RESUMO
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.
Assuntos
Aborto Animal/virologia , Encefalopatias/veterinária , Variação Genética , Infecções por Herpesviridae/veterinária , Herpesvirus Equídeo 1/genética , Doenças dos Cavalos/virologia , Transtornos Respiratórios/veterinária , Animais , Sequência de Bases , Encefalopatias/virologia , DNA Viral/genética , DNA Polimerase Dirigida por DNA/genética , Surtos de Doenças/veterinária , Equidae , Feminino , Infecções por Herpesviridae/epidemiologia , Infecções por Herpesviridae/virologia , Herpesvirus Equídeo 1/isolamento & purificação , Doenças dos Cavalos/epidemiologia , Cavalos , Filogenia , Gravidez , Transtornos Respiratórios/virologia , Reino UnidoRESUMO
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.
Assuntos
Cromossomos Humanos Par 14/genética , Códon sem Sentido , Mutagênese Insercional , Atrofia Óptica Hereditária de Leber/genética , Proteínas/genética , Animais , Criança , Pré-Escolar , Proteínas do Citoesqueleto , Análise Mutacional de DNA , Modelos Animais de Doenças , Cães , Éxons/genética , Humanos , Lactente , LinhagemRESUMO
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.
Assuntos
Cromossomos Humanos Par 10/genética , Genes , Mapeamento Físico do Cromossomo , Animais , Composição de Bases , Mapeamento de Sequências Contíguas , Ilhas de CpG/genética , Evolução Molecular , Éxons/genética , Duplicação Gênica , Variação Genética/genética , Genética Médica , Genômica , Humanos , Pan troglodytes/genética , Proteínas/genética , Pseudogenes/genética , Análise de Sequência de DNARESUMO
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.
Assuntos
Proteínas de Ligação a DNA/genética , Peixes/genética , Genes Reguladores , Sequências Hélice-Alça-Hélice , Proteínas Proto-Oncogênicas , Fatores de Transcrição , Proteínas de Peixe-Zebra , Peixe-Zebra/genética , Sequência de Aminoácidos , Animais , Animais Geneticamente Modificados , Fatores de Transcrição Hélice-Alça-Hélice Básicos , Mapeamento Cromossômico , Feminino , Regulação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Rearranjo Gênico , Dados de Sequência Molecular , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Proteína 1 de Leucemia Linfocítica Aguda de Células TRESUMO
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.
Assuntos
Genoma Humano , Projeto Genoma Humano , Análise de Sequência de DNA , Animais , Mapeamento Cromossômico , Sequência Conservada , Ilhas de CpG , Elementos de DNA Transponíveis , Bases de Dados Factuais , Indústria Farmacêutica , Evolução Molecular , Previsões , Sequência Rica em GC , Duplicação Gênica , Genes , Doenças Genéticas Inatas , Genética Médica , Humanos , Mutação , Setor Privado , Proteínas/genética , Proteoma , Setor Público , RNA/genética , Sequências Repetitivas de Ácido Nucleico , Análise de Sequência de DNA/métodos , Especificidade da EspécieRESUMO
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.
Assuntos
Sequência Conservada/genética , Enzimas de Restrição do DNA/genética , Proteínas de Ligação a DNA/genética , Proteínas Proto-Oncogênicas , Fatores de Transcrição , Animais , Composição de Bases , Sequência de Bases , Fatores de Transcrição Hélice-Alça-Hélice Básicos , DNA Mitocondrial/genética , Proteínas de Ligação a DNA/metabolismo , Desoxirribonuclease I/genética , Genes Neoplásicos , Marcadores Genéticos , Variação Genética , Humanos , Hidrólise , Leucemia-Linfoma de Células T do Adulto/genética , Camundongos , Camundongos Endogâmicos , Dados de Sequência Molecular , Homologia de Sequência do Ácido Nucleico , Células-Tronco/metabolismo , Proteína 1 de Leucemia Linfocítica Aguda de Células TRESUMO
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.
Assuntos
Cromossomos Humanos Par 20 , Animais , Sequência de Bases , Biologia Computacional , Mapeamento de Sequências Contíguas , DNA , Doenças Genéticas Inatas/genética , Variação Genética , Humanos , Camundongos , Mapeamento Físico do Cromossomo , Proteoma , Análise de Sequência de DNARESUMO
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.
Assuntos
Sequência Conservada , Proteínas de Ligação a DNA/genética , Elementos Facilitadores Genéticos , Proteínas Proto-Oncogênicas , Fatores de Transcrição/genética , Vertebrados/genética , Proteínas de Xenopus , Sequência de Aminoácidos , Animais , Animais Geneticamente Modificados , Sequência de Bases , Fatores de Transcrição Hélice-Alça-Hélice Básicos , Galinhas , Sequências Hélice-Alça-Hélice , Humanos , Camundongos , Dados de Sequência Molecular , Rombencéfalo/embriologia , Homologia de Sequência de Aminoácidos , Proteína 1 de Leucemia Linfocítica Aguda de Células T , XenopusRESUMO
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.
Assuntos
Elementos de DNA Transponíveis/genética , Peixe-Zebra/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , DNA/química , DNA/genética , Dados de Sequência Molecular , Filogenia , Sequências Repetitivas de Ácido Nucleico/genética , Alinhamento de Sequência , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos , Homologia de Sequência do Ácido Nucleico , Transposases/genéticaRESUMO
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.