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2.
Genomics ; 73(1): 10-9, 2001 Apr 01.
Article in English | MEDLINE | ID: mdl-11352561

ABSTRACT

Deletions on 3p have been described in a large number of human tumors, suggesting the presence of a tumor suppressor gene(s). Using the elimination test, we previously defined a 1-Mb segment from human 3p21.3 (C3CER1). Genomic sequencing allowed us to construct a transcription map covering 250 kb containing five genes. We have characterized a human leucine zipper containing gene, leucine zipper transcription factor-like 1 (LZTFL1), and its mouse orthologue (Lztfl1), which was also mapped to mouse chromosome 9F. The LZTFL1 gene has two transcript isoforms displaying alternative polyadenylation. We have localized the human orthologue of the yeast SAC1 (suppressor of actin) gene as well as characterized and mapped the mouse Sac1 gene. Furthermore, the XT3 gene was characterized, encoding a member of the Na(+)/Cl(-) neurotransmitter superfamily. It has been shown that the XT3 gene had an alternatively spliced brain-specific isoform, predicted to remove 1 of 12 putative transmembrane domains. The transcription map also includes the CC chemokine receptor 9 gene (CCR9) and the LIM domain containing gene 1 (LIMD1). This work partially defines the gene content of C3CER1 that is a prerequisite for delineation of its role in tumorigenesis.


Subject(s)
Chromosomes, Human, Pair 3/genetics , Leucine Zippers/genetics , Membrane Proteins , Membrane Transport Proteins , Neurotransmitter Agents , Transcription Factors/genetics , Amino Acid Sequence , Animals , Blotting, Northern , Carrier Proteins/genetics , Chromosome Deletion , DNA Primers , Genes, Tumor Suppressor , Humans , Mice , Molecular Sequence Data , Physical Chromosome Mapping , Proteins/genetics , RNA, Messenger/analysis , Sequence Alignment
3.
J Med Genet ; 38(3): 165-70, 2001 Mar.
Article in English | MEDLINE | ID: mdl-11238683

ABSTRACT

Four cases of late onset clear cell renal cell carcinoma (RCC), a case of gastric cancer, and a case of exocrine pancreatic cancer were identified in a Japanese family. In order to elucidate the underlying mechanism for tumorigenesis in this family, extensive genetic studies were performed including routine and spectral karyotyping (SKY), fluorescence in situ hybridisation (FISH), comparative genomic hybridisation (CGH), loss of heterozygosity studies (LOH), and VHL mutation analysis. A germline translocation t(1;3)(q32-q41;q13-q21) was identified by karyotyping in five members of the family including all three RCC cases tested. The translocation was refined to t(1;3)(q32;q13.3) by FISH analysis using locus specific genomic clones, and the two breakpoints were mapped to a 5 cM region in 3q13.3 and a 3.6 cM region in 1q32. Both CGH and allelotyping using microsatellite markers showed loss of the derivative chromosome 3 carrying a 1q segment in the three familial RCCs analysed. Additional chromosomal imbalances were identified by CGH, including amplifications of chromosomes 5 and 7 and loss of 8p and 9. No germline VHL mutation was found but two different somatic mutations, a splice (IVS1-2A>C) and a frameshift (726delG), were identified in two RCCs from the same patient confirming their distinct origin. Taken together, these results firmly support a three step model for tumorigenesis in this family. A constitutional translocation t(1q;3q) increased the susceptibility to loss of the derivative chromosome 3 which is then followed by somatic mutations of the RCC related tumour suppressor gene VHL located in the remaining copy of chromosome 3.


Subject(s)
Carcinoma, Renal Cell/genetics , Kidney Neoplasms/genetics , Ligases , Translocation, Genetic , Tumor Suppressor Proteins , Ubiquitin-Protein Ligases , Adenocarcinoma, Clear Cell/genetics , Adenocarcinoma, Clear Cell/pathology , Base Sequence , Carcinoma, Renal Cell/pathology , Chromosomes, Human, Pair 1/genetics , Chromosomes, Human, Pair 3/genetics , DNA/chemistry , DNA/genetics , DNA Mutational Analysis , Family Health , Female , Humans , In Situ Hybridization, Fluorescence , Karyotyping , Kidney Neoplasms/pathology , Loss of Heterozygosity , Male , Mutation , Nucleic Acid Hybridization , Pedigree , Proteins/genetics , Von Hippel-Lindau Tumor Suppressor Protein
4.
Hum Genet ; 107(2): 145-9, 2000 Aug.
Article in English | MEDLINE | ID: mdl-11030412

