Isolation and characterization of a new 110 kDa human nuclear RNA-binding protein (p110nrb)

RNA-protein interactions play key roles in many fundamental cellular processes such as RNA processing, RNA transport, and RNA translation. During our attempts to isolate the human U6 small nuclear RNA capping enzyme, we identified a new 110 kDa nuclear RNA-binding protein, designated p110nrb. The full-length cDNA clone for p110nrb was characterized, and it encodes a 963 amino acid polypeptide. It is a highly acidic protein (pI 5.28) and the carboxyl terminal portion contains two conserved RNP motifs. A databank search found a putative C. elegans protein that might be the p110nrb homologue. The p110nrb was overexpressed as a glutathione S-transferase fusion protein in insect Sf9 cells, purified by affinity chromatography and injected into rabbits to produce specific polyclonal antibodies. Immunofluorescent staining showed that p110nrb is distributed evenly throughout the nucleoplasm. Northern blots showed that the mRNA is expressed in all tissues examined. An in vitro RNA-binding assay showed that p110nrb bound to RNA. These data suggest that p110nrb may play a role in the metabolism of nuclear RNA.

Guanine nucleotide exchange factors regulate specificity of downstream signaling from Rac and Cdc42

The Rac and Cdc42 GTPases regulate diverse cellular behaviors involving the actin cytoskeleton, gene transcription, and the activity of multiple protein and lipid kinases. All of these pathways can potentially become activated when GTP-Rac or GTP-Cdc42 is formed in response to external cell signals, yet it is evident that each activity must also be able to be controlled individually. The mechanisms by which such specificity of GTPase signaling in response to upstream stimuli is achieved remains unclear. We investigated the action of several well characterized guanine nucleotide exchange factors (GEFRho) to activate Rac- and/or Cdc42-dependent kinase pathways. Coexpression studies in COS-7 cells revealed that the ability of individual guanine nucleotide exchange factors (GEFs) to activate the p21-activated kinase PAK1 could be dissociated from activation of c-Jun amino-terminal kinase, even though activation of both pathways requires the action of the GEFs on Rac and/or Cdc42. In contrast, expression of constitutively active forms of Rac or Cdc42 effectively stimulated both downstream kinases. We conclude that GEFs can be important determinants of downstream signaling specificity for members of the Rho GTPase family.

Identification of high-molecular-weight proteins with multiple EGF-like motifs by motif-trap screening

To identify large proteins with an EGF-like-motif in a systematic manner, we developed a computer-assisted method called motif-trap screening. The method exploits 5'-end single-pass sequence data obtained from a pool of cDNAs whose sizes exceed 5 kb. Using this screening procedure, we were able to identify five known and nine new genes for proteins with multiple EGF-like-motifs from 8000 redundant human brain cDNA clones. These new genes were found to encode a novel mammalian homologue of Drosophila fat protein, two seven-transmembrane proteins containing multiple cadherin and EGF-like motifs, two mammalian homologues of Drosophila slit protein, an unidentified LDL receptor-like protein, and three totally uncharacterized proteins. The organization of the domains in the proteins, together with their expression profiles and fine chromosomal locations, has indicated their biological significance, demonstrating that motif-trap screening is a powerful tool for the discovery of new genes that have been difficult to identify by conventional methods.

Molecular characterization and postsplicing fate of three introns within the single rRNA operon of the hyperthermophilic archaeon Aeropyrum pernix K1

The single rRNA operon (arnS-arnL) of the hyperthermophilic archaeon Aeropyrum pernix K1 was sequenced. The DNA sequence data and detailed RNA analyses disclosed an unusual feature: the presence of three introns at hitherto undescribed insertion positions within the rRNA genes. The 699-nucleotide (nt) intron Ialpha was located at position 908 (Escherichia coli numbering [H. F. Noller, Annu. Rev. Biochem. 53:119-162, 1984]) of the 16S rRNA, while the 202-nt intron Ibeta and 575-nt intron Igamma were located at positions 1085 and 1927 (E. coli numbering), respectively, of the 23S rRNA. They were located within highly conserved sites which have been implicated as crucial for rRNA function in E. coli. All three introns were remarkably AT rich (41.5 to 43.1 mol% G+C) compared with the mature rRNAs (67.7 and 69.2 mol% G+C for 16S and 23S rRNAs, respectively). No obvious primary sequence similarities were detected among them. After splicing from rRNA transcripts in vivo, a large quantity of intronic RNAs were stably retained in the linear monomeric form, whereas a trace of topoisomeric RNA molecules also appeared, as characterized by their behavior in two-dimensional gel electrophoresis. Secondary structural models of the Ialpha-, Ibeta-, and Igamma-containing rRNA precursors agree with the bulge-helix-bulge motif. Two of the introns, Ialpha and Igamma, contained open reading frames whose protein translation exhibited no overall similarity with proteins reported so far. However, both share a LAGLI-DADG motif characteristic of homing endonucleases.

Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro

As an extension of our cDNA analysis for deducing the coding sequences of unidentified human genes, we have newly determined the sequences of 100 cDNA clones from a set of size-fractionated human brain cDNA libraries, and predicted the coding sequences of the corresponding genes, named KIAA0611 to KIAA0710. In vitro transcription-coupled translation assay was applied as the first screening to select cDNA clones which produce proteins with apparent molecular mass of 50 kDa and over. One hundred unidentified cDNA clones thus selected were then subjected to sequencing of entire inserts. The average size of the inserts and corresponding open reading frames was 4.9 kb and 2.8 kb (922 amino acid residues), respectively. Computer search of the sequences against the public databases indicated that predicted coding sequences of 87 genes were similar to those of known genes, 62% of which (54 genes) were categorized as proteins related to cell signaling/communication, cell structure/motility and nucleic acid management. The expression profiles in 10 human tissues of all the clones characterized in this study were examined by reverse transcription-coupled polymerase chain reaction and the chromosomal locations of the clones were determined by using human-rodent hybrid panels.

UBPY: a growth-regulated human ubiquitin isopeptidase

The ubiquitin pathway has been implicated in the regulation of the abundance of proteins that control cell growth and proliferation. We have identified and characterized a novel human ubiquitin isopeptidase, UBPY, which both as a recombinant protein and upon immunoprecipitation from cell extracts is able to cleave linear or isopeptide-linked ubiquitin chains. UBPY accumulates upon growth stimulation of starved human fibroblasts, and its levels decrease in response to growth arrest induced by cell-cell contact. Inhibition of UBPY accumulation by antisense plasmid microinjection prevents fibroblasts from entering S-phase in response to serum stimulation. By increasing or decreasing the cellular abundance of UBPY or by overexpressing a catalytic site mutant, we detect substantial changes in the total pattern of protein ubiquitination, which correlate stringently with cell proliferation. Our results suggest that UBPY plays a role in regulating the overall function of the ubiquitin-proteasome pathway. Affecting the function of a specific UBP in vivo could provide novel tools for controlling mammalian cell proliferation.

