Glycobiology, 2000, Vol. 10, No. 6 637-643
© 2000 Oxford University Press
Genomic structure and promoter analysis of the human 
1,6-fucosyltransferase gene (FUT8)
2Department of Biochemistry, Room B1, Osaka University Medical School, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan, 3Department of Obstetrics and Gynecology, Asahikawa Medical School, 4-5-3-11 Nishikagura, Asahikawa 078-8510, Japan, 4Center for Research and Education, Room C10, Osaka University Medical School, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan, and 5Department of Biochemistry, Yamagata University School of Medicine, 2-2-2 Iida-Nishi, Yamagata 990-9585, Japan
Received on December 3, 1999; revised on January 14, 2000; accepted on January 17, 2000.
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GDP-L-Fuc:N-acetyl-ß-D-glucosaminide
1,6-fucosyltransferase (1,6FucT) catalyzes the transfer of a fucosyl moiety from GDP-fucose to the asparagine-linked GlcNAc residue of complex N-glycans via 1,6-linkage. We have cloned the genomic DNA which encodes the human 1,6FucT gene (FUT8) and analyzed its structure. It was found that the gene consists of at least nine exons spanning more than a 50 kbp genomic region, and the coding sequence is divided into eight exons. The translation initiation codon was located at exon 2, and thus exon 1 encodes only 5'-untranslated sequences. Transcription initiation site of FUT8 was determined by 5'-rapid amplification of the cDNA end and a primer-extension analysis using the total RNA isolated from SK-OV-3 cells, which have a high level of 1,6FucT activity. We then characterized the FUT8 promoter region by a reporter gene assay. The luciferase reporter assay indicated that the 5'-flanking region of exon 1, which covered about 1 kbp, conferred the promoter activity in SK-OV-3 cells. This region contains potential binding sites for some transcription factors, such as bHLH, cMyb, GATA-1, as well as a TATA-box, but not a CCAAT motif. 5'-Untranslated sequences found in ESTs and the cDNA for the FUT8 suggest the presence of an additional exon(s) at the upstream of the first exon identified in this study, and therefore, the transcription of the gene would be regulated by multiple promoters.
Key words: 1,6-fucosyltransferase/gene promoter system/genomic organization/alternative splicing/N-glycan
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Introduction |
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1,6-Fucosyltransferase (1,6FucT) transfers a fucosyl residue to position 6 of the asparagine-linked (N-linked) N-acetylglucosamine residue of an N-glycan, and is involved in biosyntheses of complex types of N-linked oligosaccharides in glycoproteins (Longmore and Schachter, 1982
; Kobata, 1992; Miyoshi et al., 1999a). This enzyme is widely distributed in nature and its products, 1,6-fucosylated oligosaccharides, are found in numerous glycoproteins in a variety of tissues (Miyoshi et al., 1999a).
The 1,6-fucose content of serum glycoproteins, such as ceruloplasmin and transferrin, is typically low, under normal conditions, which is probably due to the very low levels of 1,6FucT activity in the liver where these proteins are synthesized. The activity of 1,6FucT, however, is increased considerably during the development of malignant liver diseases (Huchinson et al., 1991), and, as a result, the 1,6-fucose contents of some serum glycoproteins are elevated under these conditions. In particular, sugar chains of -fetoprotein, a well-established tumor marker which is produced by hepatocellular carcinomas, are abundantly 1,6-fucosylated, whereas those produced in non-tumorous liver diseases are only slightly fucosylated, if at all (Taketa et al., 1990; Huchinson et al., 1991; Ohno et al., 1992). Thus, the expression of 1,6FucT in the liver is closely associated with changes in oligosaccharide structure during hepatocarcinogenesis. In addition, germ cell tumors such as yolk sac tumors also produce highly fucosylated -fetoprotein (Aoyagi et al., 1993).
