RESUMEN
Equine herpesvirus 1 (EHV-1) causes respiratory disease, abortion, neonatal death and neurological disease in equines and is endemic in most countries. The viral factors that influence EHV-1 disease severity are poorly understood, and this has hampered vaccine development. However, the N752D substitution in the viral DNA polymerase catalytic subunit has been shown statistically to be associated with neurological disease. This has given rise to the term "neuropathic strain," even though strains lacking the polymorphism have been recovered from cases of neurological disease. To broaden understanding of EHV-1 diversity in the field, 78 EHV-1 strains isolated over a period of 35 years were sequenced. The great majority of isolates originated from the United Kingdom and included in the collection were low passage isolates from respiratory, abortigenic and neurological outbreaks. Phylogenetic analysis of regions spanning 80% of the genome showed that up to 13 viral clades have been circulating in the United Kingdom and that most of these are continuing to circulate. Abortion isolates grouped into nine clades, and neurological isolates grouped into five. Most neurological isolates had the N752D substitution, whereas most abortion isolates did not, although three of the neurological isolates from linked outbreaks had a different polymorphism. Finally, bioinformatic analysis suggested that recombination has occurred between EHV-1 clades, between EHV-1 and equine herpesvirus 4, and between EHV-1 and equine herpesvirus 8.
Asunto(s)
Aborto Veterinario/virología , Encefalopatías/veterinaria , Variación Genética , Infecciones por Herpesviridae/veterinaria , Herpesvirus Équido 1/genética , Enfermedades de los Caballos/virología , Trastornos Respiratorios/veterinaria , Animales , Secuencia de Bases , Encefalopatías/virología , ADN Viral/genética , ADN Polimerasa Dirigida por ADN/genética , Brotes de Enfermedades/veterinaria , Equidae , Femenino , Infecciones por Herpesviridae/epidemiología , Infecciones por Herpesviridae/virología , Herpesvirus Équido 1/aislamiento & purificación , Enfermedades de los Caballos/epidemiología , Caballos , Filogenia , Embarazo , Trastornos Respiratorios/virología , Reino UnidoRESUMEN
Cone-rod dystrophy 1 (cord1) is a recessive condition that occurs naturally in miniature longhaired dachshunds (MLHDs). We mapped the cord1 locus to a region of canine chromosome CFA15 that is syntenic with a region of human chromosome 14 (HSA14q11.2) containing the retinitis pigmentosa GTPase regulator-interacting protein 1 (RPGRIP1) gene. Mutations in RPGRIP1 have been shown to cause Leber congenital amaurosis, a group of retinal dystrophies that represent the most common genetic causes of congenital visual impairment in infants and children. Using the newly available canine genome sequence we sequenced RPGRIP1 in affected and carrier MLHDs and identified a 44-nucleotide insertion in exon 2 that alters the reading frame and introduces a premature stop codon. All affected and carrier dogs within an extended inbred pedigree were homozygous and heterozygous, respectively, for the mutation. We conclude the mutation is responsible for cord1 and demonstrate that this canine disease is a valuable model for exploring disease mechanisms and potential therapies for human Leber congenital amaurosis.
Asunto(s)
Cromosomas Humanos Par 14/genética , Codón sin Sentido , Mutagénesis Insercional , Atrofia Óptica Hereditaria de Leber/genética , Proteínas/genética , Animales , Niño , Preescolar , Proteínas del Citoesqueleto , Análisis Mutacional de ADN , Modelos Animales de Enfermedad , Perros , Exones/genética , Humanos , Lactante , LinajeRESUMEN
The finished sequence of human chromosome 10 comprises a total of 131,666,441 base pairs. It represents 99.4% of the euchromatic DNA and includes one megabase of heterochromatic sequence within the pericentromeric region of the short and long arm of the chromosome. Sequence annotation revealed 1,357 genes, of which 816 are protein coding, and 430 are pseudogenes. We observed widespread occurrence of overlapping coding genes (either strand) and identified 67 antisense transcripts. Our analysis suggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count on chromosome 10. Multispecies comparative analysis indicated that we can readily annotate the protein-coding genes with current resources. We estimate that over 95% of all coding exons were identified in this study. Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence.