Group I introns found in Chlorella viruses: biological implications

More than 80 group I introns were detected and characterized in Chlorella viruses isolated from various locations in Japan; the overall average frequency of viruses containing the group I intron was 8.0%. Although most of these introns were inserted in the gene for either transcriptional elongation factor TFIIS (approximately 60%) or URF 14.2 (unidentified open reading frame coding for a 14.2-kDa polypeptide) (approximately 40%), in a few cases, the gene for the major capsid protein Vp52 contained an intron. These introns were biologically active (self-splicing) both in vivo and in vitro. Viruses that contained introns almost usually contained only one, but more than two introns coexisted in several virus isolates. Nucleotide sequence analysis showed that the intron sequences have diverged under strong constraint of the exon genes: introns in the same gene showed more than 99% sequence identity, whereas introns in different genes were only 72-78% identical. Phylogenetic analysis suggested relatedness of these introns to those found in the rRNA genes of a variety of organisms including green algae, red algae, red algae, yeasts, fungi, and protozoa.

Rearrangement of c-myc gene in rapidly induced avian lymphoid leukosis tumors

Southern blot hybridization of DNA samples from 9 primary tumors of avian lymphoid leukosis (LL) rapidly induced by ALV infection 27-74 days post inoculation was carried out to search for rearrangement of the c-myc gene with human c-myc gene exon III as a probe. Rearrangement of the c-myc gene was detected by appearance of new EcoRI fragments in 7 out of 9 tumors examined. The size of the fragments ranged from 3.1 to 4.0 kilobases (kb). In addition to these fragments, two fragments (9.0 kb and 13 kb) were observed in one tumor, and a faint fragment (3.5 kb) was observed in another tumor. Rearrangement of the c-myc gene was not detected in the remaining two tumors kept in unsuitable condition. These results suggest that rearrangement of c-myc gene was induced even in rapidly induced LL as well as that induced after long incubation period. This is the first report of involvement of c-myc gene in rapidly induced B-cell lymphoma (LL).

Antitumor effect of S-1 on DMH induced colon cancer in rats

The aim of this study was to establish an autochthonous colon cancer model in the rat as an in vivo secondary screen for the general evaluation of new anticancer agents against colorectal cancer, and also to evaluate practically the antitumor activity of 1M tegafur-0.4M 5- chloro-2,4-dihydroxypyridine-1M potassium oxonate(S-1), a new p.o. fluoropyrimidine. Thirty-two Sprague-Dawley rats received dimethlhydrazine(40 mg/kg) s.c. once weekly for 10 weeks to induce colon cancer.20 weeks after beginning the carcinogen treatment, a barium enema was performed to visualize tumors. The animals were divided into a control group and S-1 treatment group. After 5 weeks of treatment, the barium enema was repeated. The mean doubling time of 24 tumors in the control group was 19.0 + 8.4 (SD) days. Response to S-1 was judged as effective when the doubling time exceeded 35.8 days, calculated from the mean + 2SDs in the control group. The response rate of S-1 was 55%, 34% of the tumors were decreased in size after treatment. This figure was higher than that of clinically-used 5-fluorouracil(5-FU) derivatives; 5-FU;6%, Tegafur(FT):6%, 1M tegafur-4M uracil(UFT):14%, reported in our previous study. An autochthonous colon cancer model is useful to evaluate the clinical therapeutic efficacy of drugs for colorectal cancer, and S-1 is expected to have a high therapeutic effect on human colorectal cancer.

Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro

As an extension of a series of projects for sequencing human cDNA clones derived from relatively long transcripts, we herein report the entire sequences of 100 newly determined cDNA clones with the potential of coding for large proteins in vitro. The cDNA clones were isolated from size-fractionated human brain cDNA libraries with insert sizes between 4.5 and 8.3 kb. The sequencing of these clones revealed that the average size of the cDNA inserts and of their open reading frames was 5.3 kb and 2.8 kb (930 amino acid residues), respectively. Homology search against public databases indicated that the predicted coding sequences of 86 clones exhibited significant similarities to known genes; 51 of them (59%) were related to those for cell signaling/communication, nucleic acid management, and cell structure/motility. All the clones characterized in this study are accompanied by their expression profiles in 14 human tissues examined by reverse transcription-coupled polymerase chain reaction and the chromosomal mapping data.

The AML1-MTG8 leukemic fusion protein forms a complex with a novel member of the MTG8(ETO/CDR) family, MTGR1

The AML1-CBFbeta transcription factor complex is essential for the definitive hematopoiesis of all lineages and is the most frequent target of chromosomal rearrangements in human leukemia. In the t(8;21) translocation associated with acute myeloid leukemia (AML), the AML1(CBFA2/PEBP2alphaB) gene is juxtaposed to the MTG8(ETO/CDR) gene. We show here that the resultant AML1-MTG8 gene product specifically and strongly interacts with an 85-kDa phosphoprotein. Molecular cloning of cDNA indicated that the AML1-MTG8-binding protein (MTGR1) is highly related to MTG8 and similar to Drosophila Nervy. Comparison of amino acid sequences among MTGR1, MTG8, and Nervy revealed four evolutionarily conserved regions (NHR1 to NHR4). Ectopic expression of AML1-MTG8 in L-G murine myeloid progenitor cells inhibits differentiation to mature neutrophils and induces cell proliferation in response to granulocyte colony-stimulating factor (G-CSF). Analysis with C-terminal deletion mutants of AML1-MTG8 indicated that the region of 51 residues (488 to 538), which contains NHR2, is essential for the induction of G-CSF-dependent cell proliferation. Immunoprecipitation analysis indicates that this region is required for AML1-MTG8 to form a stable complex with MTGR1. Overexpression of MTGR1 stimulates AML1-MTG8 to induce G-CSF-dependent proliferation of L-G cells and to interfere with AML1-dependent transcription. These results suggest that AML1-MTG8 could function as a complex with MTGR1 and that the complex might be important in promoting leukemogenesis.

