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Hidetoshi Inoko

Publications and source records attributed to Hidetoshi Inoko.

At least 55 records · Page 3Linked to original sources
PubMed2004

Identification, expression analysis and polymorphism of a novel RLTPR gene encoding a RGD motif, tropomodulin domain and proline/leucine-rich regions.

We describe the isolation and characterization of a full-length cDNA encoded by a gene that was significantly down-regulated in the affected skin of patients with psoriasis vulgaris. The cDNA was isolated from a keratinocyte cDNA library and its sequence was found to correspond to a hypothetical locus recorded in GenBank with the accession number . The nucleotide sequence of the full-length cDNA was found to have an open reading frame of 1365 amino acids and to span approximately 12 kb of genomic DNA with 39 exons on chromosome 16q22. The deduced amino acid sequence contains four distinct structural regions, an RGD motif, a leucine-rich repeat (LRR) region, a tropomodulin domain, and a proline-rich domain. The gene was consequently designated as RLTPR (RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein). The RLTPR hypothetical protein has a functional domain organization similar to Acan125, a myosin-binding protein expressed by Acanthamoeba castellanni. RT-PCR with RLTPR PCR primers amplified products from cDNAs prepared from all of the 30 different tissues that we examined including thymus, spleen, colon, skin, skin keratinocytes, skin fibroblasts and fetal skin. During the course of screening the human keratinocyte cDNA library, some alternative splicing was also detected in three regions of the RLTPR gene. In addition, sequence analysis of the RLTPR genes from eight psoriasis patients and eight healthy controls revealed a number of synonymous and nonsynonymous SNPs that may be useful markers for future disease association studies.

Alternative Splicing↗
PubMed2004

Novel algorithm for automated genotyping of microsatellites.

Microsatellites or short tandem repeats (STRs) are abundant in the human genome with easily assayed polymorphisms, providing powerful genetic tools for mapping both Mendelian and complex traits. Microsatellite genotyping requires detection of the products of polymerase chain reaction (PCR) amplification by electrophoresis, and analysis of the peak data for discrimination of the true allele. A high-throughput genotyping approach requires computer-based automation at both the detection and analysis phases. In order to achieve this, complicated peak patterns from individual alleles must be interpreted in order to assign alleles. Previous methods consider limited types of noise peaks and cannot provide enough accuracy. By pattern recognition of various types of noise peaks, such as stutter peaks and additional peaks, we have achieved an overall average accuracy of 94% for allele calling in our actual data. Our algorithm is crucial for a high-throughput genotyping system for microsatellite markers by reducing manual editing and human errors.

Algorithms↗
PubMed2004

Rhesus macaque class I duplicon structures, organization, and evolution within the alpha block of the major histocompatibility complex.

The alpha block of the human and chimpanzee major histocompatibility complex (MHC) class I genomic region contains 10 to 11 duplicated MHC class I genes, including the HLA/Patr-A, -G, and -F genes. In comparison, the alpha block of the rhesus macaque (Macaca mulatta, Mamu) has an additional 20 MHC class I genes within this orthologous region. The present study describes the identification and analysis of the duplicated segmental genomic structures (duplicons) and genomic markers within the alpha block of the rhesus macaque and their use to reconstruct the duplication history of the genes within this region. A variety of MHC class I genes, pseudogenes, transposons, and retrotransposons, such as Alu and ERV16, were used to categorize the 28 duplicons into four distinct structural categories. The phylogenetic relationship of MHC class I genes, Alu, and LTR16B sequences within the duplicons was examined by use of the Neighbor-Joining (NJ) method. Two single-duplicon tandem duplications, two polyduplicon tandem duplications with an accompanying inversion product per duplication, eight polyduplicon tandem duplications steps, 12 deletions, and at least two recombinations were reconstructed to explain the highly complex organization and evolution of the 28 duplicons (nine inversions) within the Mamu alpha block. On the basis of the phylogenetic evidence and the reconstructed tandem duplication history of the 28 duplicons, the Mamu/Patr/HLA-F ortholog was the first MHC class I gene to have been fixed without further duplication within the alpha block of primates. Assuming that the rhesus macaque and the chimpanzee/human lineages had started with the same number of MHC class I duplicons at the time of their divergence approximately 24 to 31 MYA, then the number of genes within the alpha block have been duplicated at an approximately three times greater rate in the rhesus macaque than in either the human or chimpanzee.

