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At least 811 records · Page 45Linked to original sources
PubMed1997

Cell wall biogenesis in Chlamydomonas: molecular characterization of a novel protein whose expression is up-regulated during matrix formation.

In the unicellular eukaryote Chlamydomonas, disruption of cell-matrix interactions by treatment with a periplasmic matrix metalloproteinase, g-lysin, activates a signal transduction pathway that results in the rapid synthesis and secretion of matrix molecules, followed by their assembly into a new matrix. I have identified and partially characterized several cDNA clones for transcripts that are dramatically up-regulated following treatment of cells with g-lysin. Here I report the complete nucleotide sequence and preliminary characterization of a matrix-related molecule termed Mrp47. The cDNA clone for Mrp47 contained an insert of 2.5 kb, corresponding to a transcript of 3.0 kb that is encoded by a single-copy gene. Sequence analysis indicated that Mrp47 cDNA contains an open reading frame (ORF) that encodes a 46-kDa polypeptide. The putative polypeptide is unusually rich in the amino acids proline, alanine and serine, with prolines clustered together in a 30-amino acid N-terminal region and a 80-amino acid C-terminal region. Further analysis of the predicted amino acid sequence suggested that Mrp47 is likely to be a secreted glycoprotein. Southern hybridization analysis indicated that Mrp47 is encoded by a single-copy gene in the Chlamydomonas genome. Database searches suggested that Mrp47 shows homology to other proline-rich proteins including a surface glycoprotein in Volvox and verprolin from yeast.

Algal Proteins↗
PubMed2002

An Alu-mediated deletion at Xp11.23 leading to Wiskott-Aldrich syndrome.

Wiskott-Aldrich syndrome (WAS) is an X-linked disease characterized by thrombocytopenia, eczema and immunodeficiency of varying severity. The WASP gene, mutations of which are responsible for the phenotype, maps to Xp11.23. We describe here a patient with a large deletion in the Xp11.23 region. The deletion, which totals 15.8 kb, begins downstream of DXS1696 and encompasses 13 kb upstream of WASP and includes the distal and proximal promoters and exons 1-6. Analysis of the 5'-boundary region identified sequences missing in the Human Genome database and, as a result, the normal DNA sequence was revised to include 743 bp of novel sequence (AF466616). The patient's upstream breakpoint was localized to an AluSg element within a highly repetitive DNA region containing other Alu elements. A 26-bp recombinogenic element is located downstream of the 5' breakpoint. A 16-bp sequence just upstream of the 5' breakpoint shares close homology with the sequence that spans the 3' breakpoint in intron 6. A heptanucleotide of unknown origin, CAGGGGG, links the 5' and 3' breakpoints. To our knowledge this is the largest deletion in a WAS patient.

Alu Elements↗
PubMed1999

Identification and phylogeny of novel human endogenous retroviral sequences belonging to the HERV-W family on the human X chromosome.

A new family (HERV-W) ofhuman endogenous retroviruses (HERVs) has recently been described that is related to MSRV (multiple sclerosis related retrovirus) sequences that have been identified in particles recovered from monocyte cultures from patients with multiple sclerosis. We investigated the pol fragment of HERV-W on the human X chromosome by the polymerase chain reaction (PCR) using a monochromosomal somatic cell hybrid DNA panel and compared these with related sequences in the genome database. We identified three novel sequences on the human X chromosome, HWXI, HWX3, and HWX5, which have a high degree of homology (88-98%) with the MSRV pol fragment and with seven other sequences. HWX5, like MSRV, has an uninterrupted open reading frame. Phylogenetic analysis showed HWX5 to be related to the HWX1, HWX3, and BAC clone B353C18 sequences with 91-93% homology. The ratio of synonymous to nonsynonymous substitutions indicated that negative selective pressure is acting on HWX5. Further studies on the structure and expression of this sequence are indicated.

Amino Acid Sequence↗
PubMed2004

Functional prediction of a T-DNA tagged gene of Arabidopsis thaliana by in silico analysis.