Characterization of a human homolog (BACH1) of the mouse Bach1 gene encoding a BTB-basic leucine zipper transcription factor and its mapping to chromosome 21q22.1

Clinical interest in the genes on human chromosome 21, especially with respect to Down syndrome (DS), has provided a strong impetus for the creation of a transcript map of this chromosome. In an effort to identify new human genes on the basis of cDNA analysis, we found several cDNA clones that corresponded to chromosome 21-specific transcripts. One of these, ha2303, showed strong similarity to the murine transcription factor Bach1. We subsequently determined the entire nucleotide sequence of this cDNA clone and found it to contain the whole coding sequence. The gene, termed BACH1, encodes a 736-amino-acid polypeptide with 80.3% identity to the murine Bach1 protein and contains a Cap'n'collar (CNC)-type basic leucine zipper (bZip) domain and a protein interaction motif, the BTB domain. Northern blot analysis revealed that BACH1 was expressed in all tissues examined. Mapping using the NotI restriction map and the YAC contig map showed that the BACH1 gene is located at 21q22.1 between the NotI sites LA329 (D21S338) and LL60 (D21S389) and within approximately 400 kb of LA329. Both the prospective function and the chromosomal location suggest that this gene may be a DS candidate gene, contributing to certain DS phenotypes, and is possibly involved in certain features of monosomy 21.

Intraischemic hypothermia during pretreatment with sublethal ischemia reduces the induction of ischemic tolerance in the gerbil hippocampus

We examined whether mild brain hypothermia during pretreatment with sublethal 2-min ischemia affected the tolerance to subsequent lethal 5-min ischemia. The neuronal densities in the hippocampal CA1 sector of gerbils preconditioned at mild brain hypothermia (32% of normal) were significantly lower than those in gerbils preconditioned at brain normothermia (70% of normal). 72-kDa heat-shock protein immunoreactivity in the CA1 sector preconditioned at mild hypothermia was reduced. These results suggest that mild brain hypothermia during pretreatment with sublethal ischemia reduces the tolerance to subsequent lethal ischemia.

p140Sra-1 (specifically Rac1-associated protein) is a novel specific target for Rac1 small GTPase

Rac1 small GTPase plays pivotal roles in various cell functions such as cell morphology, cell polarity, and cell proliferation. We have previously identified IQGAP1 from bovine brain cytosol as a target for Rac1 by an affinity purification method. By using the same method, we purified a specifically Rac1-associated protein with a molecular mass of about 140 kDa (p140) from bovine brain cytosol. This protein interacted with guanosine 5'-(3-O-thio)triphosphate (GTPgammaS).glutathione S-transferase (GST)-Rac1 but not with the GDP.GST-Rac1, GTPgammaS.GST-Cdc42, or GTPgammaS.GST-RhoA. The amino acid sequences of this protein revealed that p140 is identified as a product of KIAA0068 gene. We denoted this protein as Sra-1 (Specifically Rac1-associated protein). Recombinant Sra-1 interacted with GTPgammaS.GST-Rac1 and weakly with GDP.Rac1 but not with GST-Cdc42 or GST-RhoA. The N-terminal domain of Sra-1 (1-407 amino acids) was responsible for the interaction with Rac1. Myc-tagged Sra-1 and the deletion mutant capable of interacting with Rac1, but not the mutants unable to bind Rac1, were colocalized with dominant active Rac1(Val-12) and cortical actin filament at the Rac1(Val-12)-induced membrane ruffling area in KB cells. Sra-1 was cosedimented with filamentous actin (F-actin), indicating that Sra-1 directly interacts with F-actin. These results suggest that Sra-1 is a novel and specific target for Rac1.

Effect of soluble complement receptor type 1 on porphyrin-induced phototoxicity in guinea pigs

The effect of recombinant human soluble complement receptor type 1 (sCR1) on the porphyrin-mediated phototoxic reaction was evaluated in guinea pigs. Phototoxicity was induced in the animals by intraperitoneal injection of hematoporphyrin derivative (HpD), followed by irradiation at a wavelength range of 320-450 nm. sCR1 administration decreased CH50 titers in a dose-dependent fashion, while it only moderately suppressed HpD/radiation-induced ear swelling at a high dose. These findings suggest that phototoxic dermatological changes in cutaneous porphyrias are not solely due to complement activation.

Identification and chromosome assignment of a human gene encoding a novel phosphatidylinositol-3 kinase

We identified a novel phosphatidylinositol (PI) 3-kinase by screening human brain cDNA libraries with probes designed from the conserved kinase-domain sequence. Analysis of cDNAs indicated that two different forms of transcripts are present: one is the full-length form composed of 1,044 amino acid residues and the other is the short form that the N-terminal 216 amino acid residues including a putative p85 binding domain has been truncated (828 amino acid residues). Database search revealed the sequence of the full-length form to be identical to that recently registered by D. Chantry et al. (Accession No. U86453 in GenBank release, August 1997). Northern blot analysis showed this mRNA to be ubiquitously expressed in various tissues, with relatively higher expression was observed in spleen, thymus and leukocytes. Based on fluorescence in situ hybridization and PCR-based analyses with both human/rodent mono-chromosomal hybrid cell panels and radiation hybrid mapping panels, this gene was localized to chromosome region 1p36.2. This region is frequently lost in a variety of human malignancies, including neuroblastoma. The novel PI3K could be a candidate target of the 1p36 alteration that occurs in neuroendocrine tumors.

Characterization of cDNA clones in size-fractionated cDNA libraries from human brain

To evaluate the size-fractionated cDNA libraries of human brain previously constructed (O. O'hara et al. DNA Research, 4, 53-59, 1997), the occurrence of chimeric clones and the content of clones with coding potentiality were analyzed using the randomly sampled clones with insert sizes of 5 to 7 kb. When the chromosomal location of 30 clones was determined by the radiation-hybrid mapping method, the map positions assigned from the 3'- and 5'-end sequences separately were coincident for 29 clones, suggesting that the occurrence of chimeric clones is at most 1/30. Using 91 clones mapped to chromosome 1, the content of clones that have the potentiality coding for proteins larger than 100 amino acid residues was estimated to be approximately 50% (46 out of 91 clones) on the basis of nucleotide sequence analysis and coding potentiality assay in vitro. No significant open reading frames were detected in the remaining clones. Although the clones coding for short peptides may not have been included in the above estimation, the libraries constructed from the whole brain mRNA fraction appear to contain a considerable amount of clones corresponding to the 5'-truncated transcripts in an unprocessed form and/or those with long 3'-untranslated regions.

