Genome articles within Nature

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  • News & Views |

    Scientists have begun to overhaul a yeast's genome to make it more stable, engineerable and evolvable. Remarkably, the part-natural, part-synthetic yeast cells function and reproduce without obvious ill effects. See Letter p.471

    • Peter J. Enyeart
    •  & Andrew D. Ellington

  • News & Views |

    Although some genetic mutations have clear effects, others have been considered neutral and inconsequential. Such cryptic mutations can nonetheless facilitate adaptation to new environments. See Letter p.92

    • Jeremy A. Draghi
    •  & Joshua B. Plotkin

  • Letter |

    In the nucleus, a complex of DNA ligase III (Lig3) and Xrcc1 catalyses the last step of base excision repair. Inactivation of Lig3 in the mouse leads to early embryonic lethality, but the critical role played by Lig3 in viability is unknown. This study shows, using conditional knockouts of Lig3 in the nervous system and cardiac muscle, that its essential function is maintenance of mitochondrial DNA integrity. The results also indicate distinct functional roles for Lig3 and Xrcc1.

    • Yankun Gao
    • , Sachin Katyal
    •  & Peter J. McKinnon

  • Letter |

    Studies have indicated an undefined role in DNA replication for CENP-B, a DNA binding protein associated with heterochromatin, centromeres and retrotransposon long terminal repeats (LTRs). Here it is shown that Sap1, which binds LTRs, promotes genomic instability when CENP-B activity is absent. CENP-B facilitates replication fork progression through LTRs in a way that protects against rearrangements.

    • Mikel Zaratiegui
    • , Matthew W. Vaughn
    •  & Robert A. Martienssen

  • News & Views |

    Mobile DNA sequences called L1 contribute to the brain's genetic heterogeneity and may affect neuron function. The protein MeCP2, which is mutated in Rett syndrome, seems to regulate the activity of these genomic elements. See Letter p.443

    • Lorenz Studer

  • Letter |

    Long interspersed nuclear elements-1 (L1) retrotransposons affect gene expression and neuronal function throughout brain development. These authors show that the absence of methyl-CpG-binding protein 2, a modulator of DNA methylation implicated in several neurodevelopmental disorders, increases L1 retrotransposon activity in rodent models, with this increase in susceptibility duplicated in patients with Rett syndrome. These correlations suggest that disease-related genetic mutations may influence L1 retrotransposon activity.

    • Alysson R. Muotri
    • , Maria C. N. Marchetto
    •  & Fred H. Gage

  • Technology Feature |

    The list of human genetic variations is expanding; but an understanding of how they contribute to disease is still patchy.

    • Monya Baker

  • News & Views |

    The 1000 Genomes Project has completed its pilot phase, sequencing the whole genomes of 179 individuals and characterizing all the protein-coding sequences of many others. Welcome to the third phase of human genomics. See Article p.1061

    • Rasmus Nielsen

  • Article
    | Open Access

    The goal of the 1000 Genomes Project is to provide in-depth information on variation in human genome sequences. In the pilot phase reported here, different strategies for genome-wide sequencing, using high-throughput sequencing platforms, were developed and compared. The resulting data set includes more than 95% of the currently accessible variants found in any individual, and can be used to inform association and functional studies.

    • Richard M. Durbin
    • , David Altshuler (Co-Chair)
    •  & Gil A. McVean

  • Letter |

    Cells that make up the liver are known to be polyploid. These authors show that mouse hepatocytes can increase and decrease their ploidy in vivo; increases occur as a result of failed cytokinesis, and decreases occur as a result of multipolar mitosis. The resulting genetic heterogeneity might be advantageous following hepatic injury, allowing the selection of 'genetically robust' cells from a pre-existing pool of diverse genotypes.

    • Andrew W. Duncan
    • , Matthew H. Taylor
    •  & Markus Grompe

  • Article |

    A non-coding polymorphism at a locus associated with myocardial infarction in humans creates a CCAAT/enhancer binding protein transcription factor binding site and alters the hepatic expression of the SORT1 gene. These authors show that modulating Sort1 levels in mouse liver alters levels of plasma low-density lipoprotein cholesterol and very low-density lipoprotein, potentially explaining why polymorphisms at this locus are associated with heart disease.