Animals↗
PubMed2004

MHC class IIB gene sequences and expression in quails (Coturnix japonica) selected for high and low antibody responses.

Two quail lines, H and L, which were developed for high (H) and low (L) antibody production against inactivated Newcastle disease virus antigen, were used to examine differences in the organization, structure and expression of the quail Mhc class IIB genes. Four Coja class IIB genes in the H line and ten Coja class IIB genes in the L line were identified by gene amplification using standard and long-range PCRs and sequencing of the amplified products. RFLP analysis, sequencing and gene mapping revealed that the H line was fixed for a single class IIB haplotype, which we have designated CojaII-02HL- CojaII-01HL. In contrast, evidence was found for two class IIB haplotypes segregating in the L line. Some individuals were found to be homozygous for haplotype CojaII-08L- CojaII-07L and others were found to be heterozygous CojaII-08L- CojaII-07L/ CojaII-02HL- CojaII-01HL. However, expression of CojaII-02HL- CojaII-01HL was not detected in the L line. SRBC immunization induced a measurable antibody response in the serum and a line-specific class IIB gene expression in the peripheral white blood cells. CojaII-01HL was expressed at the highest level in the H line and CojaII-07L in the L line. The expression of the class IIB mRNA reached the highest level at approximately 1 week after the primary antibody response and then declined exponentially. The antibody and class IIB gene expression data obtained in response to SRBC immunization provide further evidence that quails within the L line had reduced immunocompetence compared with those in the H line.

Amino Acid Sequence↗
PubMed2004

CHOP: visualization of 'wobbling' and isolation of highly conserved regions from aligned DNA sequences.

The web software CHOP was developed to visualize the 'wobbling' in the third codon position of aligned DNA sequences. The simple features of this tool allow users to easily find regions suspected of containing coding sequences (CDSs). The program also allows visualization of the nucleotide diversity between two genomic or gene sequences by graphically plotting the percentage identity between the two sequences. CHOP can also isolate highly conserved regions within both CDSs and non-CDSs. Highly conserved regions within CDSs include the regions with lower rates of synonymous substitution in which nucleotide sequences are expected to be under strong selective pressure. CHOP is available at http://bunsei2.med.u-tokai.ac.jp:8080/~ohtsuka/cds_finding.html.

Animals↗
PubMed2004

Comparative genomic analysis of two avian (quail and chicken) MHC regions.

We mapped two different quail Mhc haplotypes and sequenced one of them (haplotype A) for comparative genomic analysis with a previously sequenced haplotype of the chicken Mhc. The quail haplotype A spans 180 kb of genomic sequence, encoding a total of 41 genes compared with only 19 genes within the 92-kb chicken Mhc. Except for two gene families (B30 and tRNA), both species have the same basic set of gene family members that were previously described in the chicken "minimal essential" Mhc. The two Mhc regions have a similar overall organization but differ markedly in that the quail has an expanded number of duplicated genes with 7 class I, 10 class IIB, 4 NK, 6 lectin, and 8 B-G genes. Comparisons between the quail and chicken Mhc class I and class II gene sequences by phylogenetic analysis showed that they were more closely related within species than between species, suggesting that the quail Mhc genes were duplicated after the separation of these two species from their common ancestor. The proteins encoded by the NK and class I genes are known to interact as ligands and receptors, but unlike in the quail and the chicken, the genes encoding these proteins in mammals are found on different chromosomes. The finding of NK-like genes in the quail Mhc strongly suggests an evolutionary connection between the NK C-type lectin-like superfamily and the Mhc, providing support for future studies on the NK, lectin, class I, and class II interaction in birds.

Animals↗
PubMed2004

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.

Alternative Splicing↗
PubMed2004

Autoreactive CD8+ cytotoxic T lymphocytes to major histocompatibility complex class I chain-related gene A in patients with Behçet's disease.

