Showing papers by "Yutaka Suzuki published in 2001"
TL;DR: This work used mRNA start sites determined by a large-scale sequencing of the cDNA libraries constructed by the "oligo-capping" method to identify the promoters from the large volumes of genomic sequences, and retrieved adjacent sequences as potential promoter regions (PPRs) for 1031 genes.
Abstract: To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from the large volumes of genomic sequences, we used mRNA start sites determined by a large-scale sequencing of the cDNA libraries constructed by the "oligo-capping" method. We aligned the mRNA start sites with the genomic sequences and retrieved adjacent sequences as potential promoter regions (PPRs) for 1031 genes. The PPR sequences were searched to determine the frequencies of major promoter elements. Among 1031 PPRs, 329 (32%) contained TATA boxes, 872 (85%) contained initiators, 999 (97%) contained GC box, and 663 (64%) contained CAAT box. Furthermore, 493 (48%) PPRs were located in CpG islands. This frequency of CpG islands was reduced in TATA(+)/Inr(+) PPRs and in the PPRs of ubiquitously expressed genes. In the PPRs of the CGM2 gene, the DRA gene, and the TM30pl genes, which showed highly colon specific expression patterns, the consensus sequences of E boxes were commonly observed. The PPRs were also useful for exploring promoter SNPs.
274 citations
TL;DR: Using cDNA libraries made from oligo‐capped mRNAs, the ‘oligo‐capping’ method was used to identify the transcriptional start site of an individual mRNA just by sequencing the 5′‐end of the cDNA.
Abstract: Determination of the mRNA start site is the first step in identifying the promoter region, which is of key importance for transcriptional regulation of gene expression. The ‘oligo-capping’ method enabled us to introduce a sequence tag to the first base of an mRNA by replacing the cap structure of the mRNA. Using cDNA libraries made from oligo-capped mRNAs, we could identify the transcriptional start site of an individual mRNA just by sequencing the 5′-end of the cDNA. The fine mapping of transcriptional start sites was performed for 5880 mRNAs in 276 human genes. Contrary to our expectations, the majority of the genes showed a diverse distribution of transcriptional start sites. They were distributed over 61.7 bp with a standard deviation of 19.5. Our finding may reflect the dynamic nature of transcriptional initiation events of human genes in vivo.
174 citations
TL;DR: FDG-PET appears to be a powerful tool not only in the diagnosis of the primary lesion and soft tissue metastasis, but also in the diagnoses of bony metastasis among patients with breast cancer.
Abstract: The purpose of this study was to determine the potential role of positron emission tomography (PET) using 2-[ 18 F]-fluoro-2-deoxy-D-glucose (FDG) for the evaluation of bony metastasis compared with 99 Tc m -methylene diphosphonate ( 99 Tc m -MDP) bone scintigraphy in patients with breast cancer. Fifty-one female patients with breast cancer who had PET together with a bone scan within 1 month between September 1994 and March 1997 were included in this study. The median age was 49 years (range 29-79 years). The sensitivity, specificity and accuracy of the bone scan were 77.7%, 80.9% and 80.3%, respectively. On the other hand, for the detection of bone metastases PET had a sensitivity, specificity and accuracy of 77.7%, 97.6% and 94.1%, respectively. In the diagnosis of bony metastasis derived from breast cancer, FDG-PET was statistically superior to bone scintigraphy in its specificity. In conclusion, FDG-PET appears to be a powerful tool not only in the diagnosis of the primary lesion and soft tissue metastasis, but also in the diagnosis of bony metastasis among patients with breast cancer.
162 citations
TL;DR: Findings suggest that CREB-H plays an important role in transcriptional regulation of genes specifically expressed in the liver, and that the putative transmembrane domain may be associated with modulation of its function as the transcriptional activator.
Abstract: The expression of liver-specific genes is regulated by unequivocally allocated transcription factors via proper responsible elements within their promoters. We identified a novel transcription factor, CREB-H, and found that its expression was restricted in the liver among 16 human tissues tested. A region of CREB-H exhibited significant homology to the basic leucine zipper (b-Zip) domain of members of the CREB/ATF family: mammalian LZIP and Drosophila BBF-2 that binds to box-B, a Drosophila enhancer modulating the fat-body-specific gene expression. CREB-H contained a hydrophobic region representing a putative transmembrane domain, like LZIP. Constructing a variety of CREB-H fusion proteins with the GAL4 DNA-binding domain disclosed that CREB-H functioned as a transcriptional activator and its N-terminal 149 amino acids accounted for the activation ability. Gel mobility sift assays revealed that CREB-H did not bind to the C/EBP, AP-1 and NF-κB elements but specifically bound to CRE and the box-B element. Luciferase reporter assays demonstrated that like BBF-2, CREB-H activated transcription via the box-B element and that a deletion of the putative transmembrane domain increased the activation of reporter expression significantly. Furthermore, a fusion protein of GFP and full-length CREB-H was localized in reticular structures surrounding the nucleus, whereas a fusion protein of GFP and a deletion mutant lacking the putative transmembrane domain was mainly in the nucleus. These findings suggest that CREB-H plays an important role in transcriptional regulation of genes specifically expressed in the liver, and that the putative transmembrane domain may be associated with modulation of its function as the transcriptional activator.
