Search PubMed⌕ Search

Biomedical subjects

E Soeda

Publications and source records attributed to E Soeda.

At least 55 records · Page 3Linked to original sources
PubMed1993

Genomic cloning and partial characterization of human chymotrypsinogen gene.

Chymotrypsinogen is a principal precursor of pancreatic proteolytic enzymes. We previously isolated a cDNA clone for human prechymotrypsinogen from a human pancreatic cDNA library. In the present study, we used this cDNA sequences to isolate genomic DNA clones. Three overlapping cosmid clones spanning approximately 65-kb genomic sequences were isolated from a human cosmid library. The genomic DNA clones were characterized by restriction enzyme mapping and by hybridizing them to subfragments of the cDNA. The sequence tagged sites for human chymotrypsinogen gene were created by designing two oligonucleotides. Furthermore, the isolated genomic clones were confirmed to be localized on chromosome 16q23 by fluorescence in situ hybridization and G-banding analysis.

Base Sequence↗
PubMed1993

[Structural analysis of human genome by YAC technologies].

A method for construction of YAC (Yeast Artificial Chromosome) libraries with large inserts has been developed and promoted the ongoing project of human genome. Isolation by PCR screening charges the YAC clone with a unique tag of a pair of PCR primers at the defined chromosome site (Sequence Tagged Sites; STS). Current evaluation of YAC has revealed that larger YAC has more problems where rearrangements including deletion and chimera occur extensively in DNA molecules, presenting a limited use of this technology in mapping; the contig map with mega YACs will be substituted by some other system such as cosmids with which the human healthy and disease genes will be characterized.

Chimera↗
PubMed1992

Mapping of the human GSPT1 gene, a human homolog of the yeast GST1 gene, to chromosomal band 16p13.1.

The GSPT1 gene, a human homolog of the yeast GST1 gene (formerly named GST1-Hs), was mapped on human chromosome 16p13.1 by a combination of nonradioactive in situ hybridization and Giemsa staining. Southern blot hybridization with a panel of human-rodent somatic cells confirmed the location of the GSPT1 gene on chromosome 16 and also showed the existence of a homologous gene on the X chromosome. A breakpoint for nonrandom chromosome rearrangements has been found in the region of GSPT1 in patients with acute nonlymphocytic leukemia.

Blotting, Southern↗
PubMed1992

Mapping of the gene family for human heat-shock protein 90 alpha to chromosomes 1, 4, 11, and 14.

The HSP90 family of heat-shock proteins (encoded by genes for HSP90 alpha and beta) constitutes one of the major groups of proteins that are synthesized at increased rates in response to heat and other forms of stress. We previously isolated two distinct cDNA clones for HSP90 alpha from human peripheral blood lymphocytes and from HeLa cells transfected with the adenovirus E1A gene, respectively. To determine the organization of this complex multigene family in the human genome, we used three complementary approaches: Southern analysis of a panel of human/hamster somatic cell hybrids, molecular cloning of the cosmid HSP90 alpha clones from libraries prepared with DNAs from human lymphoblastoid cells, and in situ hybridization to human chromosomes. We demonstrate here that nucleotide sequences that encode HSP90 alpha map to human chromosomes 1q21.2-q22, 4q35, 11p14.1-p14.2, and 14q32.3. The chromosomal mapping of the loci, HSPCAL1, HSPCAL2, HSPCAL3, HSPCAL4, and the characterization of the respective genes should facilitate clarification of the organization of this gene family and lead to a better understanding of the biological functions of the gene product.

Animals↗
PubMed1992

Generation of 19 STS markers that can be anchored at specific sites on human chromosome 21.

Sequence-tagged sites (STSs) are short stretches of DNA that can be specifically detected by the polymerase chain reaction (PCR) and can be used to construct long-range physical maps of chromosomal DNA. These STSs can be detected by PCR assays developed by reference to data obtained from the sequencing of restriction fragment length polymorphism-DNA markers for chromosome 21, which were derived from recombinant lamba-phage and plasmid clones made from DNA of a human-hamster hybrid cell line. In this report, we describe the generation of 19 new STSs that are specific for human chromosome 21.

Base Sequence↗
PubMed1991

Human genome analysis system.

An automated DNA sequencing system, the collaborative effort of Japanese scientists and engineers, which has a potential output of up to 108,000 bases per day is described.

Base Sequence↗
PubMed1991

Physical map of the 3' region of the human immunoglobulin heavy chain locus: clustering of autoantibody-related variable segments in one haplotype.