ABSTRACT

Dyschondrosteosis (DCO) and hypochondroplasia (HCH) are common skeletal dysplasias characterized by disproportionate short stature. The diagnosis of these conditions might be difficult to establish especially in early childhood. Point mutations and deletions of the short stature homeobox containing gene (SHOX) are detected in DCO and idiopathic short stature with some rhizomelic body disproportion, whereas mutations in the fibroblast growth factor receptor 3 (FGFR3) gene are found in 40-70% of HCH cases. In this study, we performed mutational analysis of the coding region of the SHOX gene in five DCO and 18 HCH patients, all of whom tested negative for the known HCH-associated FGFR3 mutations. The polymorphic CA-repeat analysis, direct sequencing and Southern blotting were used for detection of deletions and point mutations. The auxological and radiological phenotype of these patients was carefully determined. Three novel mutations in DCO patients were found: (1) a deletion of one base (de1272G) (according to GenBank accession nos. Y11536, Y11535), resulting in a premature stop codon at position 75 of the amino acid sequence; (2) the transversion C485G resulting in the substitution Leu132Val; and (3) the transversion G549T causing an Arg153Leu substitution. These substitutions segregate with the DCO phenotype and affect evolutionarily conserved homeodomain residues, based on a comparison of homeobox containing proteins in 13 species. Moreover, these changes were not found in 80 unrelated, unaffected individuals. This strongly suggests that these mutations are pathogenic. The phenotype of our patients with DCO and HCH varied from mild to severe shortness and body disproportion. These results further support clinical and genetic heterogeneity of dyschondrosteosis and hypochondroplasia.


Subject(s)
Homeodomain Proteins/genetics , Mutation , Osteochondrodysplasias/genetics , Protein-Tyrosine Kinases , Amino Acid Sequence , DNA Mutational Analysis , Humans , Molecular Sequence Data , Polymerase Chain Reaction , Receptor, Fibroblast Growth Factor, Type 3 , Receptors, Fibroblast Growth Factor/genetics , Sequence Homology, Amino Acid , Short Stature Homeobox Protein
5.
Hum Genet ; 106(5): 506-16, 2000 May.
Article in English | MEDLINE | ID: mdl-10914680

ABSTRACT

Translocation t(11;22)(q23;q11) is the most common constitutional reciprocal translocation in man. Balanced carriers are phenotypically normal, except for decreased fertility, an increased spontaneous abortion rate and a possible predisposition to breast cancer in some families. Here, we report the high resolution mapping of the t(11;22)(q23;q11) breakpoint. We have localised the breakpoint, by using fluorescence in situ hybidisation (FISH) walking, to a region between D11S1340 and WI-8564 on chromosome 11, and D22S134 and D22S264 on chromosome 22. We report the isolation of a bacterial artificial chromosome (BAC) clone spanning the breakpoint in 11q23. We have narrowed down the breakpoint to an 80-kb sequenced region on chromosome 11 and FISH analysis has revealed a variation of the breakpoint position between patients. In 22q11, we have sequenced two BACs (BAC2280L11 and BAC41C4) apparently mapping to the region; these contain low copy repeats (LCRs). Southern blot analysis with probes from BAC2280L11 has revealed different patterns between normal controls and translocation carriers, indicating that sequences similar/identical to these probes flank the translocation breakpoint. The occurrence of LCRs has previously been associated with genomic instability and "unclonable" regions. Hence, the presence of such repeats renders standard translocation breakpoint cloning techniques ineffective. Thus, we have used high resolution fiber-FISH to study this region in normal and translocation cases by using probes from 22q11, LCRs and 11q23. We demonstrate that the LCR containing the gap in 22q11 is probably substantially larger than the previous estimates of 100 kb. Using fiber-FISH, we have localised the breakpoint in 22q11 to approximately 20-40 kb from the centromeric border of the LCR (i.e. the telomeric end of AC006547) and have confirmed the breakpoint position on 11q23.


Subject(s)
Chromosome Mapping/methods , Chromosomes, Human, Pair 11/genetics , Chromosomes, Human, Pair 22/genetics , Translocation, Genetic , Base Sequence , Chromosome Walking , DNA Primers/genetics , DNA Probes/genetics , Female , Humans , In Situ Hybridization, Fluorescence , Male , Molecular Sequence Data , Telomere/genetics
6.
Biochem Biophys Res Commun ; 273(1): 90-4, 2000 Jun 24.
Article in English | MEDLINE | ID: mdl-10873569