In order to investigate the molecular basis of the increased expression of 1,6FucT, which is associated with the cancer-associated alteration in oligosaccharide structure, we purified and characterized 1,6FucTs from pig brain and a human gastric cancer cell line, and then cloned the cDNAs for these enzymes (Uozumi et al., 1996; Yanagidani et al., 1997). The enzymes were found to be nearly identical, even though they were cloned using different mRNA sources. We also isolated a genomic clone for the human 1,6FucT gene (FUT8) and used this to map the gene on human chromosome 14q24.3 by fluorescence in situ hybridization (Yamaguchi et al., 1999). Northern blot analyses have shown that a good correlation exists between the increased 1,6FucT activities in hepatocellular carcinomas and the elevated levels of the FUT8 mRNA (Miyoshi et al., 1997; Noda et al., 1997, 1998). This supports the view that the FUT8 is certainly responsible for the increased fucosylation which is associated with hepatocellular carcinoma.
We recently reported that the overexpression of FUT8 in hepatoma cells suppresses intrahepatic metastasis after splenic injection in athymic mice (Miyoshi et al., 1999b), suggesting that the altered oligosaccharide structure resulting from excessive 1,6-fucosylation affects metastastic potential. Since the elevated expression of 1,6FucT activities has been reported in a variety of cancers, in addition to liver cancer (Miyoshi et al., 1997), FUT8 may also play a role in other malignant diseases. Thus, the expression of this enzyme is likely to contribute to the malignant characteristics of cancer cells, and, hence, an examination of the mechanism for the FUT8 expression is of importance in comprehending malignant potentials, such as invasive and metastatic capabilities of the cells.
This study was undertaken in order to elucidate the mechanism which controls the regulation of the expression of FUT8 by means of a structural and functional characterization of the gene. The human FUT8 was cloned and characterized, and its promoter activity was demonstrated via a reporter assay. The findings herein will provide useful information regarding the investigation of malignant characteristics of cells in terms of alterations in oligosaccharide structure.
The novel nucleotide sequence data reported in this study have been submitted to the DDBJ, EMBL, and GenBank sequence data banks and are available under accession numbers AB032567, AB032568, AB032569, AB032570, AB032571, AB032572, AB032573, AF038280, and AF038281.
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Isolation and characterization of the human FUT8
A human genomic DNA library (
FIXII) was screened using the entire cDNA for human FUT8 (Yanagidani et al., 1997) as a probe. The screening of ~106 plaques led to the identification of 17 independent positive clones. DNA fragments from the digestion of the genomic clones by restriction endonucleases were subjected to Southern hybridization to identify the exon-containing fragments. After subcloning the DNA fragments, which were hybridizable to the cDNA probe, into a plasmid vector, they were subjected to sequence analyses. Figure 1 shows the structure of the human FUT8, along with the restriction enzyme sites and positions covered by the isolated clones. The isolated genomic clones covered the entire coding region of the FUT8 cDNA (Yanagidani et al., 1997). The coding sequence was divided into eight exons, and, in addition, the most 5'-upstream exon, designated as exon 1 in this study, was found to encode only 5'-untranslated sequences of the cDNA. The nucleotide sequences of all exons were found to be identical to the cDNA sequences (Yanagidani et al., 1997). The exon–intron boundaries all followed the GT-AG rule that introns begin with GT and end with AG (Mount, 1982), and were in agreement with the consensus sequences for the splicing donor and acceptor sites (Table I). Although all coding exons were covered by the isolated clones, no overlap in the four intronic sequences was observed. Among the four introns, 1, 2, 5, and 8, the length of intron 8 was successfully estimated by genomic PCR, but attempts to determine the sizes of the other three introns by other methods resulted in failure. Thus, the size of the genomic region is predicted to be longer than 50 kb, but the exact size remains unknown.
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Identification of the transcription initiation site
To determine the transcriptional initiation site of the FUT8, the 5' end of the mRNA was analyzed by 5'-rapid amplification of the cDNA end (5'RACE) and a primer-extension analysis. Prior to these analyses, we surveyed several ovarian cancer cell lines using the enzyme activity assay and Northern blot analysis in order to identify a cell line that expresses a sufficiently high level of the FUT8 mRNA. As shown in Figure 2, the SK-OV-3 cells were found to express the highest level of mRNA as well as activity among the five cell lines examined.