We have constructed the physical map of the 3' region of the human immunoglobulin heavy chain variable region (VH) genes. DNA segments extending to 200 kb upstream of the JH segment were isolated in two YAC clones. Five VH segments were identified in this region in the 5' to 3' order, V(II-5), V(IV-4), V(I-3), V(I-2), and V(VI-1) segments which were all structurally normal and orientated in the same direction as the JH segments. From DNA of a different cell line we have isolated a cosmid contig containing the same DNA region which has extraordinary polymorphism. The YAC and cosmid DNAs were called haplotypes A and B, respectively. Haplotype B contained an additional VH-I segment (V(I-4.1b)) between the V(II-5) and V(IV-4) segments. V(I-4.1b) segment is almost identical to a previously published VH sequence encoding a rheumatoid factor. Another VH segment in the B haplotype (V(I-3b)) corresponding to the V(I-3) segment also showed 99.7% nucleotide sequence homology with an anti-DNA autoantibody VH sequence. However, none of the VH sequences in haplotype A showed such strong homology with autoantibody VH sequences. The results suggest that VH haplotypes may have linkage with autoantibody production.

Amino Acid Sequence↗
PubMed1991

Single DNA marker generated by "YAC-Alu PCR" that is end-specific.

A simple strategy for the rapid preparation of an end-specific linking-DNA probe from the YAC-human chromosome 21 DNA recombinant clone and the characterization of this single DNA probe are described. Synthetic oligodeoxynucleotide primers, based on the consensus Alu sequence, and the Sup4 DNA fragment in the YAC arms were used to amplify end-specific DNA sequences by the polymerase chain reaction (PCR) for screening of the linking YAC recombinant clones ("YAC-Alu PCR"). Nucleotide sequencing of the product of PCR from human genomic DNA in a YAC insert confirmed the boundary between the vector and the insert and the presence of the 3'-end Alu-like structure. The probe R1, prepared by "YAC-Alu PCR" amplification, was assigned to chromosome 21 by Southern hybridization of somatic cell hybrid DNAs. In situ hybridization allowed localization of the R1 DNA probe to the human chromosome 21q21-q22.1 region. Thus, this approach has significant advantages not only for isolation of a single DNA probe specific for human chromosome 21 but also for the screening of YAC linking recombinant clones for mapping of the human genome.

Animals↗
PubMed1991

Complete nucleotide sequence of the human RCC1 gene involved in coupling between DNA replication and mitosis.

Total genomic DNA of the human RCC1 gene was isolated from HeLa DNA and its complete nucleotide sequence (34,641 bp) was determined by the shotgun sequencing method. The exon-intron junctions were precisely assigned to this sequence by comparing the nucleotide sequence of RCC1 genomic DNA with that of its cDNA. The RCC1 gene was found to have 14 exons, 8 of which (starting from the seventh one) coded the seven repeated sequences of RCC1 protein. A single exon corresponded roughly to each repeat of the RCC1 protein except for the middle one, indicating that the RCC1 gene was generated through amplification of a primordial exon. Primer extension analysis revealed the presence of an internal promoter.

Base Sequence↗
PubMed1991

Isolation of cDNA including a reverse transcriptase-like sequence transcribed from the long interspersed repetitive DNA sequence of rat.

The mammalian genome congains long interspersed repetitive sequences, but the role of these repetitive sequence is not clear. A cDNA clone has been isolated that contains part of the L1 sequences from a cDNA library of rat liver. The DNA sequence analysis showed the homology of cDNA to several reverse transcriptases. The homology between the amino acid sequences predicted from L1 consensus sequences and reverse transcriptases has been reported previously. However, this is the first isolation of a cDNA clone containing a reverse transcriptase-like sequence.

Amino Acid Sequence↗
PubMed1990

Rapid method for construction of yeast artificial chromosome human DNA libraries involving the trapping of cells in agarose films.

A simple method for the molecular cloning of fragments of more than one hundred kilobase pairs of exogenous DNA, by the encapsulation of cells in agarose beads, was reported previously for the construction of a human genomic DNA library in a yeast artificial chromosome (YAC) vector (in situ YAC construction) [1]. The efficiency of this procedure is impaired by the step in which agarose beads that contain human DNA fragments are melted before transformation. The incomplete solubility of the ligated human DNA fragment-YAC vector often results in lower than desirable frequencies of transformation. To overcome this problem we have developed a new improved method that involves use of an agarose film. The technical manipulations involved in the construction of clones of very large segments of human DNA are discussed.

