ABSTRACT
The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.
Subject(s)
Databases, Genetic , Genes , Terminology as Topic , Animals , Bibliographies as Topic , Electronic Mail , Genomics , Humans , Information Storage and Retrieval , Internet , Molecular Biology , Proteins/classification , Proteins/genetics , SoftwareSubject(s)
Databases, Factual , Genes/genetics , Genome , Animals , Computational Biology/methods , Information Storage and Retrieval , MiceABSTRACT
The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. By combining the different types of expression data, GXD aims to provide increasingly complete information about the expression profiles of genes in different mouse strains and mutants, thus enabling valuable insights into the molecular networks that underlie normal development and disease. GXD is integrated with the Mouse Genome Database (MGD). Extensive interconnections with sequence databases and with databases from other species, and the development and use of shared controlled vocabularies extend GXD's utility for the analysis of gene expression information. GXD is accessible through the Mouse Genome Informatics web site at http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression_menu. shtml.
Subject(s)
Databases, Factual , Gene Expression Profiling , Mice/genetics , Animals , Information Services , InternetABSTRACT
The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. The database is designed as an open-ended system that can integrate different types of expression data. New expression data are made available on a daily basis. Thus, GXD provides increasingly complete information about what transcripts and proteins are produced by what genes; where, when and in what amounts these gene products are expressed; and how their expression varies in different mouse strains and mutants. GXD is integrated with the Mouse Genome Database (MGD). Continuously refined interconnections with sequence databases and with databases from other species place the gene expression information in the larger biological and analytical context. GXD is accessible through the Mouse Genome Informatics Web site at http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression_menu.shtm l
Subject(s)
Databases, Factual , Gene Expression , Mice/genetics , Alternative Splicing , Animals , Database Management Systems , RNA, Messenger/geneticsABSTRACT
The Gene Expression Database (GXD) is a community resource that stores and integrates expression information for the laboratory mouse, with a particular emphasis on mouse development, and makes these data freely available in formats appropriate for comprehensive analysis. GXD is implemented as a relational database and integrated with the Mouse Genome Database (MGD) to enable global analysis of genotype, expression and phenotype information. Interconnections with sequence databases and with databases from other species further extend GXD's utility for the analysis of gene expression data. GXD is available through the Mouse Genome Informatics Web Site at http://www.informatics.jax.org/
Subject(s)
Databases, Factual , Gene Expression/genetics , Mice/genetics , Animals , Databases, Factual/trends , Expressed Sequence Tags , Genes , Genotype , Information Storage and Retrieval , Internet , Mice, Inbred Strains , Phenotype , Terminology as TopicABSTRACT
The gene expression database (GXD) is being developed to store and integrate expression information for mouse development. GXD addresses many issues that apply to gene expression databases in general, and its data structures and supporting software tools are generalized in design and thus readily adaptable to other life stages and species. Integration of GXD with the mouse genome database (MGD) and interconnections with other relevant databases will place the gene expression data into the larger biological and analytical context. Here, we describe the design and implementation of GXD and illustrate, in particular, the gene expression annotator, an electronic system for submitting expression data to the database.Copyright 1997 Academic Press Limited Copyright 1997Academic Press Limited
Subject(s)
Cadherins/genetics , Cell Adhesion Molecules/genetics , Chromosomes , Cytoskeletal Proteins/genetics , Muridae/genetics , Trans-Activators , Animals , Base Sequence , Chromosome Mapping , Desmoplakins , Genetic Markers , Haplotypes , Mice , Mice, Inbred C57BL , Mice, Inbred Strains , Molecular Sequence Data , Polymorphism, Restriction Fragment Length , alpha Catenin , beta Catenin , gamma CateninABSTRACT
The retroviral oncogene v-myb encodes a transcriptional activator which is responsible for the activation of the mim-1 gene in myelomonocytic cells transformed by v-myb. The mim-1 promoter contains several myb consensus binding sites and has previously been shown to be regulated directly by v-myb. Here we report that the mim-1 gene is activated synergistically by v-myb and different C/EBP transcription factors. We have cloned a chicken C/EBP-related gene that is highly expressed in myeloid cells and identified it as the chicken homolog of C/EBP beta. A dominant-negative variant of chicken C/EBP beta interferes with the v-myb induced activation of the mim-1 gene in these cells, suggesting that C/EBP beta or another C/EBP transcription factor is required for the activation of mim-1 by v-myb. We found that C/EBP beta and other C/EBP transcription factors confer to fibroblasts the ability to induce the mim-1 gene in the presence of v-myb. Finally we show that, in contrast to v-myb, c-myb synergizes with C/EBP transcription factors only at low concentrations of c-myb protein. Our results suggest a role for C/EBP beta, and possibly for other C/EBP transcription factors, in v-myb function and in myeloid-specific gene activation.