We have employed a gene-knockout approach using T-DNA tagging and in vivo gene fusion in Arabidopsis thaliana for identification and isolation of specific plant genes. Screening of about 3,000 T-DNA tagged lines resulted in identification of a mutant line (no. 197) exhibiting a significant delay in flowering. From this line a 600-bp plant DNA fragment downstream of the left T-DNA junction was cloned by inverse PCR. BLAST searching in the A. thaliana genomic database indicated a putative gene, frf (flowering regulating factor), with unknown function downstream of the T-DNA insert. Bioinformatic tools were used to predict possible protein structure and function. The protein structure predicted by fold recognition indicates that frf is a transcriptional regulator, a ligand-binding receptor responsive to steroids and hormones. Analyzing the predicted results and the phenotype of the T-DNA tagged plant we hypothesized that FRF might be involved in hormone response in A. thaliana. For verification of this hypothesis we exposed the plants of line no. 197 to gibberellic acid (GA3), a potential growth regulator in higher plants. This treatment resulted in an earlier onset of flowering, almost similar to that in wild type control plants.

Amino Acid Sequence↗
PubMed2003

Isolation and identification of a novel cDNA that encodes human yrdC protein.

In the course of detecting the interaction protein of RBBP10 by yeast two-hybridization, we isolated a novel cDNA that encodes a putative human protein with yrdC domain. It is named human yrdC protein. Because the cDNA contains an open reading fragment (ORF) without a 5' in- frame stop codon, 5' RACE and 3' RACE were proceeded to produce the full-length cDNA. An 1825 bp cDNA was isolated from human placenta, which encodes a putative protein of 279 amino acids. The protein contains a sua5-yciO-yrdC domain. Blast analysis against the human genome database of Genbank revealed that the gene contains five exons, and assigned the gene to human chromosome 1p34.2. A transcript about 2.5 kb is ubiquitously expressed in human tissues. The gene is highly conserved during evolution.

Amino Acid Sequence↗
PubMed2003

Identification of a novel human doublecortin-domain-containing gene (DCDC1) expressed mainly in testis.

Mutations in the X-linked gene doublecortex (DCX) result in lissencephaly in males or subcortical laminar heterotopia (double cortex) in females. Recently, an evolutionarily conserved doublecortin (DC) domain important for microtubule binding and microtubule polymerization was defined according to detailed sequence analysis of DCX and DCX-like proteins. Subsequently we cloned a novel human cDNA that contained a DC domain during large-scale DNA sequencing of the human fetal brain cDNA library, and termed it doublecortin-domain-containing 1 (DCDC1). According to a search against the human genome database, DCDC1 was mapped to 11p13. Expression analysis showed that DCDC1 was mainly expressed in adult testis. Furthermore, the expression level of DCDC1 in fetal brain was much higher than in adult brain.

Amino Acid Sequence↗
PubMed2004

Phenotype-genotype correlation in two patients with 12q proximal deletion.

Proximal 12q deletion is a very rare chromosomal abnormality. Only five cases have been reported. Among the five, an Argentinian patient (Case 1) with del(12)(q11q13) and a Japanese patient (Case 2) with del(12)(q12q13.12) were analyzed because they shared several clinical features: growth and psychomotor developmental delay; strabismus; broad and short nose with anteverted nostrils; high, arched palate; large, lowset ears; widely set nipples; short fingers and clinodactyly of fifth fingers; and abnormality of the second and third toes. To clarify the correlation between the deleted genes and their phenotypes, we delimited their deleted regions by fluorescence in situ hybridization (FISH). The overlapped region in the deletions spanned 6.2 Mb where at least 15 genes were predicted to localize on the current human genome database. Among them, YAF2 and AMIGO2 were the most plausible candidates to affect growth and psychomotor retardation, respectively, in both cases. Regarding unique symptoms in each case, congenital fibrosis of the extraocular muscles found only in Case 1 may be caused by KIF21A deletion and hearing loss and cleft palate in Case 2 by COL2A1 defect.

Abnormalities, Multiple↗
PubMed1998

Heterozygosities and allelic frequencies of 358 dinucleotide-repeat marker loci in the Japanese population.