Prediction of the coding sequences of unidentified human genes. VIII. 78 new cDNA clones from brain which code for large proteins in vitro

As a part of our project for accumulating sequence information of the coding regions of unidentified human genes, we herein report the sequence features of 78 new cDNA clones isolated from human brain cDNA libraries as those which may code for large proteins. The sequence data showed that the average size of the cDNA inserts and their open reading frames was 6.0 kb and 2.8 kb (925 amino acid residues), respectively, and these clones produced the corresponding sizes of protein products in an in vitro transcription/translation system. Homology search against the public databases indicated that the predicted coding sequences of 68 genes contained sequences similar to known genes, 69% of which (47 genes) were related to cell signaling/communication, nucleic acid management, and cell structure/motility. The expression profiles of these genes in 14 different tissues have been analyzed by the reverse transcription-coupled polymerase chain reaction method, and 8 genes were found to be predominantly expressed in the brain.

The genomic analysis of human DAN gene

DAN gene is shown to be localized at human chromosome 1p36.11-p36.13, which resides within the consensus deletion observed in neuroblastoma. In the present study, we have isolated the genomic DNA containing the entire human DAN gene and determined its nucleotide sequence. Structural analysis revealed that DAN gene is composed of four exons and spans approximately 15 kb. Its overall structure was basically the same as that of rat DAN gene. Two distinct transcription initiation sites (major and minor) were identified by the primer extension experiment. Putative TATA and CAAT-like elements are present 38 and 366 bp upstream from the major transcription start site, respectively, however, no apparent TATA-like sequence was found in the upstream region of the minor transcription start site. The 400-bp region immediately upstream from the major transcription initiation site was strongly GC-rich (79% GC). Genomic Southern experiments demonstrated that the allelic loss of DAN gene might occur in neuroblastoma. Interestingly, there exist two dinucleotide repeats, (CA)7 and (CA)8, in the first intron of DAN gene, raising the possibility to distinguish two alleles of DAN gene in some of the cancer cells.

Analysis of the functional domain of the rat liver mitochondrial import receptor Tom20

Tom20 is an outer mitochondrial membrane protein and functions as a component of the import receptor complex for the cytoplasmically synthesized mitochondrial precursor proteins. It consists of the N-terminal membrane-anchor segment, the tetratricopeptide repeat (TPR) motif, a charged amino acids-rich linker segment between the membrane anchor and the TPR motif, and the C-terminal acidic amino acid cluster. To assess the functional significance of these segments in mammalian Tom20, we cloned rat Tom20 and expressed mutant rat Tom20 proteins in Deltatom20 yeast cells and examined their ability to complement the defects of respiration-driven growth and mitochondrial protein import. Tom20N69, a mutant consisting of the membrane anchor and the linker segments, was targeted to mitochondria and complemented the growth and import defects as efficiently as wild-type Tom20, whereas a mutant lacking the linker segment did not. In vitro protein import into mitochondria isolated from the complemented yeast cells revealed that the precursor targeted to yeast Tom70 was efficiently imported into the mitochondria via rat Tom20N69. Thus the linker segment is essential for the function of rat Tom20, whereas the TPR motif and the C-terminal acidic amino acids are not.

Nonpalpable lymph nodes of the neck: assessment with US and US-guided fine-needle aspiration biopsy

Ultrasound (US) and US-guided fine-needle aspiration biopsy (FNA) were performed in 91 nonpalpable neck nodes of 70 patients, 98% of which had known malignancy. Various sonographic findings were evaluated for predicting malignancy. The accuracy of US-guided FNA for detecting malignancy was 88%, with 96% sensitivity and 94% specificity. The ratio of minimal to maximal axial diameters of a node was most valid for predicting malignancy with US. A ratio of more than 0.55 yielded the highest accuracy (80%) (92% sensitivity, 63% specificity). Addition of any other factors to this criterion did not improve its accuracy. US and US-guided FNA are accurate for the assessment of nonpalpable neck nodes. Lymph nodes with a round configuration should be biopsied in patients with known malignancy.

The possible role of zinc and metallothionein in the liver on the therapeutic effect of IFN-alpha to hepatitis C patients

We have studies zinc deficiency in hepatitis C patients (complete responder [CR] 22, nonresponder [NR] 25) with relation to the therapeutic effect of interferon-alpha (IFN-alpha). Circadian variations in serum zinc levels were high in the morning (basal level) and then gradually decreased during the day in both chronic hepatitis C patients and healthy controls. Basal zinc levels in serum were significantly lower in chronic hepatitis C patients (73 +/- 3 micrograms/dL, n = 12) than in controls (93 +/- 5 micrograms/dL). An injection of 10 MU of IFN-alpha to hepatitis C patients augmented the serum zinc reductions, up to 40% in 8 h. Serum cortisol levels were significantly elevated 8 h (25.6 +/- 2.3 micrograms/dL) after IFN-alpha dose. Forty-seven chronic hepatitis C patients were treated with IFN-alpha for 24 wk, and serum zinc and copper levels were determined 12 and 24 wk during and after the completion of IFN-alpha therapy. Serum zinc levels and zinc/copper ratio were higher in CRs than in NRs to IFN therapy at each time-point. Hepatic metallothionein staining became prominent after IFN therapy in most of CRs, whereas it diminished NRs. These data suggest that nutritional status of zinc influences the effect of IFN on hepatitis C patients.

Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro

In this series of projects of sequencing human cDNA clones which correspond to relatively long transcripts, we newly determined the entire sequences of 100 cDNA clones which were screened on the basis of the potentiality of coding for large proteins in vitro. The cDNA libraries used were the fractions with average insert sizes from 5.3 to 7.0 kb of the size-fractionated cDNA libraries from human brain. The randomly sampled clones were single-pass sequenced from both the ends to select clones that are not registered in the public database. Then their protein-coding potentialities were examined by an in vitro transcription/translation system, and the clones that generated proteins larger than 60 kDa were entirely sequenced. Each clone gave a distinct open reading frame (ORF), and the length of the ORF was roughly coincident with the approximate molecular mass of the in vitro product estimated from its mobility on SDS-polyacrylamide gel electrophoresis. The average size of the cDNA clones sequenced was 6.1 kb, and that of the ORFs corresponded to 1200 amino acid residues. By computer-assisted analysis of the sequences with DNA and protein-motif databases (GenBank and PROSITE databases), the functions of at least 73% of the gene products could be anticipated, and 88% of them (the products of 64 clones) were assigned to the functional categories of proteins relating to cell signaling/communication, nucleic acid managing, and cell structure/motility. The expression profiles in a variety of tissues and chromosomal locations of the sequenced clones have been determined. According to the expression spectra, approximately 11 genes appeared to be predominantly expressed in brain. Most of the remaining genes were categorized into one of the following classes: either the expression occurs in a limited number of tissues (31 genes) or the expression occurs ubiquitously in all but a few tissues (47 genes).