Asunto(s)
Cromosomas Humanos Par 10/genética , Genes , Mapeo Físico de Cromosoma , Animales , Composición de Base , Mapeo Contig , Islas de CpG/genética , Evolución Molecular , Exones/genética , Duplicación de Gen , Variación Genética/genética , Genética Médica , Genómica , Humanos , Pan troglodytes/genética , Proteínas/genética , Seudogenes/genética , Análisis de Secuencia de ADNRESUMEN
The stem cell leukemia (SCL) gene encodes a tissue-specific basic helix-loop-helix (bHLH) protein with a pivotal role in hemopoiesis and vasculogenesis. Several enhancers have been identified within the murine SCL locus that direct reporter gene expression to subdomains of the normal SCL expression pattern, and long-range sequence comparisons of the human and murine SCL loci have identified additional candidate enhancers. To facilitate the characterization of regulatory elements, we have sequenced and analyzed 33 kb of the SCL genomic locus from the pufferfish Fugu rubripes, a species with a highly compact genome. Although the pattern of SCL expression is highly conserved from mammals to teleost fish, the genes flanking pufferfish SCL were unrelated to those known to flank both avian and mammalian SCL genes. These data suggest that SCL regulatory elements are confined to the region between the upstream and downstream flanking genes, a region of 65 kb in human and 8.5 kb in pufferfish. Consistent with this hypothesis, the entire 33-kb pufferfish SCL locus directed appropriate expression to hemopoietic and neural tissue in transgenic zebrafish embryos, as did a 10.4-kb fragment containing the SCL gene and extending to the 5' and 3' flanking genes. These results demonstrate the power of combining the compact genome of the pufferfish with the advantages that zebrafish provide for studies of gene regulation during development. Furthermore, the pufferfish SCL locus provides a powerful tool for the manipulation of hemopoiesis and vasculogenesis in vivo.
Asunto(s)
Proteínas de Unión al ADN/genética , Peces/genética , Genes Reguladores , Secuencias Hélice-Asa-Hélice , Proteínas Proto-Oncogénicas , Factores de Transcripción , Proteínas de Pez Cebra , Pez Cebra/genética , Secuencia de Aminoácidos , Animales , Animales Modificados Genéticamente , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico , Mapeo Cromosómico , Femenino , Regulación de la Expresión Génica , Regulación del Desarrollo de la Expresión Génica , Reordenamiento Génico , Datos de Secuencia Molecular , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Proteína 1 de la Leucemia Linfocítica T AgudaRESUMEN
The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
Asunto(s)
Genoma Humano , Proyecto Genoma Humano , Análisis de Secuencia de ADN , Animales , Mapeo Cromosómico , Secuencia Conservada , Islas de CpG , Elementos Transponibles de ADN , Bases de Datos Factuales , Industria Farmacéutica , Evolución Molecular , Predicción , Secuencia Rica en GC , Duplicación de Gen , Genes , Enfermedades Genéticas Congénitas , Genética Médica , Humanos , Mutación , Sector Privado , Proteínas/genética , Proteoma , Sector Público , ARN/genética , Secuencias Repetitivas de Ácidos Nucleicos , Análisis de Secuencia de ADN/métodos , Especificidad de la EspecieRESUMEN
Long-range comparative sequence analysis provides a powerful strategy for identifying conserved regulatory elements. The stem cell leukemia (SCL) gene encodes a bHLH transcription factor with a pivotal role in hemopoiesis and vasculogenesis, and it displays a highly conserved expression pattern. We present here a detailed sequence comparison of 193 kb of the human SCL locus to 234 kb of the mouse SCL locus. Four new genes have been identified together with an ancient mitochondrial insertion in the human locus. The SCL gene is flanked upstream by the SIL gene and downstream by the MAP17 gene in both species, but the gene order is not collinear downstream from MAP17. To facilitate rapid identification of candidate regulatory elements, we have developed a new sequence analysis tool (SynPlot) that automates the graphical display of large-scale sequence alignments. Unlike existing programs, SynPlot can display the locus features of more than one sequence, thereby indicating the position of homology peaks relative to the structure of all sequences in the alignment. In addition, high-resolution analysis of the chromatin structure of the mouse SCL gene permitted the accurate positioning of localized zones accessible to restriction endonucleases. Zones known to be associated with functional regulatory regions were found to correspond precisely with peaks of human/mouse homology, thus demonstrating that long-range human/mouse sequence comparisons allow accurate prediction of the extent of accessible DNA associated with active regulatory regions.
Asunto(s)
Secuencia Conservada/genética , Enzimas de Restricción del ADN/genética , Proteínas de Unión al ADN/genética , Proteínas Proto-Oncogénicas , Factores de Transcripción , Animales , Composición de Base , Secuencia de Bases , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico , ADN Mitocondrial/genética , Proteínas de Unión al ADN/metabolismo , Desoxirribonucleasa I/genética , Genes Relacionados con las Neoplasias , Marcadores Genéticos , Variación Genética , Humanos , Hidrólisis , Leucemia-Linfoma de Células T del Adulto/genética , Ratones , Ratones Endogámicos , Datos de Secuencia Molecular , Homología de Secuencia de Ácido Nucleico , Células Madre/metabolismo , Proteína 1 de la Leucemia Linfocítica T AgudaRESUMEN
The finished sequence of human chromosome 20 comprises 59,187,298 base pairs (bp) and represents 99.4% of the euchromatic DNA. A single contig of 26 megabases (Mb) spans the entire short arm, and five contigs separated by gaps totalling 320 kb span the long arm of this metacentric chromosome. An additional 234,339 bp of sequence has been determined within the pericentromeric region of the long arm. We annotated 727 genes and 168 pseudogenes in the sequence. About 64% of these genes have a 5' and a 3' untranslated region and a complete open reading frame. Comparative analysis of the sequence of chromosome 20 to whole-genome shotgun-sequence data of two other vertebrates, the mouse Mus musculus and the puffer fish Tetraodon nigroviridis, provides an independent measure of the efficiency of gene annotation, and indicates that this analysis may account for more than 95% of all coding exons and almost all genes.
