Katsuyuki Hashimoto | National institute of infectious diseases (original) (raw)

Papers by Katsuyuki Hashimoto

Genomics, 1998

We originally isolated LECT2 (leukocyte cell-derived chemotaxin 2) as a 16-kDa secreted protein h... more We originally isolated LECT2 (leukocyte cell-derived chemotaxin 2) as a 16-kDa secreted protein having a human neutrophil chemotactic activity, then cloned human and bovine LECT2 cDNAs and demonstrated the liver-specific expression of the protein. LECT2 is thought to be a multifunctional protein, because it was recently found to be identical to chondromodulin-II a growth stimulator of chondrocyte cells. We report here the cloning and the structural analysis of the human LECT2 gene. The gene spans approximately 8 kb and consists of four exons and three introns. Primer extension analysis revealed that several transcription initiation sites occur within 70-230 nucleotides upstream of the translation initiation codon. Several transcriptional control sequences relevant to the liver-specific expression have been identified at the 5' untranslated region of the human LECT2 gene. The human LECT2 gene was mapped to chromosome 5q31.1-q32 by fluorescence in situ hybridization. This region contains a cluster of cytokine genes including IL-4, IL-5, and IL-9.

Article, 1992

Using a synthetic, alpha satellite consensus DNA unit as a probe, we could show dicentrics as wel... more Using a synthetic, alpha satellite consensus DNA unit as a probe, we could show dicentrics as well as acentric fragmented chromosomes in metaphases of γ-irradiated lymphocyte cells and that the number of appearance of dicentrics or acentric fragments seemed to be proportional to radiation doses. To make such examination with a large number of chromosomes of metaphases, a quantitative fluorescence measurement was performed using a fluorescent microscope digital image analysis system. The relative amounts of fluoresceinated probe hybridized to alpha satellite DNA varied with chromosomes to a certain extent (1-4% of total probe-fluorescence of one metaphase). However, we could score dicentrics and acentric fragments as dots with extraordinarily higher or low percentage in plots of relative amount of probe-fluorescence on metaphase chromosome in γ-irradiated cells. The number of appearacne of acentric fragments were proportional to radiation doses of 1, 2 and 4 Gy. In the case of dicentrics, the number of appearance seemed to be proportional to square doses. Further, to reduce the variation of relative amounts of probe-fluorescence, we tried to make probe-fluorescence reflect the content of alpha satellite DNA on each chromosome more exactly, using a DNA probe amplified by polymerase chain reaction.

Journal of interferon & cytokine research, 2003

The CC chemokines are a closely related subfamily of the chemokine superfamily. Most of the CC ch... more The CC chemokines are a closely related subfamily of the chemokine superfamily. Most of the CC chemokine genes form a cluster on chromosome 11 in mice and chromosome 17 in humans. To date, 11 and 16 functional genes have been localized within the mouse and human clusters, respectively. Notably, some of the genes within these clusters appear to have no counterparts between the two species, and the orthologous relationships of some of the genes are difficult to establish solely on the basis of amino acid similarity. In this study, we have taken a comparative genomic approach to reveal some of the features that may be involved in the dynamic evolution of these gene clusters. We sequenced a 122-kb region containing five chemokine genes of the mouse CC cluster. This mouse sequence was combined with those determined by the Mouse Genome Sequencing Project, and the entire sequence of the mouse CC cluster was compared with that of the corresponding cluster in the human genome by percent identity plot and dot-plot analyses. Although no additional chemokine genes have been found in these clusters, our analysis has revealed that numerous gene rearrangements have occurred even after the diversification of rodents and primates, resulting in several species-specific chemokine genes and pseudogenes. In addition, phylogenetic analysis and comparison of the genomic sequences unambiguously identified the orthologous relationships of some of the chemokine genes in the mouse and human CC gene clusters.

To understand the mechanism of transcriptional regulation, it is essential to identify and charac... more To understand the mechanism of transcriptional regulation, it is essential to identify and characterize thepromoter, which is located proximal to the mRNA start site. To identify the promoters from the large volumesof genomic sequences, we used mRNA start sites determined by a large-scale sequencing of the cDNA librariesconstructed by the “oligo-capping” method. We aligned the mRNA start sites with the genomic sequences andretrieved adjacent sequences as potential promoter regions (PPRs) for 1031 genes. The PPR sequences weresearched to determine the frequencies of major promoter elements. Among 1031 PPRs, 329 (32%) containedTATA boxes, 872 (85%) contained initiators, 999 (97%) contained GC box, and 663 (64%) contained CAATbox. Furthermore, 493 (48%) PPRs were located in CpG islands. This frequency of CpG islands was reduced inTATA+/Inr+ PPRs and in the PPRs of ubiquitously expressed genes. In the PPRs of the CGM2 gene, the DRAgene, and the TM30pl genes, which showed highly colon specific expression patterns, the consensus sequences ofE boxes were commonly observed. The PPRs were also useful for exploring promoter SNPs.

