RESUMEN
Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
Asunto(s)
ADN Complementario/genética , Genómica , Ratones/genética , Transcripción Genética/genética , Empalme Alternativo/genética , Secuencias de Aminoácidos , Animales , Cromosomas de los Mamíferos/genética , Clonación Molecular , Bases de Datos Genéticas , Etiquetas de Secuencia Expresada , Genes/genética , Genómica/métodos , Humanos , Proteínas de la Membrana/genética , Mapeo Físico de Cromosoma , Estructura Terciaria de Proteína , Proteoma/química , Proteoma/genética , ARN sin Sentido/genética , ARN Mensajero/análisis , ARN Mensajero/genética , ARN no Traducido/análisis , ARN no Traducido/genética , Sitio de Iniciación de la TranscripciónRESUMEN
We characterized a new human ATP-binding cassette (ABC) transporter gene that is highly expressed in the liver. The gene, ABCG5, contains 13 exons and encodes a 651 amino acid protein. The predicted protein is closely related to the Drosophila white gene and a human gene, ABCG1, which is induced by cholesterol. This subfamily of genes all have a single ATP-binding domain at the N-terminus and a single C-terminal set of transmembrane segments. ABCG5 maps to human chromosome 2p21, between the markers D2S117 and D2S119. The abundant expression of this gene in the liver suggests that the protein product has an important role in transport of specific molecule(s) into or out of this tissue.
Asunto(s)
Transportadoras de Casetes de Unión a ATP/genética , Cromosomas Humanos Par 2/genética , Lipoproteínas/genética , Familia de Multigenes/genética , Sitoesteroles/sangre , Transportador de Casetes de Unión a ATP, Subfamilia G, Miembro 1 , Transportador de Casetes de Unión a ATP, Subfamilia G, Miembro 5 , Transportadoras de Casetes de Unión a ATP/química , Secuencia de Aminoácidos , Animales , Clonación Molecular , Drosophila melanogaster , Exones/genética , Marcadores Genéticos/genética , Humanos , Intrones/genética , Lipoproteínas/química , Hígado/metabolismo , Datos de Secuencia Molecular , Especificidad de Órganos , Filogenia , Estructura Terciaria de Proteína , Sitios de Empalme de ARN/genética , Mapeo de Híbrido por Radiación , Alineación de SecuenciaRESUMEN
We report here the genomic and transcriptional characterization in mouse and man of a novel transporter of the ABCA subclass, named ABCA7. As it is the case for other ABCA genes, the predicted protein encoded by ABCA7 is a full symmetric transporter, highly conserved across species. The ABCA7 gene maps to human chromosome 19 and to the homologous region at band B4-C1 on mouse chromosome 10. The preferential expression of ABCA7 in the spleen, thymus, and fetal liver is consistent with the finding, in both human and mouse promoter, of sites targeted by lymphomyeloid-specific transcription factors. This suggests that ABCA7 may play a pivotal role in the developmental specification of hematopoietic cell lineages.
Asunto(s)
Transportadoras de Casetes de Unión a ATP/genética , Exones/genética , Intrones/genética , Regiones Promotoras Genéticas/genética , Transportadoras de Casetes de Unión a ATP/química , Secuencia de Aminoácidos , Animales , Línea Celular , Cromosomas Humanos Par 19/genética , Secuencia Conservada/genética , ADN Complementario/genética , Humanos , Hibridación Fluorescente in Situ , Hígado/embriología , Hígado/metabolismo , Ratones , Datos de Secuencia Molecular , Especificidad de Órganos , ARN Mensajero/análisis , ARN Mensajero/genética , Mapeo de Híbrido por Radiación , Alineación de Secuencia , Homología de Secuencia de Ácido Nucleico , Bazo/metabolismo , Timo/metabolismoRESUMEN
The RIKEN Mouse Gene Encyclopaedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analysed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs extends known gene families and identifies new ones.