ABSTRACT

The redundancy of sequences in dbEST has approached a level where contiguous cDNA sequences of genes can be assembled, without the need to physically handle the clones from which the ESTs are derived. This is termed EST based in silico gene cloning. With the availability of sequence chromatogram files for a subset of ESTs, the quality of EST sequences can be ascertained accurately and used in contig assembly. In this report, we performed a study using this approach and isolated five novel human genes, C11orf1-C11orf5, in the 11q13-q22 region. The full open reading frames of these genes were determined by comparison with their orthologs, of which four mouse orthologs were isolated (c11orf1, c11orf2, c11orf3 and c11orf5). These genes were then analyzed using several proteomics tools. Both C11orf1 and C11orf2 are nuclear proteins with no other distinguishing features. C11orf3 is a cytoplasmic protein containing an ATP/GTP binding site, a signal peptide located in the N-terminus and a similarity to the C. elegans protein "Probable ARP 2/3 complex 20kD subunit." C11orf4 is a peptide which displays four putative transmembrane domains and is predicted to have a cytoplasmic localization. It contains signal peptides at the N- and C-termini. C11orf5 is a putative nuclear protein displaying a central coiled coil domain. Here, we propose that this purely EST-based cloning approach can be used by modestly sized laboratories to rapidly and accurately characterize and map a significant number of human genes without the need of further sequencing.


Subject(s)
Chromosomes, Human, Pair 11/genetics , Contig Mapping/methods , Expressed Sequence Tags , Genes/genetics , Genetic Linkage/genetics , Animals , Cloning, Molecular/methods , Codon, Initiator/genetics , Codon, Terminator/genetics , Computational Biology , Conserved Sequence/genetics , Databases, Factual , Humans , Mice , Molecular Sequence Data , Open Reading Frames/genetics , Sequence Homology , Sequence Tagged Sites
7.
Genomics ; 62(2): 147-55, 1999 Dec 01.
Article in English | MEDLINE | ID: mdl-10610706

ABSTRACT

We have developed an elimination test to identify chromosomal regions that contain tumor inhibitory genes. Monochromosomal human/mouse microcell hybrids are generated and passaged through SCID mice. Derived tumors are then analyzed for deletions on the transgenomic chromosome. Using this strategy, we have previously identified a 1.6-cM common eliminated region 1 (CER1) on human 3p21. 3. We now report that CER1 contains 14 markers that are deleted in 19 SCID-derived tumors. A 1-Mb PAC contig that spans CER1 was assembled. Five chemokine receptor genes (CCR1, CCR3, CCR2, CCR5, and CCR6) were localized in CER1 in a 225-kb cluster. The lactotransferrin gene (LTF, or lactoferrin, LF), which reportedly has tumor inhibitory activity, also maps to CER1. Our results create a basis for characterization and further functional testing of genes within CER1.


Subject(s)
Bacteriophage P1/genetics , Contig Mapping , Fibrosarcoma/genetics , Mice, SCID/genetics , Animals , Chromosomes, Human, Pair 3/genetics , Contig Mapping/methods , Genes , Genetic Markers , Humans , Hybrid Cells , In Situ Hybridization, Fluorescence , Mice , Molecular Sequence Data
8.
Genome Res ; 9(9): 803-14, 1999 Sep.
Article in English | MEDLINE | ID: mdl-10508838

ABSTRACT

Analysis of 600 kb of sequence encompassing the beta-prime adaptin (BAM22) gene on human chromosome 22 revealed intrachromosomal duplications within 22q12-13 resulting in three active RFPL genes, two RFPL pseudogenes, and two pseudogenes of BAM22. The genomic sequence of BAM22vartheta1 shows a remarkable similarity to that of BAM22. The cDNA sequence comparison of RFPL1, RFPL2, and RFPL3 showed 95%-96% identity between the genes, which were most similar to the Ret Finger Protein gene from human chromosome 6. The sense RFPL transcripts encode proteins with the tripartite structure, composed of RING finger, coiled-coil, and B30-2 domains, which are characteristic of the RING-B30 family. Each of these domains are thought to mediate protein-protein interactions by promoting homo- or heterodimerization. The MID1 gene on Xp22 is also a member of the RING-B30 family and is mutated in Opitz syndrome (OS). The autosomal dominant form of OS shows linkage to 22q11-q12. We detected a polymorphic protein-truncating allele of RFPL1 in 8% of the population, which was not associated with the OS phenotype. We identified 6-kb and 1.2-kb noncoding antisense mRNAs of RFPL1S and RFPL3S antisense genes, respectively. The RFPL1S and RFPL3S genes cover substantial portions of their sense counterparts, which suggests that the function of RFPL1S and RFPL3S is a post-transcriptional regulation of the sense RFPL genes. We illustrate the role of intrachromosomal duplications in the generation of RFPL genes, which were created by a series of duplications and share an ancestor with the RING-B30 domain containing genes from the major histocompatibility complex region on human chromosome 6.