(PDF) ERRATUM Identification and characterization of the potential promoter regions of 1031 kinds of human genes. Available from: https://www.researchgate.net/publication/222101688_ERRATUM_Identification_and_characterization_of_the_potential_promoter_regions_of_1031_kinds_of_human_genes#fullTextFileContent [accessed May 17 2023].

Background: As part of our investigation into the genetic basis of tumor cell radioresponse, we h... more Background: As part of our investigation into the genetic basis of tumor cell radioresponse, we have isolated several clones with a wide range of responses to X-radiation (XR) from an unirradiated human colorectal tumor cell line, HCT116. Using human cDNA microarrays, we recently identified a novel gene that was down-regulated by twofold in an XR-resistant cell clone, HCT116 Clone2_XRR. We have named this gene as X-ray radiation resistance associated 1 (XRRA1) (GenBank BK000541). Here, we present the first report on the molecular cloning, genomic characterization and over-expression of the XRRA1 gene. Results: We found that XRRA1 was expressed predominantly in testis of both human and macaque. cDNA microarray analysis showed threefold higher expression of XRRA1 in macaque testis relative to other tissues. We further cloned the macaque XRRA1 cDNA (GenBank AB072776) and a human XRRA1 splice variant from HCT116 Clone2_XRR (GenBank AY163836). In silico analysis revealed the full-length human XRRA1, mouse, rat and bovine Xrra1 cDNAs. The XRRA1 gene comprises 11 exons and spans 64 kb on chromosome 11q13.3. Human and macaque cDNAs share 96% homology. Human XRRA1 cDNA is 1987 nt long and encodes a protein of 559 aa. XRRA1 protein is highly conserved in human, macaque, mouse, rat, pig, and bovine. GFP-XRRA1 fusion protein was detected in both the nucleus and cytoplasm of HCT116 clones and COS-7 cells. Interestingly, we found evidence that COS-7 cells which over-expressed XRRA1 lacked Ku86 (Ku80, XRCC5), a non-homologous end joining (NHEJ) DNA repair molecule, in the nucleus. RT-PCR analysis showed differential expression of XRRA1 after XR in HCT116 clones manifesting significantly different XR responses. Further, we found that XRRA1 was expressed in most tumor cell types. Surprisingly, mouse Xrra1 was detected in mouse embryonic stem cells R1. Conclusions: Both XRRA1 cDNA and protein are highly conserved among mammals, suggesting that XRRA1 may have similar functions. Our results also suggest that the genetic modulation of XRRA1 may affect the XR responses of HCT116 clones and that XRRA1 may have a role in the response of human tumor and normal cells to XR. XRRA1 might be correlated with cancer development and might also be an early expressed gene.

BMC Genomics, Dec 23, 2002

In order to contribute to the establishment of a complete map of transcribed regions of the human... more In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and attempted to find novel transcripts for identification of their human homologues. The full-insert sequences of 512 cDNA clones were determined. Ultimately we found 302 non-redundant cDNAs carrying open reading frames of 300 bp-length or longer. Among them, 89 cDNAs were found not to be annotated previously in the Ensembl human database. After searching against the Ensembl mouse database, we also found 69 putative coding sequences have no homologous cDNAs in the annotated human and mouse genome sequences in Ensembl. We subsequently designed a DNA microarray including 396 non-redundant cDNAs (with and without open reading frames) to examine the expression of the full-sequenced genes. With the testicular probe and a mixture of probes of 10 other tissues, 316 of 332 effective spots showed intense hybridized sign...

Gene, Sep 1, 2007

The genetic basis of the phenotypic difference between human and chimpanzee is one of the most ac... more The genetic basis of the phenotypic difference between human and chimpanzee is one of the most actively pursued issues in current genomics. Although the genomic divergence between the two species has been described, the transcriptomic divergence has not been well documented. Thus, we newly sequenced and analyzed chimpanzee full-length cDNAs (FLcDNAs) representing 87 protein-coding genes. The number of nucleotide substitutions and sites of insertions/deletions (indels) was counted as a measure of sequence divergence between the chimpanzee FLcDNAs and the human genome onto which the FLcDNAs were mapped. Difference in transcription start/termination sites (TSSs/TTSs) and alternative splicing (AS) exons was also counted as a measure of structural divergence between the chimpanzee FLcDNAs and their orthologous human transcripts (NCBI RefSeq). As a result, we found that transposons (Alu) and repetitive segments caused large indels, which strikingly increased the average amount of sequence divergence up to more than 2% in the 3′-UTRs. Moreover, 20 out of the 87 transcripts contained more than 10% structural divergence in length. In particular, two-thirds of the structural divergence was found in the 3′-UTRs, and variable transcription start sites were conspicuous in the 5′-UTRs. As both transcriptional and translational efficiency were supposed to be related to 5′-and 3′-UTR sequences, these results lead to the idea that the difference in gene regulation can be a major cause of the difference in phenotype between human and chimpanzee.