151 citations
TL;DR: The Helix Research Institute (HRI) in Japan is releasing 4356 HUman Novel Transcripts and related information in the newly established HUNT database, which represents an essential bioinformatics contribution towards understanding of the gene function.
Abstract: The Helix Research Institute (HRI) in Japan is releasing 4356 HUman Novel Transcripts and related information in the newly established HUNT database. The institute is a joint research project principally funded by the Japanese Ministry of International Trade and Industry, and the clones were sequenced in the governmental New Energy and Industrial Technology Development Organization (NEDO) Human cDNA Sequencing Project. The HUNT database contains an extensive amount of annotation from advanced analysis and represents an essential bioinformatics contribution towards understanding of the gene function. The HRI human cDNA clones were obtained from full-length enriched cDNA libraries constructed with the oligo-capping method and have resulted in novel full-length cDNA sequences. A large fraction has little similarity to any proteins of known function and to obtain clues about possible function we have developed original analysis procedures. Any putative function deduced here can be validated or refuted by complementary analysis results. The user can also extract information from specific categories like PROSITE patterns, PFAM domains, PSORT localization, transmembrane helices and clones with GENIUS structure assignments. The HUNT database can be accessed at http://www.hri.co.jp/HUNT.
55 citations
48 citations
TL;DR: Using the oligo-capping method, a full-length-enriched cDNA library from erythrocytic stage parasites is produced and led to detection of three new gene candidates that were not previously known.
Abstract: FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum (http://133.11. 149.55/). Because of its medical importance, this organism is the first target for genome sequencing of a eukaryotic pathogen; the sequences of two of its 14 chromosomes have already been determined. However, for the full exploitation of this rapidly accumulating information, correct identification of the genes and study of their expression are essential. Using the oligo-capping method, we have produced a full-length-enriched cDNA library from erythrocytic stage parasites and performed one-pass reading. The database consists of nucleotide sequences of 2490 random clones that include 390 (16%) known malaria genes according to BLASTN analysis of the nr-nt database in GenBank; these represent 98 genes, and the clones for 48 of these genes contain the complete protein-coding sequence (49%). On the other hand, comparisons with the complete chromosome 2 sequence revealed that 35 of 210 predicted genes are expressed, and in addition led to detection of three new gene candidates that were not previously known. In total, 19 of these 38 clones (50%) were full-length. From these observations, it is expected that the database contains approximately 1000 genes, including 500 full-length clones. It should be an invaluable resource for the development of vaccines and novel drugs.
40 citations
TL;DR: This work demonstrates that genes expressed in cynomolgus monkey are highly conserved throughout primate evolution, and that virtually all had human homologs, and will be able to discover novel human genes in the human genome using monkey homologys as probes.
26 citations
Journal Article•
TL;DR: It is concluded that when tumor invasion remains within the muscle layer, lymph nodes with high RI activity can be regarded as sentinel nodes.
Abstract: The purpose of this study is to determine whether a lymph node identified with high radioisotope (RI) activity is a sentinel node. We studied 26 patients with either esophageal or gastric cancer whose preoperative imaging studies showed no lymph node metastasis. Before surgery, Tc-99m tin colloid was injected via endoscopy into the submucosa. In lymph nodes dissected at surgery, RI activity was measured by a scintillation counter, and metastatic status was examined by hematoxylin-eosin staining. The number of dissected nodes was 45 +/- 15 (mean +/- SD) per patient, and the number of nodes with high RI activity was 4 +/- 1. Nodal metastasis occurred in 11 of 26 patients. In 9 of these 11 patients, metastatic foci were found in one or more nodes with high RI activity. In one of the 2 remaining patients, endoscopic clipping was applied just above the injection sites, and in the other patient, the tumor invasion was beyond the muscle layer. For further analysis, the case with clipping was excluded, and only those in which the tumor invasion was confined within the muscle layer were evaluated. Six of 18 patients in this analysis showed nodal metastasis. Each of the 6 patients had at least one node that showed high RI activity and that was positive for metastasis. We conclude that when tumor invasion remains within the muscle layer, lymph nodes with high RI activity can be regarded as sentinel nodes.
25 citations
TL;DR: Monkey cDNA is a valuable resource for the preparation of a complete human gene catalog, which will facilitate post-genomic studies and predicted 29 new genes that had not been discovered in recent explorations for novel genes in humans.
