A ScrFI polymorphism in the human ALPL gene.
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Alkaline Phosphatase↗
Biomedical subjects
J Kudoh
Publications and source records attributed to J Kudoh.
PCR detection of a BclI RFLP in the human ALPL gene.
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Alkaline Phosphatase↗
DNA diagnosis of hydatidiform mole using the polymerase chain reaction.
We have used the polymerase chain reaction (PCR) technique for the diagnosis of hydatidiform mole, a trophoblastic disease. For this, we targeted the hypervariable 3' flanking region of the APOB gene (APOB/VNTR) because of its high heterozygosity index (0.61) in the Japanese population. We examined seven clinical cases which were tentatively diagnosed as hydatidiform moles. Five of these revealed DNA segments unique to the paternal APOB allele, allowing us to diagnose a complete mole. The PCR technique for targeting the APOB/VNTR appears useful for early diagnosis of hydatidiform mole.
Alleles↗
Linkage analysis of affective disorder using DNA markers on chromosomes 11 and X.
We have investigated two pedigrees in an attempt to detect the putative linkages between affective disorder and c-Ha-ras-1 oncogene and the insulin gene on chromosome 11, or hypoxanthine phosphoribosyltransferase (HPRT) on X chromosome. The linkage between affective disorders and the markers on chromosomes 11 and X was ruled out with the assumption of no recombination.
Bipolar Disorder↗
Localization of the human gene for 230-kDal bullous pemphigoid autoantigen (BPAG1) to chromosome 6pter----q15.
Chromosome mapping of the human gene encoding the 230-kDal autoantigen of an autoimmune skin disease, bullous pemphigoid, was performed using flow-sorted human chromosomes of cells of normal karyotype and cells carrying a reciprocal translocation t(6;16)(q15;q24). The cDNA of the autoantigen hybridized with intact chromosome 6 and translocation chromosome 6p- (6pter----q15::16q24----qter). The gene (BPA230) was located to the chromosome region 6pter----q15.
Animals↗
Mitochondrial DNA analysis of Leber's hereditary optic neuropathy.
A mitochondrial DNA (mtDNA) mutation associated with Leber's hereditary optic neuropathy (LHON) was recently observed. The presence or absence of the mutation was analyzed in 10 Japanese patients whose clinical course and fundus findings were consistent with LHON. Four of them had at least one maternally related individual who also had bilateral optic atrophy, and were diagnosed as "definite LHON". The other 6 cases lacked any record of optic nerve disease in maternally related individuals, and were diagnosed as "possible LHON". We found the mutation at the SfaNI site of mtDNA in 3 out of the former 4 cases, and in 5 out of the latter 6 cases. This result demonstrates the clinical and diagnostic importance of mtDNA analysis, especially with possible cases of LHON, and suggests that an alternative mutation associated with LHON is also present in Japanese patients.
Adolescent↗
A human testis-specific mRNA for phosphoribosylpyrophosphate synthetase that initiates from a non-AUG codon.
Two highly homologous subunits for phosphoribosylpyrophosphate synthetase are encoded by human X-linked genes, PRPS1 and PRPS2 (Taira, M., Kudoh, J., Minoshima, S., Iizasa, T., Shimada, H., Shimizu, Y., Tatibana, M., and Shimizu, N. (1989b) Somat. Cell Mol. Genet. 15, 29-37). These genes are expressed in most tissues, whereas an additional unique mRNA (1.4 kilobases) is present in the testes of rats as well as mice and humans (Taira, M., Iizasa, T., Yamada, K., Shimada, H., and Tatibana, M. (1989a) Biochim. Biophys. Acta 1007, 203-208). In this paper, cDNA cloning revealed that the human testis-specific mRNA was encoded by an autosomal gene, termed PRPS3. RNA blot analysis showed that the expression of this gene began at 4 weeks of age in rats, coinciding with the reported appearance of primary spermatocytes. A cDNA clone of PRPS3 was sequenced and found to encode a predicted product of 317 amino acids which was highly homologous to those of PRPS1 and PRPS2 (94.3% and 91.2% identities, respectively). However, the PRPS3 cDNAs lacked an ATG initiator for translation at the expected position, and instead contained an ACG triplet. In vitro transcription/translation studies, combined with in vitro site-directed mutagenesis experiments, suggested that the ACG codon at this position did serve as a start codon. Analysis of amino-terminal sequence of the radiolabeled PRPS3 product, prepared by in vitro translation, supported the predicted sequence starting with Pro-1, and, in addition, this product was labeled with N-formyl[35S]methionyl-tRNAi. These results suggested that the synthesis of the nascent polypeptide could initiate with methionine at the position corresponding to the ACG codon.