Subject(s)
Acetyltransferases , DNA-Binding Proteins/metabolism , Nuclear Proteins/metabolism , Proteins/genetics , Retroviridae Proteins, Oncogenic/metabolism , Transcription Factors/metabolism , Amino Acid Sequence , Animals , Avian Myeloblastosis Virus , Base Sequence , CCAAT-Enhancer-Binding Proteins , Cell Line , Chickens , Gene Expression Regulation , Mice , Molecular Sequence Data , Muramidase/genetics , Oligodeoxyribonucleotides , Oncogene Proteins v-myb , Promoter Regions, Genetic , Proteins/metabolism , Rats , Sequence Homology, Amino Acid , Transcriptional ActivationABSTRACT
We have recently shown that the Ca2+ dependent cell adhesion molecule uvomorulin is encoded by a single gene, localized on mouse chromosome 8. Here we describe the organization of the uvomorulin gene and give an initial characterization of the uvomorulin promoter. Uvomorulin is encoded by 16 exons, which are distributed over a region of more than 40 kb genomic DNA. The exon structure of the genes for uvomorulin and its chicken homologue L-CAM are nearly identical and thus highly conserved. The relationship between the exon structure and the structure of the uvomorulin protein is analysed. The initiation site of transcription of the uvomorulin gene is located 127 bp upstream of the translation start site in a GC-rich region with no TATA-box, but with a GC-box in position -48 and a CCAAT-box starting at position -65 with respect to the transcription start site. 1.6 kb of the uvomorulin promoter (-1492 to + 92) confer cell type specific promoter activity to the CAT reporter gene. Homologies to known cis acting elements of other promoters are discussed.
Subject(s)
Cadherins/genetics , 3T3 Cells , Amino Acid Sequence , Animals , Base Sequence , Cloning, Molecular , DNA , Exons , Gene Expression Regulation , Introns , Mice , Molecular Sequence Data , Organ Specificity/genetics , Promoter Regions, Genetic , Restriction Mapping , Sequence Alignment , Transcription, Genetic , Tumor Cells, CulturedABSTRACT
Cadherins, a multigene family of transmembrane glycoproteins, mediate Ca(2+)-dependent intercellular adhesion. They are thought to be essential for the control of morphogenetic processes, including myogenesis. Here we report the identification and characterization of the cDNA of another member of the cadherin family, M-cadherin (M for muscle), from differentiating muscle cells. The longest open reading frame of the cDNAs isolated contains almost the entire coding region of the mature M-cadherin as determined by sequence homology to the known cadherins. M-cadherin mRNA is present at low levels in myoblasts and is upregulated in myotube-forming cells. In mouse L cells (fibroblasts), M-cadherin mRNA is undetectable. This expression pattern indicates that M-cadherin is part of the myogenic program and may provide a trigger for terminal muscle differentiation.
Subject(s)
Cadherins/metabolism , Muscles/physiology , Amino Acid Sequence , Animals , Base Sequence , Blotting, Northern , Cadherins/genetics , Cell Differentiation , Cell Line , Cloning, Molecular , DNA/genetics , Fluorescent Antibody Technique , Gene Expression , Mice , Molecular Sequence Data , Muscle Proteins/genetics , Muscle Proteins/metabolism , Muscles/cytology , RNA, Messenger/geneticsABSTRACT
We have recently found that the cytoplasmic region of the cell adhesion molecule uvomorulin associates with three proteins named catenin alpha, beta, and gamma. Here we show by analysis of various mutant uvomorulin polypeptides expressed in mouse L cells that this association is mediated by a specific domain in the cytoplasmic region. A specific recognition site for catenins is located in a 72-amino acid domain. Interestingly, 69 of the 72 amino acid residues are encoded by a single exon of the uvomorulin gene. To demonstrate the direct interaction between catenins and the 72-amino acid domain, cDNA constructs composed of H-2Kd cDNA and various 3' sequences of uvomorulin were expressed in L cells. Chimeric proteins between H-2Kd and the 72-amino acid domain of uvomorulin were shown, by immunoprecipitation with anti-H-2Kd antibodies, to complex with catenin alpha, beta, and gamma. Catenins connect uvomorulin to cytoskeletal structures. We provide biochemical evidence for an association of the uvomorulin-catenin complex with actin bundles. Our results suggest that catenin alpha plays a key role in the association with actin filaments, whereas catenin beta binds more directly to the cytoplasmic region of uvomorulin. In cell aggregation assays with transfected cells expressing normal or mutant uvomorulin, the adhesive function was expressed only when uvomorulin was associated with catenins. From these results we conclude that the cytoplasmic anchorage of uvomorulin is of major biological importance.