Human small Maf proteins form heterodimers with CNC family transcription factors and recognize the NF-E2 motif

The transcription factor NF-E2, a heterodimeric protein complex composed of p45 and small Maf family proteins, is considered crucial for the regulation of erythroid gene expression and platelet formation. To facilitate the characterization of NF-E2 functions in human cells, we isolated cDNAs encoding two members of the small Maf family, MafK and MafG. The human mafK and mafG genes encode proteins of 156 and 162 amino acid residues, respectively, whose deduced amino acid sequences show approximately 95% identity to their respective chicken counterparts. Expression of mafK mRNA is high in heart, skeletal muscle and placenta, whereas mafG mRNA is abundant in skeletal muscle and is moderately expressed in heart and brain. Both are expressed in all hematopoietic cell lines, including those of erythroid and megakaryocytic lineages. In electrophoretic gel mobility shift assays binding to NF-E2 sites was found to depend on formation of homodimers or heterodimers with p45 and p45-related CNC family proteins. The results suggest that the small Maf family proteins function in human cells through interaction with various basic-leucine zipper-type transcription factors.

Construction and characterization of human brain cDNA libraries suitable for analysis of cDNA clones encoding relatively large proteins

Analysis of proteins registered in the PIR protein database implied that most of relatively large proteins are related to important functions in higher multicellular organisms, but not many large proteins have been registered to date. To establish a protocol for efficient analysis of cDNA clones coding for large proteins, we constructed a series of strictly size-fractionated cDNA libraries of human brain, where the average insert sizes of cDNA clones ranged from 3.3 kb to 10 kb. As judged by hybridization analysis with probes derived from mRNAs of known sizes, the libraries with insert sizes up to 7 kb, at least, contained the clones corresponding to full-length transcripts in addition to truncated products of longer transcripts, but few chimeric clones. Using one of the fractionated libraries with an average insert size of 7 kb, the single-pass sequences from both the ends of randomly sampled clones were determined and sarched against DNA databases. Approximately 90% of the clones were found to be new with respect to their 5'-sequences while their 3'-sequences were frequently similar to the registered expression sequence tags. Examination of the protein-coding capacity in an in vitro transcription/translation system showed that about 20% of the clones direct the synthesis of proteins with apparent molecular masses larger than 50 kDa. The set of libraries constructed here should be very useful for the accumulation of sequence data on large proteins in the human brain.

Molecular defects of the coproporphyrinogen oxidase gene in hereditary coproporphyria

Hereditary coproporphyria (HCP) is an acute hepatic porphyria, and is an autosomal dominant disorder but with a variable degree of clinical expression. Molecular cloning, sequencing and expression of the defective gene for coproporphyrinogen oxidase (CPO) in a patient with HCP were carried out. Enzyme assays revealed that CPO activity in EBV-transformed lymphoblastoid cells from the proband and one of her sisters was approximately 50% of normal. Nucleotide sequence analysis of CPO cDNAs isolated from the proband's cells demonstrated 3 base substitutions which accompanied 3 different amino acid substitutions. An A514-->C transition causing an Asn172-->His substitution occurred in one allele, while two other transitions, G265-->A and G580-->A, caused Gly89-->Ser and Val194-->Ile substitutions, respectively, in the other allele. The A514-->C and the G580-->A transitions were shown to be genetic polymorphisms. Transfection of CPO cDNA into E. coli demonstrated that cDNA with the G265-->A transition produced a protein with less than 5% of normal enzyme activity. These findings indicate that the G265-->A transition, involving the highly conserved glycine residue at the 89th position, is responsible for the CPO defect in the patient and accounts for the partial deficiency of CPO activity in this pedigree. This mutation is different from three other mutations reported in patients with HCP. Molecular defects in the porphyrias including HCP are highly heterogeneous.

Identification of a human cDNA clone for lysosomal type Ca2+-independent phospholipase A2 and properties of the expressed protein

A Ca2+-independent phospholipase A2 (PLA2) maximally active at pH 4 and specifically inhibited by the transition-state analogue 1-hexadecyl-3-trifluoroethylglycero-sn-2-phosphomethanol (MJ33) was isolated from rat lungs. The sequence for three internal peptides (35 amino acids) was used to identify a 1653-base pair cDNA clone (HA0683) from a human myeloblast cell line. The deduced protein sequence of 224 amino acids contained a putative motif (GXSXG) for the catalytic site of a serine hydrolase, but showed no significant homology to known phospholipases. Translation of mRNA produced from this clone in both a wheat germ system and Xenopus oocytes showed expression of PLA2 activity with properties similar to the rat lung enzyme. Apparent kinetic constants for PLA2 with dipalmitoylphosphatidylcholine as substrate were Km = 0.25 mM and Vmax = 1.89 nmol/h. Activity with alkyl ether phosphatidylcholine as substrate was decreased significantly compared with diacylphosphatidylcholine. Significant lysophospholipase, phospholipase A1, or 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine acetylhydrolase activity was not observed. Enzyme activity was insensitive to p-bromophenacyl bromide, bromoenol lactone, trifluoromethylarachidonoyl ketone, mercaptoethanol, and ATP, but was inhibited by MJ33 and diethyl p-nitrophenyl phosphate, a serine protease inhibitor. SDS-polyacrylamide gel electrophoresis with autoradiography of the translated [35S]methionine-labeled protein confirmed a molecular mass of 25.8 kDa, in good agreement with the enzyme isolated from rat lung. By Northern blot analysis, mRNA corresponding to this clone was present in both rat lung and isolated rat granular pneumocytes. These results represent the first molecular cloning of a cDNA for the lysosomal type Ca2+-independent phospholipase A2 group of enzymes.

Intraischemic hypothermia during pretreatment with sublethal ischemia reduces the induction of ischemic tolerance in the gerbil hippocampus

We examined whether mild brain hypothermia during pretreatment with sublethal 2-min ischemia affected the tolerance to subsequent lethal 5-min ischemia. The neuronal densities in the hippocampal CA1 sector of gerbils preconditioned at mild brain hypothermia (32% of normal) were significantly lower than those in gerbils preconditioned at brain normothermia (70% of normal). 72-kDa heat-shock protein immunoreactivity in the CA1 sector preconditioned at mild hypothermia was reduced. These results suggests that mild brain hypothermia during pretreatment with sublethal ischemia reduces the tolerance to subsequent lethal ischemia.

