Genetics articles within Nature

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  • Article |

    Copy number variants (CNVs) account for a major proportion of human genetic diversity and may contribute to genetic susceptibility to disease. Here, a large, genome-wide study of association between common CNVs and eight common human diseases is presented. The study provides a wealth of technical insights that will inform future study design and analysis. The results also indicate that common CNVs that can be 'typed' on existing platforms are unlikely to contribute much to the genetic basis of common diseases.

    • Nick Craddock
    • , Matthew E. Hurles
    •  & Peter Donnelly

  • Brief Communications Arising |

    • Julia Fischer
    • , Linda Koch
    •  & Ulrich Rüther

  • Letter
    | Open Access

    Studies of identical twins are widely used to dissect the contributions of genes and the environment to human diseases. In multiple sclerosis, an autoimmune demyelinating disease, identical twins often show differences. This might suggest that environmental effects are most significant in this case, but genetic and epigenetic differences between identical twins have been described. Here, however, studies of identical twins show no evidence for genetic, epigenetic or transcriptome differences that could explain disease discordance.

    • Sergio E. Baranzini
    • , Joann Mudge
    •  & Stephen F. Kingsmore

  • Letter |

    'Horizontal gene transfer' refers to the passage of genetic material between non-mating species. Transposable elements (transposons) may be especially prone to horizontal gene transfer, but the mechanisms by which they can spread across diverged species have been elusive. Here it is shown that transposons can spread by hitchhiking in the genomes of parasites. The amount of DNA that can be transferred in this way underscores the impact of horizontal gene transfer on genome evolution.

    • Clément Gilbert
    • , Sarah Schaack
    •  & Cédric Feschotte

  • Letter |

    Interleukin-17-producing helper T (TH17) cells are a distinct T-cell subset characterized by its role in autoimmune disease. Here it is shown that the development of TH17 cells requires the transcription factor IκBζ, as well as nuclear receptors of the ROR family. Mice lacking IκBζ have a defect in TH17 development and are resistant to the induction of experimental autoimmune encephalomyelitis. The study points to some new potential molecular targets for drugs to treat autoimmune disease.

    • Kazuo Okamoto
    • , Yoshiko Iwai
    •  & Hiroshi Takayanagi

  • Article |

    High-throughput microscopy combined with gene silencing by RNA interference is a powerful method for studying gene function. Here, a genome-wide method is presented for phenotypic screening of each of the ∼21,000 human protein-coding genes, using two-day imaging of dividing cells with fluorescently labelled chromosomes. The method enabled the identification of hundreds of genes involved in biological functions such as cell division, migration and survival.

    • Beate Neumann
    • , Thomas Walter
    •  & Jan Ellenberg

  • Article |

    Adiponectin is a protein with anti-diabetic properties; its levels are decreased in obesity, insulin resistance and type 2 diabetes. It is shown here that mice with a muscle-specific disruption of adiponectin receptor 1 (AdipoR1) are insulin resistant and less able to endure exercise. The pathway downstream of receptor activation is delineated; the findings suggest that the decreased levels of adiponectin and AdipoR1 seen in obesity may have causal roles in the mitochondrial dysfunction and insulin resistance seen in diabetes.

    • Masato Iwabu
    • , Toshimasa Yamauchi
    •  & Takashi Kadowaki

  • Letter |

    In plants, the hormone jasmonoyl-isoleucine (JA-Ile) regulates growth, development and defence against pathogens. Proteins of the JAZ family repress JA-Ile-dependent gene expression, but the mechanism has been unclear. Here, an adaptor protein, NINJA, has been identified, which recruits co-repressor proteins that are known to mediate auxin-responsive gene expression as well. Hence these co-repressors are part of general repression complexes that are recruited to several different signalling pathways.

    • Laurens Pauwels
    • , Gemma Fernández Barbero
    •  & Alain Goossens

  • Letter |

    Self-fertilisation (selfing) in plants is prevented mainly by the self-incompatibility recognition system, which consists of male and female specificity genes and modifier genes. Selfing does occur in Arabidopsis plants, but it is not known how it arose. Here it is reported that selfing in Arabidopsis results from a geographically widespread, 213-base-pair inversion within the male specificity gene. When this inversion is returned to its original orientation, selfing is prevented once more.