OBJECTIVE: To detect and characterize the autoreactive CD8+ T cells to major histocompatibility complex class I chain-related gene A (MICA), a stress-inducible antigen preferentially expressed on the epithelium and endothelium, in patients with Behcet's disease (BD). METHODS: A candidate for the antigenic MICA peptide was selected based on its predicted binding affinity for HLA-B51 and proteasomal cleavage sites. Peripheral blood T cells from 14 patients with BD and 15 healthy controls were repeatedly stimulated with the MICA peptide, and the specific T cell response was measured by peptide-induced interferon-gamma. Cytotoxic T lymphocyte activity was examined by chromium-51 release from an HLA-B51-transfected B cell line in the presence of the MICA peptide. RESULTS: A 9-mer peptide AAAAAIFVI (termed MICA transmembrane [MICA-TM]) was selected as a candidate for the antigenic peptide presented by HLA-B51. A specific T cell response to MICA-TM was detected in 4 patients with BD (29%) but in none of the 15 healthy donors. All 4 responders had HLA-B51 and active disease, and the specific T cell response was lost after the BD-related symptoms disappeared. The MICA-induced T cell response was specifically inhibited by anti-HLA class I antibody or by CD8+ cell depletion. MICA-reactive T cells recognized an HLA-B51-transfected B cell line pulsed with MICA-TM or a B cell line transfected with both HLA-B51 and MICA in the absence of exogenous peptides. Finally, MICA-stimulated T cell lines lysed the HLA-B51-expressing B cell line in the presence of MICA-TM. CONCLUSION: HLA-B51-restricted cytotoxic T lymphocytes autoreactive to MICA may be involved in the pathogenesis of BD.

Autoimmunity↗
PubMed2004

hRDH-E2 gene polymorphisms, variable transcriptional start sites, and psoriasis.

hRDH-E2 is a member of the short-chain alcohol dehydrogenase/reductase (SDR) family that converts retinol to retinaldehyde as the first and rate-limiting step in the retinoic acid synthetic pathway. This pathway is critical for the maintenance of epidermal homeostasis in vivo. Previously, we reported that the mRNA levels of hRDH-E2 in psoriatic skin were elevated significantly compared with that in healthy individual skin and psoriatic unaffected skin. The gene encoding hRDH-E2 is located on Chromosome 8 close to a candidate region for psoriasis and therefore is a functional and positional candidate for this disorder. In the present study, the transcription start sites for hRDH-E2 gene transcription in the lung were found to be more upstream of those that were identified previously in keratinocytes. Consequently, differences in the nucleotide sequence were determined for all of the coding exons, untranslated regions, and at least 2850 bp of 5'-noncoding sequence of hRDH-E2 by direct sequencing of polymerase chain reaction (PCR)-amplified DNA samples obtained from 8 psoriatic patients and 8 healthy controls. One polymorphic microsatellite marker at the noncoding 3' end of the gene and six single nucleotide polymorphisms (SNPs) (three in the 5' flanking sequence, two in the coding sequence, and one in the intronic sequence) were identified. One of the SNPs was nonsynonymous in the second exon with an allelic variation between the amino acid sequences Arg and Trp. The microsatellite marker and the six SNPs were all genotyped in 100 Japanese psoriatic patients and 120 controls. However, there were no statistically significant differences in the genotype or allele frequency distributions between the cases and controls. On this basis, we conclude that the polymorphisms that we detected for the hRDH-E2 gene do not contribute to the etiology of psoriasis but may be important in diseases of other tissues.

Aldehyde Oxidoreductases↗
PubMed2004

Possible roles of zic1 and zic4, identified within the medaka Double anal fin (Da) locus, in dorsoventral patterning of the trunk-tail region (related to phenotypes of the Da mutant).

