RESUMO
A key challenge of functional genomics today is to generate well-annotated data sets that can be interpreted across different platforms and technologies. Large-scale functional genomics data often fail to connect to standard experimental approaches of gene characterization in individual laboratories. Furthermore, a lack of universal annotation standards for phenotypic data sets makes it difficult to compare different screening approaches. Here we address this problem in a screen designed to identify all genes required for the first two rounds of cell division in the Caenorhabditis elegans embryo. We used RNA-mediated interference to target 98% of all genes predicted in the C. elegans genome in combination with differential interference contrast time-lapse microscopy. Through systematic annotation of the resulting movies, we developed a phenotypic profiling system, which shows high correlation with cellular processes and biochemical pathways, thus enabling us to predict new functions for previously uncharacterized genes.
Assuntos
Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Caenorhabditis elegans/embriologia , Caenorhabditis elegans/genética , Desenvolvimento Embrionário/genética , Genoma , Interferência de RNA , Animais , Caenorhabditis elegans/fisiologia , Biologia Computacional , Genes de Helmintos/genética , Genômica , Fenótipo , RNA de Helmintos/genética , RNA de Helmintos/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismoRESUMO
It is well known that basing phylogenetic reconstructions on uncorrected genetic distances can lead to errors in their reconstruction. Nevertheless, it is often common practice to report simply the most similar BLAST (Altschul et al. 1997) hit in genomic reports that discuss many genes (Ruepp et al. 2000; Freiberg et al. 1997). This is because BLAST hits can provide a rapid, efficient, and concise analysis of many genes at once. These hits are often interpreted to imply that the gene is most closely related to the gene or protein in the databases that returned the closest BLAST hit. Though these two may coincide, for many genes, particularly genes with few homologs, they may not be the same. There are a number of circumstances that can account for such limitations in accuracy (Eisen 2000). We stress here that genes appearing to be the most similar based on BLAST hits are often not each others closest relative phylogenetically. The extent to which this occurs depends on the availability of close relatives present in the databases. As an example we have chosen the analysis of the genomes of a crenarcheaota species Aeropyrum pernix, an organism with few close relatives fully sequenced, and Escherichia coli, an organism whose closest relative, Salmonella typhimurium, is completely sequenced.
Assuntos
Algoritmos , Bases de Dados Factuais , Crenarchaeota/genética , Escherichia coli/genética , Fases de Leitura Aberta , Filogenia , Salmonella typhimurium/genética , SoftwareRESUMO
Horizontal gene transfer is now recognized as an important mechanism of evolution. Several methods to detect horizontally transferred genes have been suggested. These methods are based on either nucleotide composition or the failure to find a similar gene in closely related species. Genes that evolve vertically between closely related species can be divided into those that retain homologous chromosomal positions (positional orthologs) and those that do not. By comparing open reading frames in the Escherichia coli and Salmonella typhi genomes, we identified 2,728 positional orthologs since these species split 100 MYA. A group of 1,144 novel E. coli genes were unusually diverged from their S. typhi counterparts. These novel genes included those that had been horizontally transferred into E. coli, as well as members of gene pairs that had been rearranged or deleted. Positional orthologs were used to investigate compositional methods of identifying horizontally transferred genes. A large number of E. coli genes with normal nucleotide composition have no apparent ortholog in S. typhi, and many genes of atypical composition do, in fact, have positional orthologs. A phylogenetic approach was employed to confirm selected examples of horizontal transmission among the novel groups of genes. Our analysis of 80 E. coli genes determined that a number of genes previously classified as horizontally transferred based on base composition and codon bias were native, and genes previously classified as native appeared to be horizontally transferred. Hence, atypical nucleotide composition alone is not a reliable indicator of horizontal transmission.
Assuntos
Códon , Transferência Genética Horizontal , Escherichia coli/genética , Funções Verossimilhança , Fases de Leitura Aberta , Filogenia , Salmonella typhi/genéticaRESUMO
A polymorphism in the igf2 gene of chickens was identified using NlaIII (GenBank accession number AF218827). In some embryos, the igf2 alleles were expressed monoallelically from either maternal or paternal alleles. These data demonstrate that genomic imprinting is not confined to mammalian vertebrates and suggest that genomic imprinting evolved at an early stage of vertebrate evolution. The observations that the igf2 gene is imprinted in a minority of embryos suggest that the imprinting in birds is unrelated to embryonic growth. Genome imprinting may provide opportunities for evolution of genes in a nonexpressed state. In poultry breeding, the presence of imprinted genes may make a major contribution to unequal performance in reciprocal matings between commercial lines.