Subject(s)
Adaptor Protein Complex 1 , Carrier Proteins/genetics , Chromosomes, Human, Pair 22 , Gene Duplication , Adaptor Protein Complex beta Subunits , Amino Acid Sequence , Base Sequence , Contig Mapping , DNA, Antisense/genetics , Female , Humans , Male , Membrane Proteins/genetics , Models, Genetic , Molecular Sequence Data , Multigene Family , Pedigree , Polymorphism, Genetic , Pseudogenes/genetics , Sequence Homology, Amino Acid , Syndrome , Tissue Distribution , Transcription, Genetic
9.
Genomics ; 57(3): 380-8, 1999 May 01.
Article in English | MEDLINE | ID: mdl-10329004

ABSTRACT

The avian tom1 (target of myb 1) gene has been previously characterized from v-myb-transformed cells. We report here cloning of the human and mouse tom1 orthologs. Both genes are expressed ubiquitously, with the highest levels in skeletal muscle, brain, and intestines, as assessed by Northern blot and mRNA in situ hybridization. The N-terminal domain of the TOM1 protein shares similarity with HGS (hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (signal-transducing adaptor molecule), which are associated with vesicular trafficking at the endosome. A putative coiled-coil domain was also detected in the central part of the TOM1 protein. This domain structure suggests that TOM1 is another member of a family of genes implicated in the trafficking regulation of growth-factor-receptor complexes that are destined for degradation in the lysosome. We also show that a human paralog of TOM1 (TOM1-like gene 1) exists. Furthermore, we provide a transcription map over a 190-kb contig of the TOM1 region. This map includes its distal neighbors HMOX1 and MCM5 and two proximal novel genes, one of which is a HMG-box-containing gene (HMG2L1), and the other of unknown function. Using a genomic PAC clone, we demonstrate that the mouse Tom1 and Hmox1 genes are part of an as yet undescribed syntenic group between mouse chromosome 8C1 and human chromosome 22q13.1.


Subject(s)
Adaptor Proteins, Signal Transducing , Chromosome Mapping , Chromosomes, Human, Pair 22 , Hepatocyte Growth Factor/genetics , Phosphoproteins/genetics , Proteins/genetics , Retroviridae Proteins, Oncogenic/genetics , Amino Acid Sequence , Animals , Base Sequence , Cloning, Molecular , DNA, Complementary , Endosomal Sorting Complexes Required for Transport , Endosomes/chemistry , Gene Expression , Humans , Intracellular Signaling Peptides and Proteins , Mice , Molecular Sequence Data , Oncogene Proteins v-myb , Promoter Regions, Genetic , Virus Integration
10.
Biochem Biophys Res Commun ; 257(3): 886-90, 1999 Apr 21.
Article in English | MEDLINE | ID: mdl-10208879

ABSTRACT

The human SMARCB1 gene (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1, previously named the INI1/hSNF5 gene) is a tumor suppressor gene located on chromosome 22q11.2 and is inactivated in malignant rhabdoid tumors. By using an EST-based approach, we cloned two splice forms of the Smarcb1 gene in mouse and a longer splice form of the human ortholog. Proteins corresponding to the longer (385 aa) and the shorter (376 aa) forms are 100% conserved between human and mouse. Meningiomas and schwannomas are tumors frequently deleting various regions on chromosome 22, including the SMARCB1 locus. We therefore directly sequenced seven SMARCB1 exons (90% of the open reading frame) in search for mutations in 41 meningiomas and 23 schwannomas. No inactivating mutations were observed, which suggests that the SMARCB1 gene is not involved in the pathogenesis of these tumors.


Subject(s)
Alternative Splicing/genetics , DNA-Binding Proteins/genetics , Amino Acid Sequence , Animals , Base Sequence , Chromosomal Proteins, Non-Histone , Chromosomes, Human, Pair 22/genetics , Conserved Sequence/genetics , Contig Mapping , Cysteine/genetics , Cysteine/metabolism , DNA Mutational Analysis , DNA-Binding Proteins/chemistry , Exons/genetics , Expressed Sequence Tags , Gene Expression Regulation, Developmental , Genome , Humans , Meningioma/genetics , Methionine/genetics , Mice , Molecular Sequence Data , Neurilemmoma/genetics , SMARCB1 Protein , Sequence Homology, Amino Acid , Software , Transcription Factors
11.
Biochem Biophys Res Commun ; 254(2): 413-6, 1999 Jan 19.
Article in English | MEDLINE | ID: mdl-9918852

ABSTRACT

This paper describes the genomic structure of the human Prostaglandin F receptor gene (FP) with its exon-intron borders and 5' flanking sequences. Furthermore, the location of the gene has been localized to a very small region on 1p31.1 using FISH and radiation hybrids analysis. The PGF receptor (FP) is highly expressed in mouse tissues especially in the corpora lutea in ovaries and in the kidney. Recently, it has been shown that homozygous knockout-mice lacking the gene for this receptor are unable to deliver normal fetuses at term. It might be speculated that the lack of the FP gene has the same effect in human as in mouse. Mutation analysis in families with difficulties in parturition would therefore be of high interest. The results presented here provides data necessary for further investigations of the FP gene.