Gene identification in 1.6-Mb region of the Down syndrome region on chromosome 21

The Down syndrome (DS) region has been defined by analyses of partial trisomy 21. The 2.5-Mb region between D21S17 and ERG is reportedly responsible for the main features of DS. Within this 2.5-Mb region, we focused previously on a distal 1.6-Mb region from an analysis of Japanese DS patients with partial trisomy 21. Previously we also performed exon-trapping and direct cDNA library screening of a fetal brain cDNA library and identified a novel gene TPRD. Further screening of a fetal heart cDNA library was performed and a total of 44 possible exons and 97 cDNA clones were obtained and mapped on a BamH1 map. By rescreening other cDNA libraries and a RACE reaction, we isolated nearly full-length cDNAs of three additional genes [holocarboxylase synthetase (HCS), G protein-coupled inward rectifier potassium channel 2 (GIRK2), and a human homolog of Drosophila minibrain gene (MNB)] and a coding sequence of a novel inward rectifier potassium channel-like gene (IRKK). The gene distribution and direction of transcription were determined by mapping both ends of the cDNA sequences. We found that these genes, except IRKK, are expressed ubiquitously and are relatively large, extending from 100 kb to 300 kb on the genome. These nearly full-length cDNA sequences should facilitate understanding of the detailed genome structure of the DS region and help to elucidate their role in the etiology of DS.

Poor correlation with loss of heterozygosity on chromosome 17p and p53 mutations in ovarian cancers

To define the target of chromosome 17p deletions, allelic losses in the 17p11.2 to 13.3 regions of 32 ovarian cancers were investigated. Twenty-one (68%) of 31 informative cancers had deletions on chromosome 17p. None of these 21 cancers involved deletions in the entire chromosome 17p even if deletions of a small chromosome region were infrequent. Of these 21, 17 cancers contained deletions at 17p13.1 or neighboring regions. The remaining 4 cancers with 17p deletions were uninformative for deletions at 17p13.1. Thus, most 17p deletions seemed to target the 17p13.1 region in ovarian cancers. Of the 30 ovarian cancers screened, 6 contained p53 mutations. One p53 allele was lost as a consequence of deletion and the other was mutated in 4 cancers. Seventeen cancers with deletions on 17p showed no evidence of p53 mutations. Thus, deletions on 17p that are common in ovarian cancers are not always accompanied by p53 gene mutations.

Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain

In this series of projects of sequencing human cDNA clones which correspond to relatively long and nearly full-length transcripts, we newly determined the sequences of 80 clones, and predicted the coding sequences of the corresponding genes, named KIAA0201 to KIAA0280. Among the sequenced clones, 68 were obtained from human immature myeloid cell line KG-1 and 12 from human brain. The average size of the clones was 5.3 kb, and that of distinct ORFs in clones was 2.8 kb, corresponding to a protein of approximately 100 kDa. Computer search against the public databases indicated that the sequences of 22 genes were unrelated to any reported genes, while the remaining 58 genes carried sequences which show some similarities to known genes. Protein motifs that matched those in the PROSITE motif database were found in 25 genes and significant transmembrane domains were identified in 30 genes. Among the known genes to which significant similarity was shown, the genes that play key roles in regulation of developmental stages, apoptosis and cell-to-cell interaction were included. Taking into account of both the search data on sequence similarity and protein motifs, at least seven genes were considered to be related to transcriptional regulation and six genes to signal transduction. When the expression profiles of the cDNA clones were examined with different human tissues, about half of the clones from brain (5 of 11) showed significant tissue-specificity, while approximately 80% of the genes from KG-1 were expressed ubiquitously.

A gene map of the human genome

The human genome is thought to harbor 50,000 to 100,000 genes, of which about half have been sampled to date in the form of expressed sequence tags. An international consortium was organized to develop and map gene-based sequence tagged site markers on a set of two radiation hybrid panels and a yeast artificial chromosome library. More than 16,000 human genes have been mapped relative to a framework map that contains about 1000 polymorphic genetic markers. The gene map unifies the existing genetic and physical maps with the nucleotide and protein sequence databases in a fashion that should speed the discovery of genes underlying inherited human disease. The integrated resource is available through a site on the World Wide Web at http://www.ncbi.nlm.nih.gov/SCIENCE96/.

Aeropyrum pernix gen. nov., sp. nov., a novel aerobic hyperthermophilic archaeon growing at temperatures up to 100 degrees C

A novel aerobic hyperthermophilic archaeon was isolated from a coastal solfataric vent at Kodakara-Jima Island, Japan. The new isolate, strain K1, is the first strictly aerobic organism growing at temperatures up to 100 degrees C. It grows optimally at 90 to 95 degrees C, pH 7.0, and a salinity of 3.5%. The cells are spherical shaped and 0.8 to 1.2 microns in diameter. Various proteinaceous complex compounds served as substrates during aerobic growth. Thiosulfate stimulates growth without producing H2S. The core lipids consist solely of C25-isopranyl archaeol (glycerol diether). The G + C content of the genomic DNA is 67 mol%. Phylogenetic analysis based on 16S rRNA sequence indicates that strain K1 is a new member of Crenarchaeota. On the basis of our results, the name Aeropyrum pernix gen. nov., sp. nov. is proposed (type strain: K1; JCM 9820).

Identification of IQGAP as a putative target for the small GTPases, Cdc42 and Rac1

Cdc42 and Rac1 have been implicated in the regulation of various cell functions such as cell morphology, polarity, and cell proliferation. We have partially purified a Cdc42- and Rac1-associated protein with molecular mass of about 170 kDa (p170) from bovine brain cytosol. This protein interacted with guanosine 5'-(3-O-thio)triphosphate (GTPgammaS).glutathione S-transferase (GST)-Cdc42 and GTPgammaS++.GST-Rac1 but not with the GDP.GST-Cdc42, GDP.GST-Rac1, or GTPgammaS.GST-RhoA). We identified p170 as an IQGAP, which is originally identified as a putative Ras GTPase-activating protein. Recombinant IQGAP specifically interacted with GTPgammaS.Cdc42 and GTPgammaS.Rac1. The C-terminal fragment of IQGAP was responsible for their interactions. IQGAP was specifically immunoprecipitated with dominant-active Cdc42(Val12) or Rac1(Val12) from the COS7 cells expressing Cdc42(Val12) or Rac1(Val12), respectively. Immunofluorescence analysis revealed that IQGAP was accumulated at insulin- or Rac1-induced membrane ruffling areas. This accumulation of IQGAP was blocked by the microinjection of the dominant-negative Rac1(Asn17) or Cdc42(Asn17). Moreover, IQGAP was accumulated at the cell-cell junction in MDCK cells, where alpha-catenin and ZO-1 were localized. These results suggest that IQGAP is a novel target molecule for Cdc42 and Rac1.