Asunto(s)
Biología Computacional , ADN Complementario , Ratones/genética , Animales , Mapeo Cromosómico , Enzimas/genética , Biblioteca de Genes , Genoma , Humanos , Ratones Endogámicos C57BL , Biosíntesis de Proteínas , Estructura Terciaria de Proteína , ARN Mensajero , Análisis de Secuencia de ADNAsunto(s)
Transportadoras de Casetes de Unión a ATP/química , Transportadoras de Casetes de Unión a ATP/genética , Adenosina Trifosfato/metabolismo , Transportador de Casetes de Unión a ATP, Subfamilia G , Transportadoras de Casetes de Unión a ATP/metabolismo , Secuencia de Aminoácidos , Animales , Clonación Molecular , Expresión Génica , Perfilación de la Expresión Génica , Humanos , Hibridación in Situ , Ratones , Datos de Secuencia Molecular , Especificidad de Órganos , Reacción en Cadena de la Polimerasa , Estructura Terciaria de Proteína , Ratas , Alineación de Secuencia , Bazo/metabolismo , Timo/metabolismoRESUMEN
In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources that operate on the data in GenBank and a variety of other biological data made available through NCBI's Web site. NCBI data retrieval resources include Entrez, PubMed, LocusLink and the Taxonomy Browser. Data analysis resources include BLAST, Electronic PCR, OrfFinder, RefSeq, UniGene, HomoloGene, Database of Single Nucleotide Polymorphisms (dbSNP), Human Genome Sequencing, Human MapViewer, GeneMap'99, Human-Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, Cancer Genome Anatomy Project (CGAP), SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheri-tance in Man (OMIM), the Molecular Modeling Database (MMDB) and the Conserved Domain Database (CDD). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih. gov.
Asunto(s)
Biotecnología , Bases de Datos Factuales , Servicios de Información , Animales , Perfilación de la Expresión Génica , Genoma , Genoma Humano , Humanos , Almacenamiento y Recuperación de la Información , Internet , Biología Molecular , National Institutes of Health (U.S.) , National Library of Medicine (U.S.) , Fenotipo , Alineación de Secuencia , Estados UnidosRESUMEN
Linkage mapping has been extensively applied in the murine and human genomes. It remains a powerful approach to mapping genes and identifying genetic variants. As genome efforts identify large numbers of single-nucleotide polymorphisms, it will be critical to validate these polymorphisms and confirm their gene assignment and chromosomal location. The presence of pseudogenes can confuse such efforts. We have used denaturing HPLC to identify polymorphisms in human genes and to genotype individuals in selected CEPH pedigrees. The same approach has been applied to the mapping of murine genes in interspecies backcross animals. This strategy is rapid, accurate and superior in several respects to other technologies.
Asunto(s)
Cromatografía Líquida de Alta Presión/métodos , Mapeo Cromosómico/métodos , Polimorfismo de Nucleótido Simple/genética , 5'-Nucleotidasa/química , Animales , Cruzamientos Genéticos , Pruebas Genéticas/métodos , Genotipo , Heterocigoto , Homocigoto , Humanos , Endogamia , Janus Quinasa 3 , Ratones , Linaje , Reacción en Cadena de la Polimerasa , Proteínas Tirosina Quinasas/genética , Reproducibilidad de los Resultados , TemperaturaRESUMEN
ATP-binding cassette (ABC) genes encode a family of transport proteins known to be involved in a number of human genetic diseases. In this study, we characterized the ABC superfamily in Mus musculus through in silico gene identification and mapping and phylogenetic analysis of mouse and human ABC genes. By querying dbEST with amino acid sequences from the conserved ATP-binding domains, we identified and partially sequenced 18 new mouse ABC genes, bringing the total number of mouse ABC genes to 34. Twelve of the new ABC genes were mapped in the mouse genome to the X chromosome and to 10 of the 19 autosomes. Phylogenetic relationships of mouse and human ABC genes were examined with maximum parsimony and neighbor-joining analyses that demonstrated that mouse and human ABC orthologs are more closely related than are mouse paralogs. The mouse ABC genes could be grouped into the seven previously described human ABC subfamilies. Three mouse ABC genes mapped to regions implicated in cholesterol gallstone susceptibility.