Subject(s)
Chromosomes, Human, Pair 1 , Receptors, Prostaglandin/genetics , Animals , Base Sequence , Centromere/genetics , Chromosome Mapping , Corpus Luteum/metabolism , Exons , Female , Genetic Markers , Humans , In Situ Hybridization, Fluorescence , Introns , Kidney/metabolism , Mice , Mice, Knockout , Molecular Sequence Data , Receptors, Prostaglandin/deficiency
12.
Hum Genet ; 105(6): 552-9, 1999 Dec.
Article in English | MEDLINE | ID: mdl-10647888

ABSTRACT

Chromosomal deletions on 3p have been described in a large number of human tumors, suggesting the presence of a tumor suppressor gene(s). Using an experimental system, called the elimination test, we previously identified a 1 Mb segment, the common eliminated region 1 (C3CER1). C3CER1 was also covered by a PAC contig. Using the sequence of two overlapping PACs from C3CER1, we localized the human KIAA0028 cDNA, encoding the precursor of mitochondrial leucyl-tRNA synthetase. We also characterized a novel human LIM domain-containing gene (LIMD1) and its mouse ortholog (Limd1). LIM domains consist of a cysteine-rich consensus sequence containing two distinct zinc-binding subdomains, which mediate protein-protein interactions. The predicted protein sequences of the human and mouse genes reveal three LIM domains located at the C-terminal end, which indicates that they belong to the group 3 of the gene family encoding LIM motifs. We characterized the genomic structure of the human LIMD1 gene and assigned the mouse Limd1 gene to the chromosome 9F subtelomeric region. Both genes are ubiquitously expressed at the mRNA level. The LIM motif has been previously identified in many developmentally important factors from various eukaryotes. These factors have been shown to play a role in intracellular signaling, transcriptional regulation and cellular differentiation during development. The human C3CER1-located LIMD1 gene should therefore be further studied for its possible role in tumor suppression.


Subject(s)
Carrier Proteins/genetics , Chromosome Deletion , Chromosomes, Human, Pair 3/genetics , Genes, Tumor Suppressor/genetics , Amino Acid Sequence , Animals , Blotting, Northern , Humans , In Situ Hybridization, Fluorescence , Intracellular Signaling Peptides and Proteins , LIM Domain Proteins , Mice , Molecular Sequence Data , Physical Chromosome Mapping , Protein Structure, Tertiary , RNA, Messenger/analysis , Sequence Alignment , Tumor Suppressor Proteins
13.
Hum Genet ; 103(2): 131-41, 1998 Aug.
Article in English | MEDLINE | ID: mdl-9760194

ABSTRACT

Genomic sequencing was combined with searches of databases for identification of active genes on human chromosome 22. A cosmid from 22q13, located in the telomeric vicinity of the PDGFB (platelet-derived growth factor B-chain) gene, was fully sequenced. Using an expressed sequence tag-based approach we characterized human (SYNGR1) and mouse (Syngr1) orthologs of the previously cloned rat synaptogyrin gene (RATSYNGR1). The human SYNGR1 gene reveals three (SYNGR1a, SYNGR1b, SYNGR1c) alternative transcript forms of 4.5, 1.3 and 0.9 kb, respectively. The transcription of SYNGR1 starts from two different promoters, and leads to predicted proteins with different N- and C-terminal ends. The most abundant SYNGR1 a transcript, the 4.5-kb form, which corresponds to RATSYNGR1, is highly expressed in neurons of the central nervous system and at much lower levels in other tissues, as determined by in situ hybridization histochemistry. The levels of SYNGR1b and SYNGR1c transcripts are low and limited to heart, skeletal muscle, ovary and fetal liver. We also characterized two additional members of this novel synaptogyrin gene family in human (SYNGR2 and SYNGR3), and one in mouse (Syngr2). The human SYNGR2 gene transcript of 1.6 kb is expressed at high levels in all tissues, except brain. The 2.2-kb SYNGR3 transcript was detected in brain and placenta only. The human SYNGR2 and SYNGR3 genes were mapped by fluorescence in situ hybridization to 17qtel and 16ptel, respectively. The human SYNGR2 gene has a processed pseudogene localized in 15q11. All predicted synaptogyrin proteins contain four strongly conserved transmembrane domains, which is consistent with the M-shaped topology. The C-terminal polypeptide ends are variable in length, display a low degree of sequence similarity between family members, and are therefore likely to convey the functional specificity of each protein.