Double anal fin (Da) is a spontaneous medaka mutant that exhibits an unique ventralizing phenotype, a mirror-image duplication across the lateral midline in the dorsal trunk-tail region. In the mutant, early D-V specification appears normal but the altered phenotype becomes evident during late embryogenesis. In this study, we genetically specified the mutation to a 174-kb region harboring two zinc-finger type transcription factors, zic1 and zic4, and compared the genomic structures of this region between wild-type and Da mutant fish. No mutation was found in the coding regions of either gene of the mutant, while two fragments, 324 bp and 3-4 kb long, were found inserted downstream of zic1 and zic4, respectively. Probably as a result of this, the expression of both genes is lost in the derivatives of the dorsal (epaxial) somite and the region dorsal to the terminal axis bending. All these tissues are morphologically affected or become ventralized in the mutants. In contrast, the expression in the head region and dorsal spinal cord remained unchanged. Detailed characterization of Da phenotypes revealed a novel defect in the axial skeleton (spina bifida occulta) that was also found in zic1-deficient mice. Finally, zic1-morpholino injection partially phenocopied early Da phenotypes. These findings strongly suggest that zic1 and/or zic4 are required for dorsal identity in the trunk-tail region and that loss of their expression in the epaxial somite derivatives and tail region causes the Da phenotypes.

Animals↗
PubMed2004

Comparative analysis of a 229-kb medaka genomic region, containing the zic1 and zic4 genes, with Fugu, human, and mouse.

Medaka is one of the prominent model animals, which also include other fishes such as Fugu and zebrafish. Its genome is relatively compact but has not been well characterized. Here we have sequenced a 229-kb region of medaka, containing the Double anal fin (Da) locus, and compared its structure to those in Fugu, human, and mouse. This region, representing a gene-poor region, contains no major rearrangements and can be readily compared among different species. Comparison of G+C contents and repeats suggested that medaka and Fugu are highly related as expected and that medaka is more similar to mammals than Fugu is. Sequence comparisons of developmental genes zic1 and zic4, identified within this region, revealed that zic1, but not zic4, is highly conserved among vertebrates. The 5' coding region of zic4 is, however, extremely homologous among fishes with little synonymous substitutions, implying its distinct function in fish.

Amino Acid Sequence↗
PubMed2004

The genomic sequence and comparative analysis of the rat major histocompatibility complex.

We have determined the sequence of a 4-Mb interval on rat chromosome 20p12 that encompasses the rat major histocompatibility complex (MHC). This is the first report of a finished sequence for a segment of the rat genome and constitutes one of the largest contiguous sequences thus far for rodent genomes in general. The rat MHC is, next to the human MHC, the second mammalian MHC sequenced to completion. Our analysis has resulted in the identification of at least 220 genes located within the sequenced interval. Although gene content and order are well conserved in the class II and class III gene intervals as well as the framework gene regions, profound rat-specific features were encountered within the class I gene regions, in comparison to human and mouse. Class I region-associated differences were found both at the structural level, the number, and organization of class I genes and gene families, and, in a more global context, in the way that evolution worked to shape the present-day rat MHC.

Animals↗
PubMed2003

Identification of NAD+-dependent isocitrate dehydrogenase 3 gamma-like (IDH3GL) gene and its genetic polymorphisms.

We have identified a novel human gene designated as IDH3GL (isocitrate dehydrogenase 3 gamma-like) that is expressed specifically in human testis. The gene corresponds in sequence to an EST (expressed sequence tag) A1476435 that was first detected by differential expression analysis using a microarray assay. The full-length cDNA sequence (1037 bp) was isolated from the human testis 5'-3'-RACE cDNA libraries and found to have 83% nucleotide sequence identity with part of the IDH3G (isocitrate dehydrogenase 3 gamma). The IDH3GL gene consists of 3 exons spanning approximately 220 kb within the region of the NELL1 gene on chromosome 11p15.1. Sequence analysis of the IDH3GL cDNA revealed the presence of a premature stop codon at nucleotide positions 337-339 that results in a truncated peptide with 112 amino acids. This stop codon is conserved in various human ethnic populations and in the chimpanzee (Pan troglodytes). In order to assess the functional status of IDH3GL, especially in relation to the presence of the putative premature stop codon, single nucleotide polymorphisms (SNPs) were screened in the upstream, coding and non-coding regions of the IDH3GL gene in a Japanese population. As a result, a total of 10 SNPs were identified, seven were novel and one of them was a non-synonymous amino acid substitution from Leu to Val. We conclude that the IDH3GL gene sequence is a splice variant of the NELL1 gene and that it probably evolved from a transposed pseudogene of the IDH3 gene.