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Total RNA extracted from the SK-OV-3 cells was reverse-transcribed, and a homopolymeric dA-tail was then attached to the resulting first-strand of cDNA using terminal nucleotidyltransferase with dATP. As shown in Figure 3A, the DNA was subjected to the first PCR using the oligo dT anchor primer and the gene specific primer SP-1, resulting in the amplification of approximately a 0.5 kbp fragment. This PCR product was then used for the second PCR with a pair of the anchor primer and the gene specific primer SP-2. The PCR products were subcloned into the plasmid vector followed by sequence analysis (Figure 3A). It was found that a putative 5' end of the mRNA for the FUT8 extended by 257 nucleotides from the translation start codon, as revealed by the results from analyses of several clones (Figure 3B). To further confirm the transcription initiation sites, a primer-extension analysis was performed. This analysis suggests that the transcription of the FUT8 starts at –259 and –256 bp upstream of the translation initiation codon in the SK-OV-3 cells (Figure 3B). Therefore, we conclude that the sites determined herein represent transcription start sites in the cell line examined.
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Nucleotide sequences and promoter activities of the 5' upstream region
Sequence analysis of ~1 kbp of the 5'-flanking region of the determined transcription initiation site revealed that the region contained a typical TATA-box sequence but not a canonical CCAAT motif (Figure 3B). In order to explore the issue of whether the upstream region functions as a promoter, we constructed a reporter plasmid in which a firefly luciferase gene was fused to the 20 bp downstream of the transcription initiation site. When SK-OV-3 cells were transfected with the plasmid containing the entire 1 kbp fragment, the reporter activity was found to be about 8 times higher than that in the case of a control plasmid with no extra DNA fragment (Figure 4). Therefore, we conclude that the identified region serves as a promoter in the FUT8. For a more detailed exploration of the region responsible for the promoter activity, several truncated forms of the promoter sequences were prepared. These were inserted into the reporter plasmids and were also subjected to the reporter assay. As shown in Figure 4, all the truncated constructs exhibited much lower luciferase activity, as compared with that in the whole 1 kbp fragment. It is thus likely that essential sequences for enhancing the FUT8 transcription are located between –1015 and –910 bp region and the downstream sequences had no significant contribution to the activity in this cell line.
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Discussion |
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Fucosyltransferases catalyze the transfer of a fucosyl moiety from GDP-fucose in
-linkage to an appropriate acceptor substrate. In mammals, fucosyltransferases involved in the formation of 1,2-(FucTH and FucTSe), 1,3-(1,3/4-) (FucTIII–FucTVII and FucTIX), and 1,6-fucose residues (1,6FucT) are also known (Breton et al., 1998; Costache et al., 1997). Among the nine human fucosyltransferase genes (FUT1–FUT9) reported to date (Larsen et al., 1990; Kelly et al., 1995; Kukowska-Latallo et al., 1990; Goelz et al., 1990; Weston et al., 1992a,b; Sasaki et al., 1994; Yanagidani et al., 1997; Kaneko et al., 1999), the ORFs of FUT1 to FUT6 are encoded by single exons, and the ORF of the FUT7 is assembled from two exons. On the other hand, our findings indicate that the ORF of the FUT8 unusually encompasses 8 exons. The human FUT8 product consists of 575 amino acid residues without a consensus N-glycosylation site, whereas the other fucosyltransferases have much fewer amino acid residues, about 400 or less. In addition, the FUT8 has been mapped to the chromosomal region 14q24.3 (Yamaguchi et al., 1999) and this localization is distinct from those of some 1,2- and 1,3-fucosyltransferases, in which the genes are clustered or located close together. Thus, it is shown that FUT8 is unique and distinct from other fucosyltransferases in terms of both its structural and genetical features.
It appears that fucosyltransferase genes have evolved from a single ancestral gene by successive duplications, followed by subsequent, divergent evolution, as suggested by Costache et al. (1997). The phylogenetic tree in their report also suggested that the FUT8 is the orthologous homologue of the common ancestor of the 1,2- and 1,3-fucosyltransferase genes. Our result concerning the genomic organization is consistent with these proposals, which have been made on the basis of the sequence comparison (Costache et al., 1997; Breton et al., 1998), that the FUT8 is the oldest gene of the fucosyltransferase family and that gene duplication of the FUT8 or its closely related ancestral gene is the origin of the diversity in this enzyme family, since it is possible that the other fucosyltransferase genes initially arose by RNA-mediated gene duplication which may yield an intronless gene from an ancestral intron-containing gene (McCarrey, 1987; McCarrey, 1990).