Subject(s)
Membrane Proteins/genetics , Nerve Tissue Proteins/genetics , Amino Acid Sequence , Animals , Base Sequence , Chromosome Mapping , DNA, Complementary , Female , Humans , Mice , Molecular Sequence Data , Multigene Family , Pseudogenes , Rats , Sequence Homology, Amino Acid , Synaptogyrins
14.
Gene ; 212(1): 13-20, 1998 May 28.
Article in English | MEDLINE | ID: mdl-9661659

ABSTRACT

Rapid progress in sequencing of human and other genomes allows high-resolution analysis of their gene content on the basis of comparison between species. We have used a combined computer and biochemical approach to characterize 135 kb of human genomic sequence from 22q12 and discovered a new 10 exon gene, termed NIPSNAP1, located between the neurofibromatosis type 2 and the pK1.3 genes. The NIPSNAP1 gene spans 26 kb of genomic sequence and shows to large introns in the 5'-region. All exon-intron junctions contain the gt/ag consensus splice site. The putative promoter of the NIPSNAP1 gene is TATA-less and resides in a GC-rich island characteristic of housekeeping genes. The NIPSNAP1 mRNA is 2.1 kb, is expressed ubiquitously at variable levels, with the highest expression in liver, is terminated by an uncommon ATTAAA polyadenylation site, and is capable of encoding a 284-amino-acid protein. This NIPSNAP1 protein has a strong sequence similarity limited to the central portion of a hypothetical protein (acc. P34492) from chromosome III of C. elegans, in which the other portions resemble a 4-nitrophenylphosphatase domain and non-neuronal SNAP25-like protein. Thus, the NIPSNAP1 gene is a member of an evolutionarily well conserved, novel gene family with two members in human and mouse that have now been characterized, and one member in C. elegans. The second human gene, NIPSNAP2, is localized in the vicinity of marker D7S499 on chromosome 7. Although the function of the NIPSNAP protein family is unknown, clues about its role may reside in the co-expression of the C. elegans orthologue, within an operon encoding protein motifs known to be involved in vesicular transport.


Subject(s)
Chromosomes, Human, Pair 22/genetics , Membrane Proteins , Multigene Family , Proteins/genetics , Amino Acid Sequence , Animals , Base Sequence , Caenorhabditis elegans/genetics , Cloning, Molecular , DNA Primers/genetics , DNA, Complementary/genetics , Exons , Humans , Intercellular Signaling Peptides and Proteins , Introns , Mice , Molecular Sequence Data , Nerve Tissue Proteins/genetics , Sequence Homology, Amino Acid , Species Specificity , Synaptosomal-Associated Protein 25
15.
Biochem Mol Biol Int ; 44(3): 589-94, 1998 Mar.
Article in English | MEDLINE | ID: mdl-9556220

ABSTRACT

In this report we describe a sequence (PNG22) highly similar to the Phospholipase C beta3 Neighboring Gene (PNG). We also report that PNG22 is located in the q12 region on chromosome 22 between markers D22S1144 and D22S280. This finding explains that PNG probes cross hybridize to sequences on chromosome 22. Fine mapping using our sequence data and the complete sequence of a PAC clone (DJ515N1), located in this region, determined that PNG22 is located in intron 15 of the LIMK-2 gene. PNG22 is 93% homologous to PNG, however it do not have the introns described for the PNG gene, instead matching the cDNA sequence. This leads us to suggest that PNG22 probably represents a PNG pseudogene. In this report we also list the exon intron borders and the genomic structure of LIMK-2 and place it on the Sanger Center chromosome 22 Physical map. It also explains the finding that PNG probes cross hybridize to sequences on chromosome 22.


Subject(s)
Chromosomes, Human, Pair 22 , DNA-Binding Proteins , Protein Kinases/genetics , Proteins/genetics , Base Sequence , Cloning, Molecular , Humans , Introns , Lim Kinases , Molecular Sequence Data , Protein Phosphatase 1 , Protein Serine-Threonine Kinases , Pseudogenes , Sequence Homology, Nucleic Acid
16.
Hum Genet ; 100(5-6): 611-9, 1997 Oct.
Article in English | MEDLINE | ID: mdl-9341881

ABSTRACT

Multiple endocrine neoplasia type 1 (MEN1) is tightly linked to the muscle-type glycogen phosphorylase (PYGM) gene in 11q13. This region of the human genome contains additional disease-related loci implicated in the development of insulin-dependent diabetes mellitus, familial paraganglioma type 2, spinocerebellar ataxia type 5, Bardet-Biedl syndrome and translocation t(11;17) described in B-cell non-Hodgkin's lymphoma. We approached cloning of candidate disease genes from 11q13 by large-scale genomic sequencing. We obtained > 106 kb of sequence around the PYGM gene and established a transcriptional map that includes: (i) two genes previously localized to 11q13, PYGM and a zinc-finger protein (ZFM1) gene; (ii) the germinal center kinase (GCK, human B-lymphocyte serine/threonine protein kinase) gene; (iii) a novel human CDC25-like (HCDC25L) gene; (iv) a dystrophia myotonica protein kinase-like (DMPKL) gene; and (v) a novel ubiquitously expressed gene of unknown function (germinal center kinase- neighboring gene, GCKNG).