Asunto(s)
Transportadoras de Casetes de Unión a ATP/genética , Transportadoras de Casetes de Unión a ATP/química , Transportadoras de Casetes de Unión a ATP/clasificación , Secuencia de Aminoácidos , Animales , Mapeo Cromosómico , Etiquetas de Secuencia Expresada , Femenino , Humanos , Masculino , Ratones , Ratones Endogámicos C57BL , Datos de Secuencia Molecular , Filogenia , Homología de Secuencia de AminoácidoRESUMEN
PTEN/MMAC1 (phosphatase, tensin homologue/mutated in multiple advanced cancers) is a tumor suppressor protein that has sequence homology with dual-specificity phosphatases, which are capable of dephosphorylating both tyrosine phosphate and serine/threonine phosphate residues on proteins. The in vivo function of PTEN/MMAC1 appears to be dephosphorylation of phosphotidylinositol 3,4, 5-triphosphate. The PTEN/MMAC1 gene is mutated in the germline of patients with rare autosomal dominant cancer syndromes and in subsets of specific cancers. Here we review the mutational spectra of the PTEN/MMAC1 gene in tumors from various tissues, especially endometrium, brain, prostate, and ovary, in which the gene is inactivated very frequently. Germline and somatic mutations in the PTEN/MMAC1 gene occur mostly in the protein coding region and involve the phosphatase domain and poly(A)(6) stretches. Compared with germline alterations found in the PTEN/MMAC1 gene, there is a substantially increased frequency of frameshift mutations in tumors. Glioblastomas and endometrial carcinomas appear to have distinct mutational spectra, probably reflecting differences in the underlying mechanisms of inactivation of the PTEN/MMAC1 gene in the two tissue types. Also, depending on the tissue type, the gene appears to be involved in the initiation or the progression of cancers. Further understanding of PTEN/MMAC1 gene mutations in different tumors and the physiologic consequences of these mutations is likely to open up new therapeutic opportunities for targeting this critical gene.
Asunto(s)
Genes Supresores de Tumor/genética , Mutación , Neoplasias/genética , Fosfatos de Fosfatidilinositol/metabolismo , Proteínas Serina-Treonina Quinasas/metabolismo , Neoplasias Encefálicas/genética , Análisis Mutacional de ADN , Neoplasias Endometriales/genética , Femenino , Mutación del Sistema de Lectura , Mutación de Línea Germinal , Humanos , Masculino , Neoplasias/enzimología , Neoplasias/metabolismo , Neoplasias Ováricas/genética , Fosforilación , Neoplasias de la Próstata/genéticaRESUMEN
Tyramide signal amplification (TSA)-FISH was used to map one mouse and two human DNA probes of less than 1 kb in size. The two human probes were 319 and 608 bp, and the mouse probe was 855 bp. Probes, made from PCR products, were labeled by incorporating biotin-11-dUTP (human) and biotin-16-dUTP (mouse) during PCR amplification. Signals were readily observed in both interphase and metaphase cells following TSA-FISH for all three genes, whereas conventional FISH experiments produced no signals. The two human ATP-binding cassette (ABC) genes, EST883227 (GenBank Accession No. AA243820) and EST990006 (GenBank Accession No. AA348546), mapped to human chromosomes 7p21 and 17q25. The mouse gene, cmyc (exon 2) mapped to band D2 of mouse chromosome 15. These findings demonstrate the ability of this technique to map small probes (PCR products and expressed sequence tags) of less than 1 kb through highly increased signal amplification.
Asunto(s)
Biotina/análogos & derivados , Mapeo Cromosómico , Sondas de ADN , Hibridación Fluorescente in Situ/métodos , Reacción en Cadena de la Polimerasa , Tiramina/análogos & derivados , Animales , Cromosomas Humanos Par 17 , Cromosomas Humanos Par 7 , Nucleótidos de Desoxiuracil , Genes myc/genética , Humanos , Linfocitos/ultraestructura , Ratones , Bazo/ultraestructuraRESUMEN
We characterized a new human ATP-binding cassette (ABC) transporter gene that is highly expressed in the placenta. The gene, ABCP, produces two transcripts that differ at the 5' end and encode the same 655-amino acid protein. The predicted protein is closely related to the Drosophila white and yeast ADP1 genes and is a member of a subfamily that includes several multidrug resistance transporters. ABCP, white, and ADP1 all have a single ATP-binding domain at the NH2 terminus and a single COOH-terminal set of transmembrane segments. ABCP maps to human chromosome 4q22, between the markers D4S2462 and D4S1557, and the murine gene (Abcp) is located on chromosome 6 28-29 cM from the centromere. ABCP defines a new syntenic segment between human chromosome 4 and mouse chromosome 6. The abundant expression of this gene in the placenta suggests that the protein product has an important role in transport of specific molecule(s) into or out of this tissue.