To identify genes that can repress the expression of growth regulatory molecules, a human fetal c... more To identify genes that can repress the expression of growth regulatory molecules, a human fetal cDNA library was screened with a degenerate oligonucleotide that corresponds to the conserved stretch of 6 amino acids connecting successive zinc-finger regions in the Wilms' tumor suppressor/Egr-1 family of DNA-binding proteins. One clone, designated zinc-finger protein 174 (ZNF174), corresponds to a putative transcription factor with three zinc fingers and a novel finger-associated domain, designated the SCAN box. The three Cys 2-His 2type zinc fingers are positioned at the carboxyl terminus, while the 65-amino acid finger-associated SCAN box is located near the amino terminus. Chromosomal localization using somatic cell hybrid analysis and fluorescent in situ hybridization mapped the gene for ZNF174 to human chromosome 16p13.3. The 2.5-kilobase transcript from this gene is expressed in a variety of human organs, but most strongly in adult testis and ovary. Fusion of the upstream regulatory region of ZNF174 to the DNA-binding domain of GAL4 revealed that the gene could confer a repression function on the heterologous DNA-binding domain. ZNF174 selectively repressed reporter activity driven by the platelet-derived growth factor-B chain and transforming growth factor-␤ 1 promoters and bound to DNA in a specific manner. This member of the C 2 H 2-type zinc-finger family is a novel transcriptional repressor.

Gene, May 12, 1998

A novel protein, BCNT, originally isolated from bovine brain and named after Bucentaur, contains ... more A novel protein, BCNT, originally isolated from bovine brain and named after Bucentaur, contains an internal portion that is translated from part of bovine LINE repetitive sequence (Bov-B LINE). Human cDNA highly homologous to the bovine bcnt (bbcnt) cDNA has been isolated but does not contain a sequence similar to the Bov-B LINE insert (Nobukuni, T

Journal of Virology

We have isolated four clones of integrated human papillomavirus type 16 (HPV-16) DNA from four di... more We have isolated four clones of integrated human papillomavirus type 16 (HPV-16) DNA from four different primary cervical cancer specimens. AU clones were found to be monomeric or dimeric forms of HPV-16 DNA with cellular flanking sequences at both ends. Analysis of the viral sequences in these clones showed that E6/E7 open reading frames and the long control region were conserved and that no region specific for the integration was detected. Analysis of the cellular flanking sequences revealed no significant homology with any known human DNA sequences, except Alu sequences, and no homology among the clones, indicating no cellular sequence specific for the integration. By probing with single-copy cellular flanking sequences from the clones, it was demonstrated that the integrated HPV-16 DNAs, with different sizes in the same specimens, shared the same cellular flanking sequences at the ends. Furthermore, it was shown that the viral sequences together with cellular flanking sequences were amplified. The possible process of viral integration into cell chromosomes in cervical cancer is discussed. * Corresponding author. digested with appropriate restriction enzymes, separated by electrophoresis on 0.5 or 1.0% agarose gels, and transferred to nitrocellulose filters (Schleicher & Schuell, Inc., Federal Republic of Germany) by the method of Southern (23), with some modifications (16). As a viral probe, the prototype of HPV-16 (21) was used. As cellular probes, Alu sequences and single-copy cellular sequences (see below) were used. DNA probes were prepared by labeling gel-purified DNA fragments with 32P by nick translation to specific activities of 108 cpm/,ug of DNA. Hybridization under stringent condition was performed with 107 cpm of the probe in 50% formamide-3x SSC (lx SSC is 0.15 M NaCl plus 0.015 M sodium

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Nippon rinsho. Japanese journal of clinical medicine

For flow karyotyping and sorting, chromosomes are stained in suspension with appropriate DNA fluo... more For flow karyotyping and sorting, chromosomes are stained in suspension with appropriate DNA fluorochromes, and passed singly through a beam of laser light. The emitted pulses of fluorescence and scattered light are measured and stored in the form of a histogram displaying the number of pulses versus fluorescence or scattered light intensity. A data processing system was devised to remove signals from cell debris or chromosome fragments. A selective window was set in a dot plot of fluorescence versus scattered light intensities and a program was made to count pulses from the gated area only. As application of chromosome fractionation, flow cytometry has been used for karyotype analysis, gene mapping, and chromosomal DNA library construction.

Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme