putative binding sites for the transcription factors Sp1, AP-2, AP-3, Ets-1, PEA3, NF-1, p53, c-Myc, NF-kappa B, and the glucocorticoid receptor. The activity of the rat MPG promoter was found to be inducible by the tumor promoter TPA and UV light, but not to a significant extent by methylating agents and ionizing radiation.

Molecular Cloning and Genomic Analysis of Mouse Galβ1,3GalNAc-specific GalNAc α2,6-Sialyltransferase

cDNA and genomic clones encoding mouse Galbeta1, 3GalNAc-specific GalNAc alpha2,6-sialyltransferase (ST6GalNAc II) were isolated, and the structure organization of the gene was determined. The predicted amino acid sequence is 57.4% identical to the chick ST6GalNAc II sequence but 33.8% identical to the chick ST6GalNA I (GalNAc alpha2, 6-sialyltransferase) sequence. The ST6GalNAc II gene is constitutively expressed in various mouse tissues but highly expressed in lactating mammary gland and adult testis. The gene contains nine exons spanning about 25 kilobases of genomic DNA and encodes a messenger RNA of 1995 nucleotides. Primer extension and S1 nuclease protection analysis of submaxillary gland mRNA showed that the transcription of the ST6GalNAc II gene starts from 68 nucleotides upstream from the translation start site. Characterization of 5'-flanking genomic regions indicated that the Galbeta1,3GalNAc-specific GalNAc alpha2,6-sialyltransferase promoter is embedded in a G+C-rich domain and contains no TATA or CAAT box but has putative binding sites for transcription factors Sp1 and AP-2. Transient transfection experiments involving luciferase reporter genes demonstrated promoter activity in NIH3T3 cells.

Genomic Organization and Glucocorticoid Transcriptional Activation of the Rat Na+/H+ Exchanger Nhe3 Gene

The activity of the apical membrane Na+/H+ exchanger NHE3 isoform of renal or intestinal epithelial cells is chronically regulated by a wide variety of stimuli, including acidosis, cAMP, glucocorticoids, and thyroid hormone. To understand the molecular mechanisms responsible for long term regulation of this cation transporter, we have isolated and determined the structure of this gene from a rat genomic library. The Nh3 gene spans > 40 kilobases and contains 17 exons that are flanked by typical splice donor and acceptor sequences at the exon-intron boundaries. The transcription initiation site was mapped by S1 nuclease protection analyses of mRNA from rat kidney and intestine. Multiple start sites were clustered between nucleotides -100 and -96 relative to the translation initiation codon. An atypical TATA-box and CCAAT-box are centered 30 and 147 nucleotides, respectively, upstream of the predominant transcription initiation site. Sequence analysis of approximately 1.4 kilobases of the 5'-flanking promoter region also revealed the presence of other putative cis-acting elements recognized by various transcription factors (e.g. AP-1, AP-2, C/EBP, NF-I, OCT-1/OTF-1, PEA3, Sp1, glucocorticoid, and thyroid hormone receptors), some of which may participate in the chronic regulation of this gene. The glucocorticoid responsiveness of the Nhe3 gene was assessed by fusing its 5' regulatory region to the firefly luciferase reporter gene and then by measuring the expression of the chimeric gene in transiently transfected renal epithelial OK and LLC-PK1 cells. Glucocorticoid treatment significantly increased the luciferase activity of the chimeric gene in both cell lines, thereby indicating that glucocorticoid regulation of Nhe3 is mediated primarily by a transcriptional mechanism.

Fully edited and partially edited nad9 transcripts differ in size and both are associated with polysomes in potato mitochondria.

Two classes of nad9 transcripts are present at different abundances in the steady-state RNA pool of potato mitochondria. The 5'- and 3' termini of the transcripts were determined by primer extension and S1 nuclease protection analyses respectively. Using two primer pairs that will either specifically amplify the larger transcript or amplify both the larger and the smaller transcripts in RT-PCR analyses it was found that the larger nad9 transcripts are partially edited, while the smaller transcripts are fully edited. Both the larger and the smaller transcripts were found to be associated with mitochondrial polysomes. The polysome association was found to be sensitive to EDTA and puromycin treatment. Therefore, both fully and partially edited nad9 transcripts appear to be engaged in translation.