Subject(s)
Cell Cycle Proteins/genetics , Chromosome Mapping , Chromosomes, Human, Pair 11/genetics , DNA-Binding Proteins , Phosphoprotein Phosphatases/genetics , Phosphorylases/genetics , Protein Serine-Threonine Kinases/genetics , Transcription Factors , Amino Acid Sequence , Carrier Proteins/genetics , Cloning, Molecular/methods , Exons/genetics , Genes/genetics , Germinal Center Kinases , Humans , Introns/genetics , Molecular Sequence Data , Multiple Endocrine Neoplasia Type 1/genetics , Muscles/enzymology , Myotonic Dystrophy , Myotonin-Protein Kinase , Nuclear Proteins/genetics , RNA Splicing Factors , RNA, Messenger/analysis , Sequence Analysis, DNA , Sequence Homology, Amino Acid , ras-GRF1
17.
J Gastroenterol ; 32(4): 442-52, 1997 Aug.
Article in English | MEDLINE | ID: mdl-9250889

ABSTRACT

Nitric oxide (NO) synthesized from L-arginine interacts with prostaglandins (PG) and sensory neuropeptides in the regulation of mucosal integrity, but the role of L-arginine, a substrate for NO-synthase, in gastroprotection and healing of chronic gastric ulcers has been little studied. In this study we compared the effects of intragastric (i.g.) and systemic (i.v.) administration of L-arginine or D-arginine on gastric secretion and acute gastric lesions provoked in rats by i.g. application of 100% ethanol, acidified aspirin (ASA), or the exposure to 3.5h of water immersion and restraint stress (WRS). In addition, the effects of L-arginine on ulcer healing and the formation of new vessels (angiogenesis) were determined, using monoclonal antibody (MAb E-9). L-arginine (10-200 mg/kg i.g.) failed to significantly affect gastric secretion but dose-dependently reduced the gastric lesions induced by 100% ethanol. ASA, and WRS, the doses inhibiting 50% of these lesions being 65, 94, and 72 mg/kg, respectively. This protection was accompanied by a significant rise in the gastric blood flow (GBF), whereas L-arginine given i.v. failed to affect the ethanol-lesions and the GBF. D-arginine or the NO-related amino acids--L-glutamine, L-citrulline, or L-ornithine--failed to significantly influence these lesions. Suppression of the generation of mucosal PG by indomethacin or capsaicin-denervation attenuated the protection and hyperemia induced by L-arginine. The inhibition of constitutive NO synthase by L-NNA had no significant effect on the protection afforded by L-arginine, but reduced the gastric hyperemia accompanying this protection. L-arginine (150 mg/kg per day, i.g.) accelerated the ulcer healing and increased GBF at the ulcer margin, and angiogenesis, whereas treatment with L-NNA had an opposite effect. L-arginine added to NG-nitro-L-arginine (L-NNA) restored the ulcer healing, hyperemia, and angiogenesis. We conclude that: (1) the protective activity of L-arginine involves gastric hyperemia mediated by NO and a mild irritant effect due to enhanced generation of endogenous PG, and (2) the ulcer healing properties of L-arginine depend upon its hyperemic and angiogenic actions, possibly involving NO.


Subject(s)
Arginine/pharmacology , Gastric Acid/metabolism , Gastric Mucosa/drug effects , Ulcer/drug therapy , Animals , Capsaicin/pharmacology , Citrulline/pharmacology , Dose-Response Relationship, Drug , Endothelium/immunology , Endothelium/metabolism , Gastric Mucosa/blood supply , Gastric Mucosa/metabolism , Gastric Mucosa/pathology , Glutamine/pharmacology , Immunohistochemistry , Indomethacin/pharmacology , Male , Neovascularization, Pathologic/drug therapy , Neovascularization, Pathologic/metabolism , Neurons, Afferent/drug effects , Nitroarginine/pharmacology , Ornithine/pharmacology , Pepsin A/metabolism , Rats , Rats, Wistar , Ulcer/chemically induced
18.
Nat Genet ; 15(1): 95-8, 1997 Jan.
Article in English | MEDLINE | ID: mdl-8988177