A FASTA search of the GenBank database identified 20 ESTs encoding human FUT8. Of these ESTs, five, all of which were derived from the retina, encode sequences containing exons 6 and 9 but lack exons 7 and 8, suggesting that the latter two exons are alternatively spliced out in these transcripts (Figure 5). The lack of exons 7 and 8 causes a frame-shift in exon 9, resulting in the premature termination of translation. As a result, this splicing variant of the transcript encodes a much shorter protein, which contains only 308 amino acid residues. The variant protein would be unable to catalyze 1,6-fucosylation because it lacks the protein domain which has been predicted to play an essential role in enzyme activity through the binding of the donor substrate (Breton et al., 1998; Perrin et al., 1999). Although many ESTs for the FUT8 have been reported in several tissues, the ESTs for the splicing variant were found only in retina. Thus, it seems likely that the variant is produced via retina-specific alternative splicing and may have a role which is independent of the fucose-transferring activity. Although we attempted to screen human adult and fetal retina cDNA libraries, the cDNA for the splicing variant has not been isolated.
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The reporter assay indicated that approximately a 1.0 kb 5'-flanking region of the transcription initiation site actually serves as a promoter in SK-OV-3 cells. However, the identified transcription initiation site appears to be located more downstream than would have been expected by the position of typical TATA-box (Figure 3B), because the motif is generally localized within a 30 nucleotide sequence upstream of the transcription initiation site of the genes. The luciferase reporter assays using successively truncated forms of the 5'-flanking region demonstrated that the region between –1015 to –910 is responsible for enhancing the expression of the FUT8 in SK-OV-3 cells, an ovarian cancer cell line. This region contains consensus sequences for bHLH and GM-CSF-responsive elements. In many ovarian cancer cells, it is known that GM-CSF often forms an autocrine loop as well as other cytokines such as IL-1, IGF-1, M-CSF, GM-CSF, and TNF-
(Burke et al., 1996).
A search of the database also identified four human FUT8 ESTs which have sequences of 200–450 bp upstream from the transcription initiation site determined here. Hence, it is entirely possible that an additional upstream exon(s) and other promoter(s) in the human FUT8 exist, although we identified only one promoter region localized upstream of the noncoding exon next to the exon containing the translational initiation codon. An increasing number of vertebrate genes have been found to be regulated by multiple promoters, and, in the case of glycosyltransferases, multiple promoters have also been reported for many genes such as the 2,3-sialyltransferase ST3Gal IV (Kitagawa et al., 1996), the N-acetylglucosaminyltransferase III (Koyama et al., 1996), the N-acetylglucosaminyltransferase V (Saito et al., 1995), a ß1,4-galactosyltransferase (Shaper et al., 1995; Rajput et al., 1996) and 1,3-fucosyltransferases (Cameron et al., 1995). The FUT8 could also be possibly transcribed from multiple promoters to regulate its expression in a cell-type- or tissue-specific manner.
Identification of the promoter region(s) responsible for the cancer-associated elevation of 1,6FucT level would be one of the most important issues. A comprehensive study involving the possible multiple promoter system would be required to understand the more detailed mechanism for the regulation of 1,6FucT gene expression.
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Materials and methods |
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Screening of a genomic library
A human genomic DNA library constructed in
FIXII (Stratagene, La Jolla, CA) was screened with the full-length cDNA clone which encodes for the human FUT8 (Yanagidani et al., 1997) as a probe. Hybridization was carried out with the 32P-labeled cDNA probe overnight at 42°C in a hybridization solution which contained 50% formamide. The filters were then washed three times in 2x SSC containing 0.1% SDS at 55°C, and were exposed to x-ray films at –80°C overnight. Phages were purified by glycerol density-gradient ultracentrifugation and subjected to proteinase K digestion. After phenol/chloroform extraction, the phage DNAs were precipitated in 80% ethanol and subjected to further analyses.