Genomic Organization of the Human ATP1AL1 Gene Encoding a Ouabain-Sensitive H,K-ATPase

The human ATP1AL1 gene belongs to the family of Na,K-ATPase and H,K-ATPase (X,K-ATPases) genes. It encodes a catalytic subunit of hitherto unknown human ouabain-sensitive H,K-ATPase that represents a novel third group of X,K-ATPases distinct from the known Na,K-ATPase and gastric H,K-ATPase. Cloning of the ATP1AL1 gene is described in this report. The exon–intron structure of ATP1AL1 was found to be very similar to that of related genes. It contains 23 exons and spans approximately 32 kb of genomic DNA. All ATP1AL1 exons and 12 of its 22 introns were entirely sequenced. A total of nineAlurepeats were identified in introns. The transcription initiation site was mapped 187 bp upstream of the ATG initiation codon by primer extension and S1nuclease protection analyses of RNA from human skin and colon. Sequence analysis of the 5′-flanking region (1.48 kb) revealed numerous potential binding sites for transcription factors Sp1 and AP2 and one putative NF-κB binding site. The 0.85-kb region from position −484 (5′-flanking region) to position +369 (intron 1) meets the structural criteria of a CpG island. It is suggested that the ATP1AL1 gene contains two poly(A) addition sites that may function in a tissue-specific manner.

Escherichia coli RNase II: characterization of the promoters involved in the transcription of rnb.

The rnb gene encodes ribonuclease II (RNase II), one of the two major Escherichia coli exonucleases involved in mRNA degradation. In this paper, the rnb transcript is characterized regarding its promoter and terminator regions. The combined results from S1 nuclease protection analysis, DNase I footprinting and gene fusions with lacZ have shown that rnb is expressed from two promoters. S1 nuclease protection analysis and DNA footprinting have shown that rnb has two promoters, P1 and P2. Transcriptional and translational lacZ reporter fusions, constructed to the rnb gene, revealed that P2, the rnb proximal promoter, is stronger than P1. However, P2 is not transcribed in vitro, suggesting that an additional factor is required in vivo. The 3' end of the rnb transcript mapped to a stem-loop structure immediately after the translated region.

Transcription of the beta-galactoside alpha 2,6-sialyltransferase gene in B lymphocytes is directed by a separate and distinct promoter.

A single human gene, SIAT1, encodes the beta-galactoside alpha 2,6-sialyltransferase from which multiple mRNA isoforms are generated. In rat, expression of the hepatic mRNA isoform (Form 1) has been defined with respect to the transcriptional initiation site and promoter region. We show here that a similar hepatic SIAT1 mRNA isoform exists in human. Another human mRNA isoform, a mature B-cell-specific mRNA isoform (Form 2), was previously reported. Here, we used 5'-RACE and S1 nuclease protection analysis to define the 5'-untranslated region of Form 2 human SIAT1 mRNA. We demonstrate conclusively that Form 2 mRNA is initiated from a point completely distinct from that of Form 1 mRNA. A number of cis-acting regulatory elements residing immediately 5'of the Form 2 initiation site includes AP-1, AP-2, NF-kappa B, NF-IL6, C/EBP, and CREB. A TATAA box is also present 29 bp 5' of the transcriptional initiation site. CAT reporter gene expression from serially-truncated segments of the 5'-flanking region of the Form 2 initiation site indicates that the segment between -784 and +125 was sufficient to promote high level CAT expression in Louckes, a mature B-cell line. The 5'-flanking region to the human Form 1 initiation site is competent in expression of CAT upon transfection of the fusion construct into HepG2, a human hepatoma cell line. Cellular specificity of expression is apparently retained. Louckes cells expressed CAT efficiently from Form 2 promoter but only marginally from the Form 1 promoter. In contrast, CAT expression from Form 1 promoter is more efficient than from the Form 2 promoter in HepG2 cells.

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.

IGF-II dependent autocrine growth in cell lines derived from renal tumours of childhood

Aims-To determine the role of insulin-like growth factors (IGF) in the proliferation of tumour cells, by studying the mitogenic response to IGFs of three cell lines of differing phenotype established from both malignant rhabdoid and Wilms tumour, representing a range of cell types (GOS 4, G401, and T3/73).Methods-Production of IGF-II and IGF-I was measured by radioimmunoassay, and the presence of IGF binding protein complexes was observed by gel exclusion chromatography. Following growth analyses in serum-free media to ascertain the dependence of the cell lines on exogenous IGFs, the generation of autocrine growth was measured by a density dependence assay of proliferation in culture. Receptors were measured by radioligand cross linking and autocrine growth through these receptors assayed by the use of blocking antibodies.Results-While GOS 4 and G401 were able to proliferate in serum-free medium over a period of 5 d, T3/73 showed an absolute dependence on IGFs added daily at 1-10 ng/ml. Plating at clonal density showed that cell growth was directly density dependent in serum-free medium. The serum independent proliferation of G401 and GOS 4 was blocked by the addition of an antibody to the type 1 IGF receptor (alpha-IR3) suggesting that the effects of autocrine factors are mediated through type 1 IGF receptors. S1 nuclease protection analysis indicated that all three cell lines produced significant amounts of mRNA derived mainly from the P3 IGF-II promoter, but transcripts for IGF-I were undetectable. Radioimmunoassay of IGFs from conditioned media showed that all the lines made assayable IGF-II (8.6, 8.4, and 6.1 ng/ml/24 h/10(6) cells for GOS 4, G401, and T3/73 respectively). The presence of species consistent with both type 1 and type II IGF receptors was demonstrated using radioligand binding to cell membranes followed by cross linking.Conclusions-Autocrine IGF-II may contribute to the serum independence of GOS 4 and G401 cells, whereas T3/73 may depend on exogenous IGF-II for proliferation.