We examined 64 normal Japanese chromosomes to determine the heterozygosities and allelic frequencies of 358 dinucleotide-repeat marker loci spanning the whole human genome. Comparisons of the data for each marker in the Japanese population sample with data for the same markers among Caucasian samples in the Genome Database (GDB) revealed a slightly lower average of heterozygosity in Japanese (71% vs 79%). Although the majority of the markers were as informative as in Caucasians, some in our sample were uninformative due to low heterozygosity; 38 loci revealed heterozygosities lower than 50% and 11 of these were less than 30%. Furthermore, allelic distributions at many of the marker loci were quite different in the two racial groups. Since such differences will influence statistical analyses between markers and disease loci, our data will be essential for linkage analyses, sib-ship pair analyses, and association studies involving the Japanese population. Therefore we have archived this database on a home page on the Internet (http:@www.ims.u-tokyo.ac.jp/nakamura/Yamane.html++ +).

Alleles↗
PubMed2002

A novel splice variant of the cell adhesion molecule contactin 4 ( CNTN4) is mainly expressed in human brain.

Axon-associated cell adhesion molecules (AxCAMs) of the immunoglobulin superfamily play important roles in the formation, maintenance, and plasticity of functional neuronal networks. Contactin4 ( CNTN4, BIG-2) is a member of the TAG-1/F3 subgroup of AxCAMs. We have cloned a novel splice variant of CNTN4, and term it CNTN4A. The complete nucleotide sequence of CNTN4 is also obtained by combining the insert sequences of two clones, which were isolated when screening the human fetal brain cDNA library with CNTN4A as a probe. CNTN4A protein has an N-terminal cleavable signal peptide, two FNIII-like domains, and a glycosyl phosphatidylinositol-anchoring domain. According to the search of the human genome database, CNTN4 was mapped to 3p25-26, a region very close to the breakpoints of the 3p syndrome. Expression analysis of CNTN4A shows that CNTN4A is mainly expressed in brain.

Alternative Splicing↗
PubMed2003

Identification of a novel human angiopoietin-like gene expressed mainly in heart.

The angiopoietins are an important family of growth factors specific for vascular endothelium. Most of them bind to the TIE2 receptor and are related to regulation of angiogenesis. During large-scale DNA sequencing of the human fetal brain cDNA library, we cloned a novel human angiopoietin-like cDNA and termed it human angiopoietin-like 5 ( ANGPTL5). Like other members of the angiopoietin family, ANGPTL5-deduced protein also has an N-terminal cleavable signal peptide, a predicted coiled-coil domain, and a fibrinogen-like domain. The search against the human genome database indicated that ANGPTL5 maps to 11q22. Expression analysis of ANGPTL5 shows that it is mainly expressed in adult human heart.

Amino Acid Sequence↗
PubMed2000

Analysis of the fit-1 gene encoding a ECM protein, flectin, in Caenorhabditis elegans.

Flectin is a new type of extracellular matrix protein and its function was suggested to provide a microenvironment of great elasticity. The C. elegans genome database revealed the presence of a flectin homologue, fit-1, which shows approximately 40% similarity (20% identity) to chick flectin. Here we propose a new gene structure for the fit-1 based on our experiments and the partial cDNA clones obtained from Y. Kohara and further suggest that the previous gene prediction is incorrect. FLT-1 is shown to be expressed in various neurons, hypodermal cells, distal tip cells and vulva epithelial cells. Immunostaining results with anti-FLT-1 antibody, further confirm the FLT-1 expression in vulva epithelial cells. The lipophilic dye, DiI, was used to identify the head neurons expressing GFP and results indicated that none of the head neurons expressing GFP are the 6 chemosensory neurons. In order to determine the function of flt-1 gene, RNA-mediated interference (RNAi) experiments were conducted.

Animals↗
PubMed2005

Structural analysis of cDNAs coding for 4SNc-Tudor domain protein from fish and their expression in yellowtail organs.