Restriction mapping of the FUT8
A restriction map of cloned FUT8 was established using the FLASH nonradioactive gene mapping kit (Stratagene) according to the manufacturer’s instructions. Briefly, phage DNAs were digested to completion with NotI and then partially digested with EcoRI, XbaI, and SacI. These partially digested DNAs were separated on agarose gels and their blots were performed in duplicate. The membranes were subjected to hybridization using a alkaline phosphatase-conjugated probes, which were specific to either of the T3 and T7 promoters. The blots were reacted with a chemiluminescent substrate for alkaline phosphatase, and then exposed to x-ray films.
Determination of exon/intron boundaries
The phage DNAs were digested with various restriction enzymes and characterized by Southern hybridization. The restriction enzyme-digested DNA fragments, which were hybridizable to the cDNA probe, were subcloned into pBluescript II KS+. The entire exons and exon/intron boundaries were directly sequenced for both strands in an ABI PRISM 310 DNA Genetic Analyzer using a DNA sequencing kit (PE Biosystems Inc., USA). Intron sizes were determined by Southern blotting, restriction mapping, and long accurate polymerase chain reaction (LA-PCR) analyses of the genomic DNAs using an LA-PCR kit (Takara, Shiga, Japan).
Cell culture
All cells were maintained at 37°C in 5% CO2. SK-OV-3 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal calf serum, and 200 µg/ml kanamycin. OVCAR-3, A2780 and Kuramochi cells were maintained in RPMI1640 supplemented with 5% FCS and 200 µg/ml kanamycin. PA-1 cells were maintained in Eagle’s minimal essential medium supplemented with 5% fetal calf serum and 200 µg/ml kanamycin.
Protein determination
The protein concentration was determined with a Bio-Rad protein assay kit using bovine serum albumin as the standard.
Assay for 1,6FucT activity
1,6FucT activity was analyzed using a 4-(2-pyridylamino)-butylamine-labeled oligosaccharide as previously described (Uozumi et al., 1996). The reaction was performed in 100 mM MES-NaOH buffer (pH 7.0) containing 1% Triton X-100, 500 µM GDP-fucose as the donor substrate, and 5 µM of the 4-(2-pyridylamino)-butylamine-labeled sugar chain as the acceptor substrate. After the sample addition, the mixture was incubated at 37°C for 2 h and then boiled for 1 min to terminate the reaction. The reacted mixture was centrifuged for 10 min at 10,000 x g and the resulting supernatant was applied to a high-performance liquid chromatography apparatus equipped with a TSK-gel and ODS-80TM column (4.6 x 150 mm) (Tosoh, Tokyo, Japan) in order to separate and quantify the product. The elution was isocratically performed at 55°C with 20 mM sodium acetate buffer containing 0.15% butanol (pH 4.0). Fluorescence of the column elute was detected with a fluorescence detector (Shimadzu, Kyoto, Japan, model RF-10AXL) at excitation and emission wavelengths of 320 and 400 nm, respectively. The amount of the product was estimated from the fluorescence intensity.
RNA isolation and Northern blotting
Total RNAs were isolated from several lines of ovarian cancer cells with TRIzol Reagent (Life Technologies Inc.). A total of 106 cells were homogenized in 1 ml of TRIzol Reagent and were incubated for 5 min at room temperature. After chloroform extraction, the total RNAs were precipitated in 50% isopropyl alcohol. Twenty micrograms of the total RNAs were electrophoresed on a 1% agarose gel containing 2.2 M formaldehyde and then transferred onto a Zeta-probe membrane (Bio-Rad, Hercules, CA) by capillary action. The membrane was hybridized with the 32P-labeled 2.7 kbp fragment of the FUT8 cDNA as a probe. Hybridization was carried out overnight at 42°C in the hybridization solution, which contained 50% formamide. The membrane was then washed three times with 2x SSC containing 0.1% SDS at 55°C, and exposed overnight to x-ray films at –80°C.