Subject(s)
Cadherins/physiology , Cell Adhesion Molecules/metabolism , Proteins/metabolism , Actins/metabolism , Amino Acid Sequence , Animals , Base Sequence , Binding Sites , Blotting, Western , Cadherins/ultrastructure , Calcium/physiology , Cell Adhesion Molecules/ultrastructure , Cell Aggregation , Cloning, Molecular , Cytoplasm/metabolism , DNA/genetics , DNA Mutational Analysis , L Cells , Macromolecular Substances , Molecular Sequence Data , Precipitin TestsABSTRACT
The adhesive function of Ca2(+)-dependent CAMS has in the past been studied only indirectly, mainly using immunological techniques. The molecular cloning and information about the primary structure of several CAMs has been an important step in a more detailed molecular analysis. If there is a homophilic interaction between CAMs of neighbouring cells, an important question concerns the specificity of each CAM-mediated adhesiveness. Has each CAM a unique specificity and can this specificity be linked to a defined amino acid sequence? It will be important to elucidate the molecular mechanism of how each CAM interacts with the other. The experiments of Volk et al. (1987) suggest that an interaction of two different CAMs can occur. Since during development a given cell can express more than one CAM such an heterophilic interaction could play some regulatory role. Alternative splicing mechanisms or different protein forms during development or on different cell types have not yet been observed for Ca2(+)-dependent CAMs. However, uvomorulin is assumed to have a slightly different function during development and in adult tissues. During development uvomorulin is involved in the condensation, the pattern formation, and the sorting out of cells. In these processes the uvomorulin-mediated adhesiveness should be controlled, since cells reorganize and migrate during development. For the maintenance of the histoarchitecture in adult tissues uvomorulin might act more as a glue. This argues for the existence of mechanisms to regulate the strength of adhesiveness, and the cytoplasmic domain might be involved in these processes. The association of the cytoplasmic domain of uvomorulin with catenins could be an important observation in this respect.(ABSTRACT TRUNCATED AT 250 WORDS)
Subject(s)
Calcium/physiology , Cell Adhesion Molecules , Cell Adhesion , Animals , Cell Adhesion Molecules/physiology , Cell Adhesion Molecules/ultrastructure , Humans , Models, Biological , Protein ConformationABSTRACT
The gene coding for the mouse cell adhesion molecule uvomorulin has been mapped to chromosome 8. Uvomorulin cDNA clone F5H3 identified restriction fragment length polymorphisms in Southern blots of genomic DNA from mouse species Mus musculus domesticus and Mus spretus. By analyzing the segregation pattern of the gene in 75 offspring from an interspecific backcross a single genetic locus, Um, was defined on chromosome 8. Recombination frequency between Um and the co-segregating loci serum esterase 1 (Es-1) and tyrosine aminotransferase (Tat) places Um about 14 centimorgan (cM) distal to Es-1, and 5 cM proximal to Tat. In situ hybridization of uvomorulin [3H]cDNA to mouse metaphase chromosomes located the Um locus close to the distal end of chromosome 8 (bands C3-E1). Since uvomorulin is evolutionarily highly conserved, its chromosomal assignment adds an important marker to the mouse genetic map.
Subject(s)
Calcium-Binding Proteins/genetics , Chromosomes, Bacterial/physiology , Genes , Membrane Glycoproteins/genetics , Animals , Cadherins , Chromosome Mapping , Crosses, Genetic , DNA/genetics , Karyotyping , Mice , Mice, Inbred C57BL , Mice, Inbred Strains , Polymorphism, Restriction Fragment LengthABSTRACT
We have determined the amino acid sequence of the Ca2+-dependent cell adhesion molecule uvomorulin as it appears on the cell surface. The extracellular part of the molecule exhibits three internally repeated domains of 112 residues which are most likely generated by gene duplication. Each of the repeated domains contains two highly conserved units which could represent putative Ca2+-binding sites. Secondary structure predictions suggest that the putative Ca2+-binding units are located in external loops at the surface of the protein. The protein sequence exhibits a single membrane-spanning region and a cytoplasmic domain. Sequence comparison reveals extensive homology to the chicken L-CAM. Both uvomorulin and L-CAM are identical in 65% of their entire amino acid sequence suggesting a common origin for both CAMs.
Subject(s)
Antigens, Surface , Calcium-Binding Proteins/genetics , Calcium/pharmacology , Cell Adhesion/drug effects , Membrane Glycoproteins/genetics , Amino Acid Sequence , Animals , Base Sequence , Cadherins , Cell Adhesion Molecules , Cell Line , Genes , Membrane Glycoproteins/physiology , Mice , Molecular Sequence Data , Nucleic Acid Hybridization , TeratomaABSTRACT
A clone (F20) containing coding sequences for the cell adhesion molecule uvomorulin was isolated by immunological techniques from cDNA library in the expression vector lambda gt11. The beta-galactosidase-uvomorulin fusion protein was used to affinity purify anti-uvomorulin antibodies. Affinity-purified antibodies recognized uvomorulin from cell lysates of embryonal carcinoma cells and reacted with the cell surface of embryonal carcinoma cells. The 1.8-kilobase cDNA insert hybridized to a single 4.3-kilobase poly(A)+ RNA species found only in cells expressing uvomorulin. Part of the nontranslated 3' sequences of the cloned uvomorulin cDNA is homologous to the interspersed B1 repeat of the mouse genome.