Chromosomes↗
PubMed1990

Comparison of the promoter regions of H-2Kb and H-2Kbm1 class I MHC genes.

The 2.0 kb-long nucleotide sequences of the promoter regions of two closely related class I genes of the mouse major histocompatibility complex (H-2Kb and H-2Kbm1) have been determined and compared. The promoter sequence of the H-2Kbm1 gene differs from that of the H-2Kb gene by a single deletion of a 'C' at position -456 in the upstream region of H-2Kbm1 gene. The actual existence of this deletion of a single base in genomic DNA has been verified by genomic DNA hybridization, using oligonucleotide probes specific for H-2Kbm1 or H-2Kb respectively. The effect on the enhancer activity of H-2Kbm1 promoter region of the difference at position -456 has been analyzed by the chloramphenicol acetyltransferase (CAT) assay, using appropriate DdeI fragments (-533 to -408 for H-2Kbm1; -534 to -408 for H-2Kb) cloned downstream of pH-2(367)CAT gene construct. The CAT activity determined by the H-2Kbm1 fragment was about 3-fold higher than that of H-2Kb, a result which probably accounts for the higher level of the H-2Kbm1 transcript and antigen in lymph node cells.

Animals↗
PubMed1990

Identification of sequences responsible for positive and negative regulation by E1A in the promoter of H-2Kbm1 class I MHC gene.

The mechanism of transcriptional regulation of the H-2Kbm1 major histocompatibility complex (MHC) class I gene by adenovirus type 12 E1A (Ad12-E1A) was studied in transfected rat embryonal fibroblasts. Results of long-term expression of the chloramphenicol acetyl transferase (CAT) gene placed under the control of the 5'-flanking region of the mouse MHC class I gene. H-2Kbm1, and the results of nuclear run-on transcription assays, yield evidence for both positive and negative regulation of H-2Kbm1 by E1A gene product. Deletion studies in the H-2Kbm1 promoter region revealed that a proximal 58 bp upstream sequence (-194 to -136, relative to the cap site) and a distal 316 bp sequence (-1837 to -1521) respectively contribute to positive and negative regulation mediated by the E1A gene product. Both regulatory elements of MHC class I gene promoter region are responsible for the differential expression of the H-2Kbm1 gene in Ad12 transformed cells. A nuclear factor binding to the negative element has been detected only in extracts derived from cells expressing Ad12-E1A.

Adenovirus Early Proteins↗
PubMed1990

Encapsulation of cells in agarose beads for use in the construction of human DNA libraries as yeast artificial chromosomes (YAC).

A simple and general method for the molecular cloning of fragments of over one hundred kilobase pairs of exogenous DNA, by the encapsulation of cells in agarose beads, was developed for the construction of a human genomic DNA library in a yeast artificial YAC chromosome vector (in situ YAC construction). The main advantages of this method for use in the construction of a human genome library are as follows. First, linear DNA molecules of up to several hundred kilobase pairs in size can easily be prepared by the partial restriction enzyme digestion of the DNA encapsulated in agarose beads in vitro. Second, less than 2 x 10(6) cells scraped from tissue culture plates are sufficient for preparation of the linear DNA molecule for construction of the genome library. The technical manipulations involved in construction of clones of very large segments of DNA, including encapsulation of cells in agarose beads, restriction enzyme digestion, ligation with the YAC vector, transformation into host yeast cells, and stable propagation are discussed.

Blotting, Southern↗
PubMed1990

Molecular cloning of cDNA encoding a human heat-shock protein whose expression is induced by adenovirus type 12 E1A in HeLa cells.

We have identified by differential plaque hybridization, human cDNA clones encoding a member of a heat-shock protein family (hsp 90 alpha) in the cDNA library of Adenovirus Type 12 E1A transfected HeLa cells. The complete nucleotide sequence of one of the clones (pHB76-114A) was identified. The sequence of 2912 base pairs had a single reading frame with a coding potential for an 84,672-Da protein. The amino acid sequence was highly homologous, but not identical, to that of the human hsp 90 alpha gene isolated from human peripheral blood lymphocytes [M. Yamazaki, K. Akaogi, T. Miwa, T. Imai, E. Soeda and K. Yokoyama, Nucleic Acids Res., 17, 7108 1989)]. This cDNA hybridized with RNA species which increased 5- to 20-fold upon heat shock and more than 5-fold in the differentiation stage of human Tera 2 cells.

Adenoviruses, Human↗