Abnormal serum porphyrin levels in patients with the acquired immunodeficiency syndrome with or without hepatitis C virus infection

OBJECTIVE

To define the contributions of human immunodeficiency virus (HIV) and hepatitis C virus infections to the development of porphyria cutanea tarda.

DESIGN

Analysis of serum porphyrin levels in a cohort of 167 subjects. Serum samples were divided into 4 groups corresponding to the status of HIV and hepatitis C virus infections: positive-positive, positive-negative, negative-positive, and negative-negative.

SETTING

Serum samples positive for HIV were obtained from the serum bank of an acquired immunodeficiency syndrome-HIV research center, and HIV-negative samples were obtained from a regional blood center.

MAIN OUTCOME MEASURES

Spectrofluorometric measurement of serum porphyrin levels.

RESULTS

The median values of porphyrin were 2.31 nmol/L (interquartile range [difference between the 25th and 75th percentiles]: 4.55) in the positive-positive group, 1.99 nmol/L (interquartile range: 1.63) in the positive-negative group, 1.31 nmol/L (interquartile range: 1.58) in the negative-positive group, and 1.14 nmol/L (interquartile range: 0.92) in the negative-negative group. The fluorescence emission spectra of samples with elevated porphyrin levels were identical with that reported for porphyria cutanea tarda. Elevated porphyrin levels were significantly associated with HIV infection (P < .001) and were observed in patients with an elevated level of alanine aminotransferase (P = .03). Infection with hepatitis C virus was also associated with an elevation in porphyrin levels, although the increase was not statistically significant (P = .16). Porphyrin levels in patients positive for HIV were not correlated with serum urea nitrogen or creatinine levels. None of the patients had symptomatic porphyria cutanea tarda.

CONCLUSIONS

Factors associated with increased serum porphyrin levels included HIV infection, elevated alanine aminotransferase levels, and, to a lesser extent, hepatitis C virus infection. These findings suggest that patients with the above risk factors are potentially predisposed to the development of symptomatic porphyria cutanea tarda on further exposure to hepatotoxic agents.

RN-tre identifies a family of tre-related proteins displaying a novel potential protein binding domain

Eps8 is a recently identified SH3-containing substrate for tyrosine kinase receptors. To understand the role of eps8 in receptor-mediated signaling, we cloned cDNAs encoding proteins that bind to its SH3 domain. One of these cDNAs predicts the synthesis of an 828 amino acid protein with homology to the N-terminal region of the tre oncogene. We designated this protein RN-tre for Related to the N-terminus of tre. RN-tre is ubiquitously expressed and maps to 10p13, a region known to be involved in translocations in various leukemias. In addition, a 10p13 monosomy syndrome, characterized by developmental alterations, has been reported. The regional homology between RN-tre and tre, which is limited to their N-terminal portion, prompted us to investigate the origin of the tre oncogene transcriptional unit. We were able to show that tre is the fusion product of a 5' genetic element, homologous to RN-tre and a 3' element, encoding a de-ubiquinating enzyme. Moreover, we identified, within the N-terminus of RN-tre and tre, a domain (named TrH, for Tre Homology), which is conserved within several proteins from yeast to mammals and has protein-binding properties in vitro.

RN-tre specifically binds to the SH3 domain of eps8 with high affinity and confers growth advantage to NIH3T3 upon carboxy-terminal truncation

We isolated a cDNA encoding a protein, RN-tre, which shows homology to the N-terminus of the tre oncogene product and has SH3-binding ability as well as an evolutionarily conserved domain, termed TrH, with protein-binding ability in vitro. In the present study, we identify the product of the RN-tre gene as a 97-100 kDa protein. We demonstrate stable association in vivo and in vitro between RN-tre and eps8, mediated by the SH3 domain of the latter. In vitro, RN-tre displayed remarkable preference for binding to the eps8-SH3, as compared to eight other SH3s. The Kd for the in vitro interaction between RN-tre and eps8-SH3 was between 10(-8) and 10(-7) M. A role for RN-tre in cell proliferation was suggested by the finding that a C-terminal truncated mutant was able to confer proliferative advantage and reduced serum-requirement to NIH3T3 fibroblasts. Finally, comparison of the structure and biological activities of RN-tre and of the tre oncogene product, provided insight into the mechanism of oncogenic activation of tre.

Inhibitory effect of a synthetic prostacyclin analogue, beraprost, on urokinase-type plasminogen activator expression in RC-K8 human lymphoma cells

Plasminogen activation by urokinase-type plasminogen activator (uPA) is implicated in tumor invasion and metastasis by the breakdown of extracellular matrix. We have recently demonstrated the inhibitory effect of cAMP on uPA gene transcription in RC-K8 human lymphoma cells (Biochim Biophys Acta 1268: 293-9, 1995). Prostacyclin produced by endothelial cells is shown to increase cellular cAMP levels by activating adenylate cyclase. We, therefore, examined the effect of a stable analogue of prostacyclin, Beraprost, on uPA production in RC-K8 cells. uPA activity gradually increased in the conditioned medium with time. Beraprost (0.1 nM-1.0 microM) inhibited uPA accumulation in a dose-dependent manner without affecting cell viability. Fibrinzymography demonstrated that high and low molecular forms of uPA were present in the conditioned medium and that after Beraprost-treatment all forms of uPA decreased and no PA/PA inhibitor complex was present. Northern blot analysis revealed that after exposure to Beraprost, uPA mRNA levels increased transiently and then rapidly decreased to below control levels. Treatment with Beraprost resulted in a rapid activation of cellular cyclic AMP-dependent protein kinase (PKA). Beraprost completely negated uPA gene expression induced by phorbol myristate acetate, an activator of protein kinase C (PKC). These results suggest that Beraprost inhibits uPA production by suppressing uPA gene expression through the PKA pathway and that PKA-mediated signals are dominant in uPA gene expression as compared to those medicated by PKC. This inhibition of uPA expression by a prostacyclin analogue may be an important fact to explain the mechanism of anti-metastatic effects of prostacyclin.