Amino Acid Sequence↗
The pyrimidine/purine-biased region of the epidermal growth factor receptor gene is sensitive to S1 nuclease and may form an intramolecular triplex.
The pyrimidine/purine-biased region located upstream of the EGF (epidermal growth factor) receptor gene transcription initiation sites was sensitive to S1 nuclease when under superhelical tension. The structural basis of this specific reactivity to S1 nuclease was probed by the use of diethyl pyrocarbonate. The patterns of modification suggested that the H-form proposed by Mirkin, Lyamichev, Drushlyak, Dobrynin, Filippov & Frank-Kamenetskii [Nature (London) (1987) 330, 495-497], which includes an intramolecular triplex and a single-stranded region, was the most plausible model for the sequence tested. The results of dimethyl sulphate modification also supported this model.
Base Sequence↗
Isolation of giant DNA fragments from flow-sorted human chromosomes.
We have established a method using a conventional cell sorter equipped with a single argon laser to sort intact human chromosomes that can be used as a source for the production of giant DNA fragments. Various improvements were made to both the equipment and sorting method to enhance the sorting resolution and avoid destruction of chromosomal DNA. Using this improved method chromosomes 21 and 22 were sorted from the B-lymphoblastoid line GM00130B, digested with the rare cutting restriction endonuclease NotI, and analyzed by pulsed field gel electrophoresis followed by Southern hybridization using the Alu repetitive sequence as a probe. More than 25 discrete NotI giant DNA fragments ranging from 50 kb to longer than 2.5 Mb were separated and the size distribution pattern was unique for each chromosome, indicating successful sorting of intact chromosomes. The cumulative size of these Alu-positive NotI DNA fragments were 22.7 Mb and 25.5 Mb for chromosomes 21 and 22, respectively. These values are 47% and 49% of the estimated size of chromosomes 21 (48 Mb) and 22 (52 Mb).
Cell Line, Transformed↗
Four genes for the calpain family locate on four distinct human chromosomes.
Calcium dependent proteases (calpains, CAPNs, E.C.3.4.22.17) constitute a family of proteins which share a homologous cysteine-protease domain (large subunits, L1, L2, and L3) and an E-F hand Ca2(+)-binding domain (L1, L2, L3, and small subunit, S). We have mapped the genes for four calpain proteins (L1, L2, L3, and S) on four distinct human chromosomes by a combination of spot-blot hybridization to flow-sorted chromosomes and Southern hybridization of DNAs from a human x mouse hybrid cell panel. The genes for calpain L1 (CAPN1, large subunit of calpain I), L2 (CAPN2, large subunit of calpain II), L3 (CAPN3, a protein related to the large subunits), and S (CAPN4, a small subunit common to calpains I and II) were assigned to human chromosomes 11, 1, 15, and 19, respectively.
Calpain↗
[DNA diagnosis of Leber's hereditary optic neuropathy].
The point mutation at nt11778 in mitochondrial DNA is highly associated with Leber's hereditary optic neuropathy and eliminates a restriction enzyme SfaNI site in American blacks and Caucasians. DNA diagnosis was applied to a male Japanese patient with this disorder and his mother as a carrier. The mitochondrial DNA fragments (255bp) including this mutation were amplified by polymerase chain reaction. SfaNI digested the DNA fragments of normal Japanese subjects, but did not digest those of the patient or the carrier, The mutation within the SfaNI site is also associated with Japanese suffering from this disorder.