Asunto(s)
Cromosomas Humanos Par 20 , Animales , Secuencia de Bases , Biología Computacional , Mapeo Contig , ADN , Enfermedades Genéticas Congénitas/genética , Variación Genética , Humanos , Ratones , Mapeo Físico de Cromosoma , Proteoma , Análisis de Secuencia de ADNRESUMEN
The SCL gene encodes a highly conserved bHLH transcription factor with a pivotal role in hemopoiesis and vasculogenesis. We have sequenced and analyzed 320 kb of genomic DNA composing the SCL loci from human, mouse, and chicken. Long-range sequence comparisons demonstrated multiple peaks of human/mouse homology, a subset of which corresponded precisely with known SCL enhancers. Comparisons between mammalian and chicken sequences identified some, but not all, SCL enhancers. Moreover, one peak of human/mouse homology (+23 region), which did not correspond to a known enhancer, showed significant homology to an analogous region of the chicken SCL locus. A transgenic Xenopus reporter assay was established and demonstrated that the +23 region contained a new neural enhancer. This combination of long-range comparative sequence analysis with a high-throughput transgenic bioassay provides a powerful strategy for identifying and characterizing developmentally important enhancers.
Asunto(s)
Secuencia Conservada , Proteínas de Unión al ADN/genética , Elementos de Facilitación Genéticos , Proteínas Proto-Oncogénicas , Factores de Transcripción/genética , Vertebrados/genética , Proteínas de Xenopus , Secuencia de Aminoácidos , Animales , Animales Modificados Genéticamente , Secuencia de Bases , Factores de Transcripción con Motivo Hélice-Asa-Hélice Básico , Pollos , Secuencias Hélice-Asa-Hélice , Humanos , Ratones , Datos de Secuencia Molecular , Rombencéfalo/embriología , Homología de Secuencia de Aminoácido , Proteína 1 de la Leucemia Linfocítica T Aguda , XenopusRESUMEN
We describe here Tdr2, a new class of Tc1-like transposons in zebrafish. Tdr2 was identified from the genomic sequence of a zebrafish PAC (P1 artificial chromosome) clone, and fragments of Tdr2 were found in several zebrafish EST (expressed sequence tag) sequences. Predicted translation of the Tdr2 transposase gene showed that it was most closely related to Caenorhabditis elegans Tc3A, suggesting an ancient origin of the Tdr2 transposon. Tdr2 spans 1. 1kb and is flanked by inverted repeats of approx. 100bp. The 5' repeat is itself composed of an inverted repeat, raising the possibility of the formation of a cruciform DNA structure. Tdr2 transposons may facilitate the development of novel transposon-based tools for the genetic analysis of zebrafish.
Asunto(s)
Elementos Transponibles de ADN/genética , Pez Cebra/genética , Secuencia de Aminoácidos , Animales , Secuencia de Bases , ADN/química , ADN/genética , Datos de Secuencia Molecular , Filogenia , Secuencias Repetitivas de Ácidos Nucleicos/genética , Alineación de Secuencia , Análisis de Secuencia de ADN , Homología de Secuencia de Aminoácido , Homología de Secuencia de Ácido Nucleico , Transposasas/genéticaRESUMEN
Using exon trapping, we have identified a new human gene in Xp22 encoding a 3-kb mRNA. Expression of this RNA is detectable in a range of tissues but is most pronounced in skeletal muscle and heart. The gene, designated "sex comb on midleg-like-1" (SCML1), maps 14 kb centromeric of marker DXS418, between DXS418 and DXS7994, and is transcribed from telomere to centromere. SCML1 spans 18 kb of genomic DNA, consists of six exons, and has a 624-bp open reading frame. The predicted 27-kDa SCML1 protein contains two domains that each have a high homology to two Drosophila transcriptional repressors of the polycomb group (PcG) genes and their homologues in mouse and human. PcG genes are known to be involved in the regulation of homeotic genes, and the mammalian homologues of the PcG genes repress the expression of Hox genes. SCML1 appears to be a new human member of this gene group and may play an important role in the control of embryonal development.