Translatability of family concepts into the Japanese culture: using the Family Environment Scale

Family concepts and their measurements interest many family researchers. There is a question about the extent to which family concepts are universal or influenced by the culture in which the instrument originated. Using the Family Environment Scale (FES), the authors examine the translatability of family concepts into the Japanese culture. Forward- and back-translation processes and cross-cultural assessment of reliability and validity are discussed. We suggest that there may be different degrees of translatability for each of the family concepts used in the FES and that evaluation of families in different societies necessitates culturally appropriate constructs and instruments. The discussion is built around Japanese data, which are compared to the American results.

Identification and characterization of a new gene physically linked to the ATM gene

Ataxia telangiectasia (AT) is an autosomal recessive disease of unknown etiology associated with cerebellar ataxia, oculocutaneous telangiectasia, immunodeficiency, and hypersensitivity to ionizing radiation. Although AT has been divided into four complementation groups by its radioresistant-DNA synthesis phenotype, the ATM gene has been isolated as the candidate gene responsible for all AT groups. We identified a new gene, designated NPAT, from the major AT locus on human chromosome 11q22-q23. The gene encoded a 1421-amino-acid protein containing nuclear localization signals and phosphorylation target sites by cyclin-dependent protein kinases associated with E2F. The messenger RNA of NPAT was detected in all human tissues examined, and its genomic sequence was strongly conserved through eukaryotes, suggesting that the NPAT gene may be essential for cell maintenance and may be a member of the housekeeping genes. Analysis of the genomic region of NPAT surprisingly revealed that the gene existed only 0.5 kb apart from the 5' end of the ATM transcript with opposite transcriptional direction. It may be possible to propose the idea that the promoter region could be shared by both housekeeping genes and that each gene could influence the expression of the other.

Genetic organization of a DNA-processing region required for mobilization of a non-self-transmissible plasmid, pEC3, isolated from Erwinia carotovora subsp. carotovora

A non-self-transmissible multiple-copy plasmid, pEC3, isolated from the phytopathogenic bacterium, Erwinia carotovora subsp. carotovora, can be mobilized by an IncP-type plasmid. The hybrid plasmid vector, pETC3, constructed from pEC3 by fusion to markers conferring TcR and CmR, was transferred by conjugation from Escherichia coli (Ec) to various genera of Enterobacteriaceae and to other genera of Gram(-) bacteria which included Xanthomonas, Agrobacterium and Rhizobium. Deletion analysis and successive subcloning of pEC3 revealed that a cis-acting locus, oriT and a trans-acting locus, mob, were involved in mobilization of pEC3. Five open reading frames (ORFs) were found in the mob region, of which four were identified as mobA, B, C and D. The mobA gene overlapped with mobC, B, D and ORF1 that were transcribed polycistronically from upstream from mobC. The nature of the four products of mob genes, MobA, B, C and D, was verified by use of the T7 promoter system in Ec.

Metallothionein synthesis induced by interferon alpha/beta in mice of various zinc status

We studied the ability of interferon alpha/beta (IFN) to induce metallothionein (MT) synthesis in mice. Male mice were injected intraperitoneally with mouse IFN (5 x 10(5) IU/mouse). Plasma Zn levels were reduced at 4 hr after injection, reached a minimum value at 6 hr, and then returned to the control level at 8 hr. Hepatic MT concentrations began to increase at 4 hr and reached maximum values at 6 hr. Induction of MT gene expression and protein synthesis was confirmed by Northern blot analysis and radioimmunoassay, respectively. The induction of MT synthesis in the liver by IFN was dose-dependent. The data suggest that induction of MT-mRNA and the protein in the liver by IFN occurs rapidly but is rather transient. Furthermore, MT synthesis was not induced by IFN in the liver of mice given a Zn-deficient diet, whereas IFN induced increases in the activity of 2',5'-oligoadenylate synthetase in the spleen were unaffected by Zn status. Thus, induction of hepatic MT synthesis by IFN is influenced by Zn status.

Identification of a novel human gene containing the tetratricopeptide repeat domain from the Down syndrome region of chromosome 21

The Down syndrome (DS) region on chromosome 21, which is responsible for the DS main features, has been defined by analysis of DS patients with partial trisomy 21. Within the DS region, we constructed a 1.6-Mb P1 contig map previously. To isolate gene fragments from the 1.6-Mb region, we performed direct cDNA library screening and exon trapping using the P1 clones and a human fetal brain cDNA library, and obtained 67 cDNA fragments and 52 possible exons. Among them, 23 cDNA fragments and 4 exons were interpreted to be derived from a single gene by localization on P1 clones and by Northern analysis. To obtain the full-length cDNA sequence, longer cDNA clones were further screened from another human cDNA library which was enriched with longer cDNA species. These clones were sequenced and assembled to a sequence of 9045 bp. This transcribed sequence encodes a novel 2025 amino-acid protein containing tetratricopeptide repeat (TPR) motifs and therefore the gene was designated as TPRD (a gene containing the TPR motifs on the Down syndrome region). The TPR domain has been found in a certain protein phosphatase and in other proteins involved in the regulation of RNA synthesis or mitosis. The TPRD gene, the novel gene which was proved to be in the 1.6-Mb region and to have the interesting features described above, is a candidate for genes responsible for the DS phenotypes.

Prediction of the coding sequences of unidentified human genes. V. The coding sequences of 40 new genes (KIAA0161-KIAA0200) deduced by analysis of cDNA clones from human cell line KG-1

As part of our continuing efforts to accumulate information on the coding region of unidentified human genes, we newly determined the sequences of 40 cDNA clones of human cell line KG-1 which correspond to relatively long and nearly full-length transcripts, and predicted the coding sequences of the corresponding genes, named KIAA0161 to 0200. The average size of the cDNA clones analyzed was approximately 5.0 kb. A computer search of the sequences in public databases indicated that the sequences of 20 genes were unrelated to any reported genes, while the remaining 20 genes carried sequences which show some similarities to known genes. Among the genes in the latter category, KIAA0167 contained a Zn-finger motif with significant structural similarity to that of the yeast transcription factor GCS1, and KIAA0189 was classified into the RhoGAP gene family. Stretches of typical CAG (Gln) repeats, which were often correlated with genetic disorders, were found in KIAA0181 and KIAA0192. Another novel repeat composed of alternating Arg and Glu was identified in KIAA0182. Northern hybridization analysis demonstrated that 10 genes are expressed in a cell- or tissue-specific manner.