We cloned complementary DNAs for 4SNc-Tudor protein (SN4TDR) from yellowtail (Seriola quinqueradiata), torafugu (Takifugu rubripes), and zebrafish (Danio rerio). This protein contains 4 staphylococcal nuclease domains at the N terminus followed by a Tudor domain. We also identified the 4SNc-Tudor proteins highly homologous to that in yellowtail from the Takifugu genomic database. According to the smart database, these fish proteins had an overlapping Tudor domain (smart00333) with a complete 5 SNc domain (smart00318). In addition, 2 possible translation start sites were observed at the 5' sequences in all 3 fish species. Northern blot analysis of different yellowtail organs showed that the full SN4TDR messenger RNA was approximately 4000 nucleotides long and that its expression was highest in liver and gallbladder, being about 2 to 5 times higher than in kidney, brain, ovary, and gills, and exceedingly low in spleen, heart, and muscle. A minor 2000-nucleotide transcript observed in kidney, spleen, and gallbladder, was attributable to an alternatively spliced variant of this gene. Total proteins extracted from yellowtail liver were fractionated by heparin affinity column chromatography and separated by sodium dodecylsulfate polyacrylamide gel electrophoresis. Analyses by SDS-PAGE and liquid chromatography with tandem mass spectroscopy identified the polypeptide encoded by SN4TDR as a single molecule of 102 kDa.

Amino Acid Sequence↗
PubMed2006

Upstream regulatory region of zebrafish lunatic fringe: isolation and promoter analysis.

Lunatic fringe (Lfng), one modulator of Notch signaling, plays an essential part in demarcation of tissues boundaries during animal early development, especially somitogenesis. To characterize the promoter of zebrafish lfng and generate somite-specific transgenic zebrafish, we isolated the upstream regulatory region of zebrafish lfng by blast search at the Ensembl genome database ( http://www.ensembl.org ) and analyzed the promoter activity using green fluorescent protein (GFP) as a reporter. Promoter activity assay in zebrafish shows that the 0.2-kb fragment containing GC-box, CAAT-box, and TATA-box can direct tissue-specific GFP expression, while the 0.4-kb and 1.2-kb fragments with further upstream sequence included drive GFP expression more efficiently. We produced lfngEGFP-transgenic founders showing somite-specific expression of GFP and consequently generated a hemizygous lfngEGFP-transgenic line. The eggs from lfngEGFP-transgenic female zebrafish show strong GFP expression, which is consistent to the reverse-transcription polymerase chain reaction PCR (RT-PCR) detection of lfng transcripts in the fertilized eggs. This reveals that zebrafish lfng is a maternal factor existing in matured eggs, suggesting that fish somitogenesis may be influenced by maternal factors.

Animals↗
PubMed2004

Extracellular matrix family proteins that are potential targets of Dd-STATa in Dictyostelium discoideum.

Dd-STATa is a functional Dictyostelium homologue of metazoan STAT (signal transducers and activators of transcription) proteins, which is activated by cAMP and is thereby translocated into the nuclei of anterior tip cells of the prestalk region of the slug. By using in situ hybridization analyses, we found that the SLF308 cDNA clone, which contains the ecmF gene that encodes a putative extracellular matrix protein and is expressed in the anterior tip cells, was greatly down-regulated in the Dd-STATa-null mutant. Disruption of the ecmF gene, however, resulted in almost no phenotypic change. The absence of any obvious mutant phenotype in the ecmF-null mutant could be due to a redundancy of similar genes. In fact, a search of the Dictyostelium whole genome database demonstrates the existence of an additional 16 homologues, all of which contain a cellulose-binding module. Among these homologues, four genes show Dd-STATa-dependent expression, while the others are Dd-STATa-independent. We discuss the potential role of Dd-STATa in morphogenesis via its effect on the interaction between cellulose and these extracellular matrix family proteins.

Amino Acid Sequence↗
PubMed2005

A novel zinc finger gene ZNF468 with two co-expressional splice variants, ZNF468.1 and ZNF468.2.