    • Takashi Tsuchimatsu
    • , Keita Suwabe
    •  & Kentaro K. Shimizu

  • Letter
    | Open Access

    The genome of the zebra finch — a songbird and a model for studying the vertebrate brain, behaviour and evolution — has been sequenced. Comparison with the chicken genome, the only other bird genome available, shows that genes that have neural function and are implicated in the cognitive processing of song have been evolving rapidly in the finch lineage. Moreover, vocal communication engages much of the transcriptome of the zebra finch brain.

    • Wesley C. Warren
    • , David F. Clayton
    •  & Richard K. Wilson

  • Editorial |

    Nearly a decade on from the completion of the draft sequence of the human genome, researchers should work with the same intensity and focus to apply the results to health.

  • Opinion |

    Genomic data will soon become a commodity; the next challenge — linking human genetic variation with physiology and disease — will be as great as the one genomicists faced a decade ago, says J. Craig Venter.

    • J. Craig Venter

  • Opinion |

    Looking back over the past decade of human genomics, Francis Collins finds five key lessons for the future of personalized medicine — for technology, policy, partnerships and pharmacogenomics.

    • Francis Collins

  • News & Views |

    An exceptionally large-scale project aimed at assigning function to all protein-coding genes in the human genome is reported on page 721 by Neumann et al.1. Here are two complementary views on the experimental design and analysis, and on how useful the findings will be to cell biologists.

    • Jason R. Swedlow
    • , Cecilia Cotta-Ramusino
    •  & Stephen J. Elledge

  • News Feature |

    The more biologists look, the more complexity there seems to be. Erika Check Hayden asks if there's a way to make life simpler.

    • Erika Check Hayden

  • Column |

    The Human Genome Project attracted investment beyond what a rational analysis would have predicted. There are pros and cons to that, says Philip Ball.

    • Philip Ball

  • Letter
    | Open Access

    The genome of the black truffle - one of the most popular truffles on the market - has been sequenced. This is the first genome of a symbiotic ascomycete to be analysed. Comparison with the genome of another ectomycorrhizal symbiotic fungus indicates that a genetic predisposition to symbiosis evolved differently in ascomycetes and basidiomycetes. The study also offers insight into fungal sex and fruiting.

    • Francis Martin
    • , Annegret Kohler
    •  & Patrick Wincker

  • Letter
    | Open Access

    Ancient mitochondrial DNA from a hominin individual who lived in the mountains of Central Asia between 48,000–30,000 years ago has been sequenced. Comparative genomics suggest that this mitochondrial DNA derives from an out-of-Africa migration distinct from the ones that gave rise to Neanderthals and modern humans. It also seems that this hominin lived in close spatio-temporal proximity to Neanderthals and modern humans.

    • Johannes Krause
    • , Qiaomei Fu
    •  & Svante Pääbo

  • Article |

    Zscan4 is shown to be involved in maintaining telomeres in embryonic stem (ES) cells. Only 5% of ES cells express Zscan4 at a given time, but nearly all ES cells activate Zscan4 at least once within nine passages. The transient Zscan4-positive state is associated with rapid telomere extension by telomere recombination and upregulation of meiosis–specific homologous recombination genes. Knocking down Zscan4 shortens telomeres, increases karyotype abnormalities and spontaneous sister chromatid exchange, and slows down cell proliferation until reaching crisis by eight passages.

    • Michal Zalzman
    • , Geppino Falco
    •  & Minoru S. H. Ko

  • Letter |

    Here, large-scale genome-wide association studies were carried out with the naturally occurring inbred lines of Arabidopsis thaliana, which can be genotyped once and phenotyped repeatedly. The results range from significant associations, usually corresponding to single genes, to findings that are more difficult to interpret, because confounding by complex genetics and population structure makes it hard to distinguish true associations from false.