5'-Rapid amplification of the cDNA end (5'RACE)
Five µg of the total RNA from SK-OV-3 cells were reverse-transcribed with SuperScript II (Life Technologies Inc.) using random primers under the reaction conditions recommended by the supplier. The 5'-end of the human FUT8 cDNA was cloned by a 5'RACE experiment (Ohara et al., 1989) using the 5'/3' RACE Kit (Boehringer Mannheim, Mannheim, Germany) according to the manufacturer’s instructions. Briefly, a homopolymeric dA-tail was appended to the 3'end of the first-strand cDNA using a terminal nucleotidyl transferase and dATP. The poly dA-tailed cDNA was amplified by PCR using the oligo dT-anchor primer (5'-GACCACGCGTATCGATGTCGACTTTTTTTTTTTTTTTTV-3') and the gene specific primer SP-1 (5'-CTGATCAATAGGGCCTTCTGGTATC-3'; corresponds to nucleotides 204 to 228). The reaction conditions were: initial denaturation for 2 min at 94°C, followed by 10 cycles of 15 s at 94°C, 30 s at 55°C, and 40 s at 72°C; and 25 cycles of 15 s at 94°C, 30 sec at 55°C, 40 s + cycle elongation of 20 s for each cycle at 72°C; and then 7 min at 72°C. Ten microliters of the PCR product was further amplified using the PCR anchor primer (5'-GACCACGCGTATCGATGTCGAC-3') and the gene specific primer SP-2 (5'-TTGTCCTGTACTTCATGCGCTCTACATG-3'; which corresponds to nucleotides –228 to –201). The second PCR product was purified from the agarose gel using a DNA Cell (Daiichi Pure Chemicals, Tokyo, Japan), subcloned into T-vector pT7Blue (R) (Novagen, Darmstadt, Germany), and sequenced.
Primer extension
The 30-mer oligonucleotide primer, 5'-TATTGTCCTGTACTTCATGCGCTCTACATG-3', of which the sequence corresponds to the position of –199 to –228 from the translation initiation codon and locates in exon 2, was labeled with 32P at the 5' end by T4 polynucleotide kinase. The labeled oligonucleotide (5 x 105 c.p.m.) was mixed with 50 µg of total RNA from SK-OV-3 cells in 20 µl of 10 mM Tris/HCl, pH8.3, 1 mM EDTA, 250 mM KCl and their hybridization was carried out by heating at 60°C for 1 h followed by incubation at room temperature for 1.5 h. To this mixture, 60 µl of reverse-transcription buffer (16.7 mM KCl, 13.3 mM MgCl2, 23.3 mM Tris/HCl, pH 8.3, 13.3 mM dithiothreitol, 0.33 mM dNTPs, and 0.133 mg/ml actinomycin D), 20 U of Molony mouse leukemia virus reverse transcriptase (RNase H–), and 20 U of RNase inhibitor were added, and the extension reaction was carried out at 37°C for 1 h. The reaction mixture was subjected to the ethanol-precipitation and then analyzed by urea-denatured polyacrylamide gel electrophoresis.
Construction of reporter plasmid with the firefly luciferase gene
The full-length promoter (–1015 to +20) and 4 deletion constructs (–909, –830, –777, –232 to +20) of the FUT8 were subcloned into a firefly luciferase reporter plasmid, the PicaGene basic plasmid vector, pPGV-B (Toyo Ink Inc., Tokyo, Japan) which contains neither a eukaryotic promoter nor an enhancer element.
Transfections and reporter assays
Twenty micrograms of the pPGV-B DNA carrying various lengths of the 5'-upstream sequences to be examined and 0.8 µg of the pRL-TK DNA containing sea pansy luciferase, the transcription of which is driven by thymidine kinase promoter, were introduced into approximately 2 x 105 SK-OV-3 cells by electroporation (Chu et al., 1987). The activities of the firefly luciferase as a reporter were determined 48 h after the transfection. Sea Pansy luciferase activities were assayed as an internal control for normalization of the results. Differential activity determination of these luciferases was carried out according to manufacturer’s instructions (Kitamura et al., 1999).
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We thank Keiji Okuda for his technical assistance. This work was supported in part by a Grant-in-Aid for Scientific Research on Priority Areas, No. 10178104, from the Ministry of Education, Science, Sports and Culture of Japan.
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Abbreviations |
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FucT, fucosyltransferase; FUT, FucT gene; LA-PCR, long accurate polymerase chain reaction; 5'RACE, 5'-rapid amplification of the cDNA end.
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1 To whom correspondence should be addressed
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