Abstract: Background
The complete assignment of the protein-coding regions of the human genome is a major challenge for genome biology today. We have already isolated many hitherto unknown full-length cDNAs as orthologs of unidentified human genes from cDNA libraries of the cynomolgus monkey (Macaca fascicularis) brain (parietal lobe and cerebellum). In this study, we used cDNA libraries of three other parts of the brain (frontal lobe, temporal lobe and medulla oblongata) to isolate novel full-length cDNAs.
15 citations
TL;DR: A genomic DNA fragment carrying the UTF1 gene is isolated and it is found that the gene contains two exons interrupted by a short intron, leading to the identification of two different species.
TL;DR: The fact that slowly progressive ataxia is often observed in EA2 indicates that a small glutamine expansion in the SCA6 gene also disturbs the function of P/Q-type calcium channels, leading to selective neuronal degeneration in the cerebellum.
Abstract: The autosomal dominant cerebellar ataxias (ADCAs) are a group of neurodegenerative disorders which can be classified into three major categories on the basis of their clinical features and mode of inheritance.1 ADCA type III is a pure cerebellar syndrome that is genetically heterogeneous and includes spinocerebellar ataxia type 5 (SCA5),2 SCA6,3SCA10,4 5 and SCA11.6 The gene responsible for SCA6 has been identified as coding for the α1Asubunit of the P/Q type voltage dependent calcium channel ( CACNA1A ). Moderate CAG expansion in the coding region causes the disorder, with the number of CAG repeats being originally reported as 21-27 in mutant alleles (n=8) and 4-16 in control alleles (n=950).3 Subsequent studies have indicated that the range of pathological expansion in SCA6 alleles varies from 207 to 33.8 The CACNA1A gene was first identified during the search for specific mutations causing familial hemiplegic migraine (FHM) and episodic ataxia type 2 (EA2).9 The gene product has four transmembrane domains and glutamine repeats are located at the C-terminal side of the intracellular segment. Missense mutations of these transmembrane domains and deletions or splice mutations leading to a truncated protein are responsible for FHM and EA2, respectively. The CACNA1A gene is predominantly expressed in Purkinje cells and granule cells of the cerebellum and is essential for the survival and maintenance of normal function by these neurones.10 11 Biochemical mechanisms leading to the development of SCA6 are not fully understood. However, the fact that slowly progressive ataxia is often observed in EA2 indicates that a small glutamine expansion in the SCA6 gene also disturbs the function of P/Q-type calcium channels, leading to selective neuronal degeneration in the cerebellum.
The pathogenic expansion in SCA6 is relatively small compared with those in other SCAs caused by …
TL;DR: DSCR5 may be the first candidate to elucidate the pathophysiology of tongue malformation observed in DS by combination of computational gene prediction and cDNA screening.
Abstract: For understanding the pathogenesis of Down syndrome (DS), it is important to identify and characterize the genes on Chromosome (Chr) 21, especially those in the Down syndrome critical region (DSCR) on Chr 21q222 Recently we have determined 335 Mb (more than 99%) of DNA sequence of Chr 21 and, from these sequence data, we identified a novel gene, DSCR5 (transcript = 08 kb), from DSCR by combination of computational gene prediction and cDNA screening For functional analysis of DSCR5, we identified a mouse homolog of the DSCR5 cDNA, and termed it mDscr5 (transcript length = 08 kb) The gene was mapped to mouse Chr 16 C3-C4, the syntenic region of human Chr 21, and encodes an amino acid of 132 residues with 90% identity to DSCR5 In situ hybridization showed that mDscr5 is predominantly expressed in the developing tongue To our best knowledge, no other gene in DSCR is reported to be expressed in tongue, so that DSCR5 may be the first candidate to elucidate the pathophysiology of tongue malformation observed in DS
TL;DR: The cDNA sequence database of oligo-capping clones enabled high throughput selection of full-length cDNA clones and was found to be due to the large redundancy of the UniGene database.
Abstract: We compared in detail the characteristics of the sequences of the cDNA clones obtained by the oligo-capping method (oligo-capping clones) with that of the sequences in the UniGene database. To compare the completeness of the sequences, three new variables, "fullness-proportion of clones" (the ratio of complete clones to total clones in a library), "fullness-proportion of genes" (the ratio of complete genes to total genes in a library), and "fullness-proportion of database" (the ratio of complete genes to total genes in a database sampled from a library), were defined. The fullness-proportion of clones of oligo-capping clones was 57.3%, 2.2 times larger than that of UniGene (25.9%). The fullness-proportion of genes of oligo-capping clones was 41.8%, 2.4 times larger than that of UniGene (17.8%). When gene length was restricted to > or = 1.5 kb, the fullness-proportion of genes of oligo-capping clones was four times larger than that of UniGene. The fullness-proportion of database of oligo-capping clones was approximately the same as that of UniGene. By simulating the clone redundancy, this coincidence was found to be due to the large redundancy of the UniGene database. Consequently, the cDNA sequence database of oligo-capping clones enabled high throughput selection of full-length cDNA clones.
26 Sep 2001