Amino Acid Sequence↗
PubMed2003

Nucleotide sequencing analysis of the swine 433-kb genomic segment located between the non-classical and classical SLA class I gene clusters.

Genome analysis of the swine leukocyte antigen ( SLA) region is needed to obtain information on the MHC genomic sequence similarities and differences between the swine and human, given the possible use of swine organs for xenotransplantation. Here, the genomic sequences of a 433-kb segment located between the non-classical and classical SLA class I gene clusters were determined and analyzed for gene organization and contents of repetitive sequences. The genomic organization and diversity of this swine non-class I gene region was compared with the orthologous region of the human leukocyte antigen ( HLA) complex. The length of the fully sequenced SLA genomic segment was 433 kb compared with 595 kb in the corresponding HLA class I region. This 162-kb difference in size between the swine and human genomic segments can be explained by indel activity, and the greater variety and density of repetitive sequences within the human MHC. Twenty-one swine genes with strong sequence similarity to the corresponding human genes were identified, with the gene order from the centromere to telomere of HCR - SPR1 - SEEK1 - CDSN - STG - DPCR1 - KIAA1885 - TFIIH - DDR - IER3 - FLOT1 - TUBB - KIAA0170 - NRM - KIAA1949 - DDX16 - FLJ13158 - MRPS18B - FB19 - ABCFI - CAT56. The human SEEK1 and DPCR1 genes are pseudogenes in swine. We conclude that the swine non-class I gene region that we have sequenced is highly conserved and therefore homologous to the corresponding region located between the HLA-C and HLA-E genes in the human.

Animals↗
PubMed2003

Genetic polymorphism of the swine major histocompatibility complex ( SLA) class I genes, SLA-1, -2 and -3.

In order to identify and characterize genetic polymorphism of the swine major histocompatibility complex ( Mhc: SLA) class I genes, RT-PCR products of the second and third exons of the three SLA classical class I genes, SLA-1, SLA-2 and SLA-3 were subjected to nucleotide determination. These analyses allowed the identification of four, eight and seven alleles at the SLA-1, SLA-2 and SLA-3 loci, respectively, from three different breeds of miniature swine and one mixed breed. Among them, 12 alleles were novel. Construction of a phylogenetic tree using the nucleotide sequences of those 19 alleles indicated that the SLA-1 and -2 genes are more closely related to each other than to SLA-3. Selective forces operating at single amino acid sites of the SLA class I molecules were analyzed by the Adaptsite Package program. Ten positive selection sites were found at the putative antigen recognition sites (ARSs). Among the 14 positively selected sites observed in the human MHC ( HLA) classical class I molecules, eight corresponding positions in the SLA class I molecules were inferred as positively selected. On the other hand, four amino acids at the putative ARSs were identified as negatively selected in the SLA class I molecules. These results suggest that selective forces operating in the SLA class I molecules are almost similar to those of the HLA class I molecules, although several functional sites for antigen and cytotoxic T-lymphocyte recognition by the SLA class I molecules may be different from those of the HLA class I molecules.

Alleles↗
PubMed2003

Evolution of the proto-MHC ancestral region: more evidence for the plesiomorphic organisation of human chromosome 9q34 region.

The present day structure of the vertebrate major histocompatibility complex (MHC) and its three paralogous regions has always been a focus of interest. In a recent study, nine human anchor genes located in the MHC region were cloned from a Branchiostoma floridae (amphioxus) cosmid library. The identification and analysis of 31 surrounding genes led to the most probable model of two rounds of en bloc duplication giving rise to these regions. These events were estimated to have occurred after the cephalochordata-craniata divergence [approximately 766 million years ago (Mya)] and before the Gnathostomata radiation (approximately 528 Mya). Furthermore, it was also shown that after this large-scale duplication one of these regions, corresponding to the human 9q33-q34, had retained an ancestral organisation. In the present study, four new cosmids in the amphioxus proto-MHC region were identified by the chromosomal walking technique. These cosmids were sequenced, and their structural annotation was performed, leading to the prediction of eleven genes. Their phylogenetic relationships among species corroborate the results obtained previously and provide more evidence for the plesiomorphic state of the human chromosome 9q33-34 MHC paralogous region.

Animals↗