Adult↗
A human muscle adenine nucleotide translocator gene has four exons, is located on chromosome 4, and is differentially expressed.
The human heart-skeletal muscle adenine nucleotide translocator (ANT1) gene was isolated and sequenced. It spans 5.8 kilobases and contains four exons. The 5'-nontranscribed region contains typical CCAAT and TATA sequences, a 22-nucleotide pair inverted repeat and a 13-nucleotide pair sequence homologous to a similar region in the ATP synthase beta subunit gene. The region surrounding the first exon and intron is G+C-region surrounding the first exon and intron is G+C-rich, and the intron contains three Sp1 binding motifs. ANT1 was assigned to chromosome 4 using both flow-sorted chromosomes and segregating human-mouse hybrid cells. Additional ANT sequences were found on at least two other chromosomes. ANT1 transcripts were present at high levels in human heart and skeletal muscle but were almost undetectable in liver, kidney, and brain. By contrast, fibroblast ANT (ANT2) mRNAs were present in all five tissues. The unique nature and arrangement of the ANT1 transcriptional control elements may account for this differential expression.
Adult↗
Complete nucleotide sequence of the chromosomal gene for human IL-4 and its expression.
We have isolated a chromosomal DNA segment of the human IL-4 gene based on homology with a human IL-4 cDNA sequence and determined its complete nucleotide sequence. The human IL-4 gene, which occurs as a single copy in the haploid genome, is mapped on chromosome 5. It is composed of four exons and three introns and is approximately 10 kilobase pairs in size. 5'-Flanking regions of human and mouse IL-4 genes share about 85% homology extending more than 500 base pairs upstream of a "TATA" like sequence. Several patches of sequences are found in the 5'-flanking region of the human IL-4 gene which are homologous to sequence in the 5'-flanking regions of the IL-2, IL-3, IL-5, and granulocyte-macrophage (GM)-CSF genes. The IL-4 gene is inducible after treatment of human T cell clone by phorbol-12-myristate-13-acetate (TPA) and calcium ionophore A23187. The 2.3-kb 5'-flanking region of the human IL-4 gene transiently transfected into Jurkat human T cell leukemia cells is activated efficiently in response to TPA and A23187 stimulation and, although less efficiently, by human T cell leukemia virus type I-encoded p40x or BPV-encoded E2 protein. Combination of TPA/A23187 and p40x or E2 protein further augmented the level of expression.
Amino Acid Sequence↗
Localization of human phosphoribosylpyrophosphate synthetase subunit I and II genes (PRPS1 and PRPS2) to different regions of the X chromosome and assignment of two PRPS1-related genes to autosomes.
Complementary DNA clones for phosphoribosylpyrophosphate synthetase subunits I and II (PRS I and PRS II) were used to determine the chromosomal localization of the corresponding human genes. Southern blot analysis of genomic DNAs isolated from human placenta and a panel of human-mouse somatic cell hybrids revealed that the rat PRS I cDNA probe detected at least five human specific DNA segments (23, 20, 14.5, 6.7, and 4.3 kb) in BamHI digests. The 23-, 14.5-, and 6.7-kb DNA segments were detected only if the hybrids contained human chromosome X or translocation chromosome 7p+ (7qter greater than 7p22::Xq21 greater than Xqter), indicating the location of these segments to Xq21-qter (PRPS1). The 20- and 4.3-kb DNA segments did not cosegregate with the other three segments, and spot blot hybridization analysis using flow-sorted human chromosomes indicated that these are the PRPS1-related genes (PRPS1L1 and PRPS1L2) and could be assigned to chromosomes 7 and 9, respectively. The human-specific PRS II cDNA probe revealed a BamHI DNA segment (17 kb), which segregated condordantly with the X chromosome but not with the PRPS1 gene. We surmise that the gene for PRS II (PRPS2) is located at a different region of the X chromosome, namely Xpter-a21.