A novel human zinc finger protein encoding gene ZNF468 was obtained from a fetal brain cDNA library. By BLAST-N analysis we found two different splice variants. We termed the two splice variants ZNF468.1 and ZNF468.2. By BLAST search against the human genome database, ZNF468 was mapped to 19q13.4. The ZNF468.1 cDNA has four exons, and the ZNF468.2 cDNA has one more, between the third and fourth exon. This extra exon creates a difference between the deduced protein N-termini of the two splice variants. The ZNF468.1 cDNA is 3906 bp in length, encoding a 522a a protein, and ZNF468.2 is 4024 bp, encoding a 469-aa-protein. Both proteins contain 11 C2H2-type zinc finger motifs at their C-termini. The N-terminus of the deduced protein of ZNF468.1 has a well-conserved Krüppel-associated box (KRAB) domain that consists of KRAB boxes A and B, whereas the protein of ZNF468.2 does not have the KRAB domain. Tissue distribution of the ZNF468 gene indicates that the two splice variants are widely expressed in normal human tissues, except in heart and brain, and they are also co-expressional.

Alternative Splicing↗
PubMed2006

Identification and characterization of the human SCAN domain zinc-finger gene ZNF449.

Zinc-finger proteins play important roles in various cellular functions, including cell proliferation, differentiation, and apoptosis. In this study, we identified a gene encoding a zinc finger protein named ZNF449, which was isolated from human testis cDNA library and mapped to Xq26.3 by searching the UCSC genomic database. The ZNF449 cDNA consists of 4035 nucleotides and has a 518-amino acids open reading frame. The predicted protein contains a leucine-rich region (LER or SCAN domain) at the N-terminus. At the C-terminus of the protein, there are 7 C(2)H(2) (Cys2-His2) zinc-finger motifs. The expression pattern of ZNF449 showed that it was ubiquitously expressed in 18 human adult tissues. ZNF449 protein was located in the nucleus when overexpressed in cultured cells. These results indicate that ZNF449 is a member of the zinc-finger family and it may function as a transcription factor.

Amino Acid Sequence↗
PubMed2006

Cloning and characterization of the human gene DERP6, which activates transcriptional activities of p53.

We report here the cloning and characterization of the human gene DERP6, isolated from human testis cDNA library, and mapped to 17p13.1 by searching the UCSC genomic database. The DERP6 cDNA consists of 1486 nucleotides and has a 316-amino acids open reading frame. The Northern hybridization analysis showed that DERP6 was ubiquitously expressed in all the 16 adult tissues, especially highly expressed in heart, brain, liver, skeletal muscle and testis. DERP6 protein was located in cytoplasm when overexpressed in cultured cells. Reporter gene assays showed that overexpression of DERP6 in cells activated the transcriptional activities of p53. These results indicate that the human gene DERP6 may be involved in p53-mediated gene transcription.

Amino Acid Sequence↗
PubMed2006

Identification and characteristics of a novel testis-specific gene, Tsc21, in mice and human.

Testis-specific genes are essential for spermatogenesis in mammalian male reproduction. We have identified a novel gene, Tsc21, exclusively expressed in mice and human testes from the results of the Affymetrix Genechip analysis in the six developmental stages of testis of postnatal Balb/C mice. The full cDNA length of Tsc21 was 810 bp, with a 543 bp open reading frame encoding a 180 amino acids protein with a predicted molecular weight of 21.040 kDa. A Blast search in the mouse genome database localized the Tsc21 gene to mice chromosome 6C3. Multiple amino acid sequence alignment of human, mouse, and rat homologous genes showed that mice Tsc21 protein was highly homologous with the human Tsc21 gene (70%) and rat Tsc21 gene (86%). The results of reverse transcriptase-polymerase chain reaction analysis showed that the mice Tsc21 is exclusively expressed in the testis and epididymis of mice, and its expression is only detected after the mice is 35 days old. Human Tsc21 is also exclusively expressed in testis of human. Considering the expression profile Tsc21 in mice and human, we propose that Tsc21 may play a role during mammalian male spermatogenesis. Our study should be a basis for function characterization of the Tsc21 gene, leading to the elucidation of the molecular events underlying mammalian male reproduction.

Amino Acid Sequence↗