ABSTRACT

Dermatofibrosarcoma protuberans (DP), an infiltrative skin tumour of intermediate malignancy, presents specific features such as reciprocal translocations t(17;22)(q22;q13) and supernumerary ring chromosomes derived from the t(17;22). In this report, the breakpoints from translocations and rings in DP and its juvenile form, giant cell fibroblastoma (GCF), were characterised on the genomic and RNA level. These rearrangements fuse the platelet-derived growth factor B-chain (PDGFB, c-sis proto-oncogene) and the collagen type I alpha 1 (COL1A1) genes. PDGFB has transforming activity and is a potent mitogen for a number of cell types, but its role in oncogenic processes is not fully understood. COL1A1 is a major constituent of the connective tissue matrix. Neither PDGFB nor COL1A1 have so far been implicated in any tumour translocations. These gene fusions delete exon 1 of PDGFB, and release this growth factor from its normal regulation.


Subject(s)
Cloning, Molecular , Collagen/genetics , Dermatofibrosarcoma/genetics , Platelet-Derived Growth Factor/genetics , Proto-Oncogene Proteins/genetics , Skin Neoplasms/genetics , Chromosome Breakage , Chromosomes, Human, Pair 17 , Chromosomes, Human, Pair 22 , Collagen Type I, alpha 1 Chain , DNA, Neoplasm , Gene Library , Humans , Molecular Sequence Data , Proto-Oncogene Mas , Proto-Oncogene Proteins c-sis , Ring Chromosomes , Translocation, Genetic
19.
Genomics ; 36(1): 112-7, 1996 Aug 15.
Article in English | MEDLINE | ID: mdl-8812422

ABSTRACT

Adaptins are major structural components of heterotetrameric protein complexes called adaptors, which are essential in intracellular receptor transport via clathrin-coated vesicles. beta-adaptins constitute one of three known classes (alpha, beta, gamma) of adaptins, including beta and beta' subtypes. We previously cloned the human beta'-adaptin gene (BAM22) (GDB symbol, ADTB1) from chromosome 22q12 and proposed its involvement in the development of meningiomas. Here we describe the genomic organization of this gene, which consists of 22 exons spanning over approximately 100 kb. We also report results from point mutation screening of 7 randomly chosen exons analyzed in 110 sporadic meningiomas. As part of the genomic characterization of the BAM22 locus, we sequenced 40 kb covering exons 1-4 and 12 kb upstream from the start of gene transcription. Analysis of the sequence suggests that the BAM22 gene has a CG-rich promoter.


Subject(s)
Adaptor Protein Complex 1 , Chromosomes, Human, Pair 22/genetics , Genes/genetics , Membrane Proteins/genetics , Meningeal Neoplasms/genetics , Meningioma/genetics , Promoter Regions, Genetic/genetics , Adaptor Protein Complex beta Subunits , Base Composition , Base Sequence , CpG Islands/genetics , DNA/chemistry , DNA Mutational Analysis , Exons/genetics , Genes, Tumor Suppressor/genetics , Humans , Introns/genetics , Molecular Sequence Data , Point Mutation/genetics , Polymorphism, Restriction Fragment Length , Sequence Analysis, DNA
20.
Biochem Biophys Res Commun ; 223(2): 335-40, 1996 Jun 14.
Article in English | MEDLINE | ID: mdl-8670283

ABSTRACT

We describe the isolation and expression of a murine homologue of the Phospholipase C beta3 Neighboring Gene (PNG), located in the MEN1 region on chromosome 11q13. The PNG cDNA was isolated using a human PNG cDNA clone (SOM172). Human and mouse PNG do not have any marked similarity to other known genes on the DNA level, but the predicted protein display similarity to the C-terminal part of Phospholipase C beta2. Northern blots with mouse PNG probes revealed expression of a 1 kb message in multiple tissues, and an additional 2.3 kb band in testis. The predicted murine protein contains 203 amino acids. In situ hybridization histochemistry displayed png mRNA expression in several tissues of the midstage mouse embryo, including the central nervous system. In late stage embryos, png was highly expressed in skeletal muscle, retina and neocortex. In the adult animal, expression was restricted to testis and thymus.


Subject(s)
Brain/metabolism , Chromosome Mapping , Protein Biosynthesis , Proteins/genetics , Aging/metabolism , Amino Acid Sequence , Animals , Animals, Newborn , Base Sequence , Humans , In Situ Hybridization , Isoenzymes/genetics , Male , Mice , Molecular Sequence Data , Oligonucleotide Probes , Organ Specificity , Phospholipase C beta , Protein Phosphatase 1 , Proteins/chemistry , RNA, Messenger/biosynthesis , Sequence Homology, Amino Acid , Transcription, Genetic , Type C Phospholipases/genetics
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