    • Susanna Atwell
    • , Yu S. Huang
    •  & Magnus Nordborg

  • News |

    Tiny particles carrying short strands of RNA can interfere with protein production in tumours.

    • Janet Fang

  • Letter |

    In multicellular organisms, apoptotic cells are removed from tissues by phagocytes, which recognize and engulf the dying cells. The molecular mechanisms underlying the subsequent degradation of the cells have been unclear. Here, two evolutionarily conserved genes have been identified that are required for such processing in Caenorhabditis elegans and mammals. An understanding of these events could lead to new treatments for diseases associated with poor engulfment and destruction of dying cells.

    • Jason M. Kinchen
    •  & Kodi S. Ravichandran

  • Article
    | Open Access

    Fungi from the genus Fusarium are important pathogens of animals and crop plants. Some have a wide host range, whereas others are more specific in the organisms they infect. Here, clues are provided as to how differences in specificity come about. The genomes of two Fusarium fungi with differing host ranges have been sequenced, and compared with the genome of a third species. Experiments show that transferring two whole chromosomes turns a non-pathogenic Fusarium strain into a pathogenic one.

    • Li-Jun Ma
    • , H. Charlotte van der Does
    •  & Martijn Rep

  • News & Views |

    Pipefish and related species provide rare examples of extreme male parental care. Controlled breeding experiments allow the resulting conflicts of interest between female, male and offspring to be explored.

    • Anders Berglund

  • Letter |

    An extensive genome-wide survey of over 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf, was conducted to shed light on the process of dog diversification. The results reveal that much of genome diversity came from Middle Eastern progenitors, combined with interbreeding with local wolf populations, and that recent evolution involved limited genetic variation to create the phenotypic diversity of modern dogs.

    • Bridgett M. vonHoldt
    • , John P. Pollinger
    •  & Robert K. Wayne

  • Letter |

    Variation in the regulation of gene transcription between individuals is thought to be a major cause of phenotypic diversity. Here, individual differences in the binding of transcription-factor proteins are studied. A well-known transcription factor in the yeast pheromone pathway is used as an example, and the underlying genetic loci responsible for variation in its binding are mapped. The study reveals new insights into the mechanisms of gene regulation, and new regulators of the yeast pheromone pathway.

    • Wei Zheng
    • , Hongyu Zhao
    •  & Michael Snyder

  • Letter
    | Open Access

    The freshwater cnidarian Hydra is a significant model for studies of axial patterning, stem cell biology and regeneration. Its (A+T)-rich genome has now been sequenced. Comparison of this genome with those of other animals provides insights into the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, pluripotency genes and more.

    • Jarrod A. Chapman
    • , Ewen F. Kirkness
    •  & Robert E. Steele

  • Letter |

    There is much interest in understanding the genetic mechanisms that underlie individual variations in gene expression. Here, RNA sequencing has been used to study gene expression in lymphoblastoid cell lines derived from Nigerian individuals for whom extensive genotype information is known. Numerous genetic determinants of variation in gene expression were identified, including variation in transcription, splicing and allele-specific expression.

    • Joseph K. Pickrell
    • , John C. Marioni
    •  & Jonathan K. Pritchard

  • Letter |

    Here, sequencing has been used to characterize the mRNA fraction of the transcriptome in Caucasian individuals, to provide a fine-scale view of transcriptomes and to identify genetic variants that affect alternative splicing. Measuring allele-specific expression identified rare expression quantitative trait loci (eQTLs) and allelic differences in transcript structure, revealing new properties of genetic effects on the transcriptome.

    • Stephen B. Montgomery
    • , Micha Sammeth
    •  & Emmanouil T. Dermitzakis

  • Letter
    | Open Access

    Here, the genomes of birds representing eight populations of domestic chickens are compared with the genome of their wild ancestor, the red jungle fowl. The results reveal selective sweeps of favourable alleles and mutations that may have contributed to domestication. One selective sweep, for instance, occurred at the locus encoding the thyroid stimulating hormone receptor, which is important in metabolism and in the timing of vertebrate reproduction.

    • Carl-Johan Rubin
    • , Michael C. Zody
    •  & Leif Andersson

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