Animals↗
Isolation of cDNAs encoding a substrate for protein kinase C: nucleotide sequence and chromosomal mapping of the gene for a human 80K protein.
An acidic phosphoprotein of Mr 80,000, the 80K protein, is a substrate for protein kinase C in fibroblasts and epidermal carcinoma cells. We purified the 80K protein from human squamous carcinoma Ca9-22 cells and fractionated it into two distinct molecular species, designated the 80K-L and 80K-H proteins. The amino acid sequences of the NH2-terminal region and cyanogen bromide-cleaved fragments of the 80K-H protein were determined and a corresponding oligonucleotide sequence was synthesized. Using this as a probe, two cDNA clones, lambda 80H-1 and lambda 80H-2, were selected from a lambda gt10 cDNA library from human A431 cells. The nucleotide sequence has an open reading frame of 1581 nucleotides encoding a protein of 527 amino acids. The deduced amino acid sequence revealed an extremely Glu-rich region. RNA blot analysis with the lambda 80H-1 cDNA clone detected two polyadenylated transcripts of 2.3 and 3.5 kb in Ca9-22 cells. Spot blot hybridization using flow-sorted human chromosomes provided evidence that the gene (G19P1) encoding 80K-H protein maps to human chromosome 19.
Amino Acid Sequence↗
The human ATP synthase beta subunit gene: sequence analysis, chromosome assignment, and differential expression.
In humans, the functional F0F1-ATP synthase beta subunit gene is located on chromosome 12 in the p13----qter region. Other partially homologous sequences have been detected on chromosomes 2 and 17. The bona fide beta subunit gene has 10 exons encoding a leader peptide of 49 amino acids and a mature protein of 480 amino acids. Thirteen Alu family DNA repeats are found upstream from the gene and in four introns. The gene has four "CCAAT" sequences upstream and in close proximity to the transcriptional initiation site. A 13-bp motif is found in the 5' nontranscribed region of both the beta subunit gene and an ADP/ATP translocator gene that is expressed in high levels in cardiac and skeletal muscle. Analysis of the beta subunit mRNA levels reveals marked differences among tissues. The highest levels are found in heart, lower levels in skeletal muscle, and the lowest levels in liver and kidney. These findings suggest that the tissue-specific levels of ATP synthase beta subunit mRNA may be generated through transcriptional control.
Amino Acid Sequence↗
Assignment of the myeloperoxidase gene MPO to human chromosome 17 using somatic cell hybrids and flow-sorted chromosomes.
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Chromosome Mapping↗
Mega base map of the epidermal growth factor (EGF) receptor gene flanking regions and structure of the amplification units in EGF receptor-hyperproducing squamous carcinoma cells.
We have established a mega base scale physical map of the 5'- and 3'-flanking regions of the epidermal growth factor (EGF) receptor gene using CpG-recognition rare-cutting restriction enzymes and pulsed-field gel electrophoresis. In this map, a methylation-free CpG island (HTF island) is located within an 8-kilobase pair (kb) EcoRI fragment which includes exon 1 of the EGF receptor gene. From this HTF island, a 390-kb NotI fragment was identified as the longest 5'-flanking region and a 540-kb MluI fragment as the longest 3'-flanking region. Utilizing this map information, we have analyzed the structure of the flanking regions of amplified EGF receptor genes which are found in various squamous carcinoma cells. Among seven cell lines tested, four cell lines carrying EGF receptor genes in amounts more than 20 times that of normal cells showed amplification together with large 5'- and 3'-flanking regions. The amplified 5'-flanking regions were rearranged in different forms but were distinct in each cell line. The amplified 3'-flanking regions were at least 540 kb in size and common to all the cell lines, except that A431 had rearrangement points within 540 kb downstream of the HTF island. Thus, the size of amplification units appears to be large and different in each cell line.
Carcinoma, Squamous Cell↗