    • Kiran Musunuru
    • , Alanna Strong
    •  & Daniel J. Rader

  • Article |

    Lipid concentration in the serum is one of the most important risk factors for coronary artery disease and can be targeted for therapeutic intervention. A genome-wide association study in >100,000 individuals of European ancestry now finds 95 significantly associated loci that also affect lipid traits in non-European populations. Among associated loci are those involved in cholesterol metabolism, known targets of cholesterol-lowering drugs and those that contribute to normal variation in lipid traits and to extreme lipid phenotypes.

    • Tanya M. Teslovich
    • , Kiran Musunuru
    •  & Sekar Kathiresan

  • Letter |

    DNA replication occurs only once per cell cycle, and numerous pathways prevent re-replication. Here it is shown that mutations in ARABIDOPSIS TRITHORAX-RELATED PROTEIN5 (ATXR5) and ATXR6 — which encode histone methyltransferases — lead to re-replication of specific genomic locations, notably those corresponding to transposons and other repetitive and silenced elements. ATXR5 and ATXR6 are proposed to be components of a pathway that prevents over-replication of heterochromatin in Arabidopsis.

    • Yannick Jacob
    • , Hume Stroud
    •  & Steven E. Jacobsen

  • Letter |

    The European corn borer consists of two sex pheromone races, leading to strong reproductive isolation which could represent a first step in speciation. Female sex pheromone production and male behavioural response are under the control of different genes, but the identity of these genes is unknown. These authors show that allelic variation in a gene essential for pheromone biosynthesis accounts for the phenotypic variation in female pheromone production, leading to race-specific signals.

    • Jean-Marc Lassance
    • , Astrid T. Groot
    •  & Christer Löfstedt

  • News Feature |

    The completion of the draft human genome sequence was announced ten years ago. Nature's survey of life scientists reveals that biology will never be the same again. Declan Butler reports.

    • Declan Butler

  • Editorial |

    The successful transplantation of a synthesized genome highlights unresolved ethical and security issues posed by synthetic biology.

  • Opinion |

    Nature asked eight synthetic-biology experts about the implications for science and society of the “synthetic cell” made by the J. Craig Venter Institute (JCVI). The institute's team assembled, modified and implanted a synthesized genome into a DNA-free bacterial shell to make a self-replicating Mycoplasma mycoides.

  • Letter |

    Most human gene promoters are embedded within CpG islands that lack DNA methylation and coincide with sites at which histone H3 lysine 4 is trimethylated (H3K4me3 sites). Here, a zinc-finger protein, Cfp1, is found to be associated with non-methylated CpG islands and H3K4me3 sites throughout the genome in the mouse brain. A primary function of non-methylated CpG islands might be to genetically determine the local chromatin modification state by interaction with Cfp1 and perhaps other CpG-binding proteins.

    • John P. Thomson
    • , Peter J. Skene
    •  & Adrian Bird

  • News & Views |

    A challenge in biology is to understand complex traits, which are influenced by many genetic variants. Studies in yeast provide the prospect of analysing such genetic variation in detail in other organisms, including humans.

    • David B. Goldstein
    •  & Mohamed A. F. Noor

  • Letter |

    Mutations in mitochondrial DNA (mtDNA) are a common cause of human genetic disease. It has been shown in non-human primates that nuclear transfer techniques might be an approach to prevent the transmission of mtDNA mutations. The proof of principle has now been extended to human embryos. Pronuclei were transferred between human zygotes, which developed onwards to the blastocyst stage in vitro. Carry-over of mtDNA from the donor zygotes to the recipients was minimal.

    • Lyndsey Craven
    • , Helen A. Tuppen
    •  & Douglass M. Turnbull

  • Brief Communications Arising |

    • Julia Fischer
    • , Linda Koch
    •  & Ulrich Rüther

  • 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

  • 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

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