Analysis of the 5′ end of the rat plasma membrane Ca 2+-ATPase isoform 3 gene and identification of extensive trinucleotide repeat sequences in the 5′ untranslated region

We have characterized the 5′ end of the rat gene encoding isoform 3 of the plasma membrane Ca 2+-ATPase using S1 nuclease protection and DNA sequence analysis. The 5′-untranslated region consists of over 900 nucleotides and includes a 217-nucleotide sequence composed of alternating tracts of TCC and ACC trinucleotides. Analysis of genomic sequences 5′ to the transcription initiation site revealed potential binding sites for transcription factors that are active in muscle and brain.

Localization of a transcription promoter within the second exon of the cytochrome P-450c27/25 gene for the expression of the major species of two-kilobase mRNA.

The rat P-450c27/25 (CYP27) gene is expressed as two distinctly sized mRNAs of 2 and 2.3 kb (kilobase). The 2 kb mRNA is the predominant form in the liver with negligible 2.3 kb species. Rat kidney and hepatoma, on the other hand, contain significant levels of the 2.3 kb species. Rat CYP27 gene contains 11 exons of 80-415 nucleotides that are separated by 10 introns of 83 bases to approximately 10 kb. S1 nuclease protection and primer extension analyses using liver RNA showed a prominent 5' terminus 86 nucleotides downstream from the start of exon 2. This site, designated as +1, is the start site for the 2 kb mRNA. 5' RACE analysis of rat kidney and hepatoma RNAs showed the presence of a 5' extended mRNA with a sequence complementary to the Spi2 mRNA. A cryptic TATA box (TTTAAA) is located 24 nucleotides upstream of the 2 kb mRNA transcription initiation site at +1. A 106 bp DNA fragment (sequence -83 to +23) that houses the putative TATA motif forms three differently migrating complexes with nuclear extract from the murine 3T3 cells. DNAse I footprinting and competition with synthetic DNA showed that complex A represents the bound Sp1 factor and complexes B and C are due to unknown factors binding to the -83 to -71 and -20 to -12 sequences, respectively. In vivo transcription analysis using -840/+23 DNA and its 5' deletions cloned in a CAT reporter plasmid suggests that the basal promoter elements are located within sequence -45 to +23 of the gene. Finally, in vitro transcription analysis in HeLa cell nuclear extract showed that intact TTTAAA motif and complex C-forming sequence from this region are essential for transcription initiation at the +1 position of the promoter. Our results demonstrate that the 2 kb mRNA is transcribed as an independent transcript driven by an immediate upstream promoter located within exon 2.

The Mouse APLP2 Gene: CHROMOSOMAL LOCALIZATION AND PROMOTER CHARACTERIZATION

Senile plaques are primarily comprised of deposits of the beta-amyloid precursor-like proteins APLP1 and APLP2. proteins (APPs). APP is a member of a gene family, including amyloid precursor-like proteins APLP1 and APLP2. Using interspecific mouse backcross mapping, we localized the mouse APLP2 gene to the promixmal region of mouse chromosome 9, syntenic with a region of human 11q. We cloned an approximately 1.2-kilobase mouse genomic fragment containing the APLP2 gene promoter. The APLP2 promoter lacks a typical TATA box, is GC-rich, and contains several sequences for transcription factor binding. S1 nuclease protection analysis revealed the presence of multiple transcription start sites. The lack of a TATA box, the presence of a high GC content, and multiple transcription start sites place the APLP2 promoter in the class of promoters of "housekeeping genes." Regulatory regions within the promoter were assayed by transfection of mouse N2a and Ltk- cells with constructs containing progressive 5'-deletions of the APLP2 promoter fused to the bacterial chloramphenicol acetyl transferase (CAT) reporter gene. A minimal region that includes sequences 99 bp upstream of the predominant transcription start site of the APLP2 promoter was sufficient to direct high levels of CAT expression.