Genetics articles within Nature

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  • Letter |

    The Escherichia coli isocitrate dehydrogenase kinase/phosphatase (AceK) is a bifunctional enzyme that can phosphorylate or dephosphorylate isocitrate dehydrogenase (ICDH) to either inactivate or activate it in response to environmental changes. Now the structures of AceK and the AceK–ICDH complex have been solved, revealing the conformational changes that occur when AceK changes from a kinase to a phosphatase and vice versa.

    • Jimin Zheng
    •  & Zongchao Jia

  • Letter |

    The initiation of protein synthesis requires the eukaryotic translation initiation factor (eIF) 2, which uses energy from the hydrolysis of GTP. Another factor, eIF5, accelerates the GTP-hydrolysing activity of eIF2. Here, two other roles for eIF5 have been defined. One involves stabilizing GDP, the product of GTP hydrolysis, on eIF2. In its other role, eIF5 works with phosphorylated eIF2 to inhibit the guanine-nucleotide exchange factor eIF2B. These results clarify our understanding of how the initiation of translation is regulated.

    • Martin D. Jennings
    •  & Graham D. Pavitt

  • Careers and Recruitment |

    Rapid technological developments have spurred big changes in the requisite genome-sequencing jobs. Kelly Rae Chi assesses the sequencing assembly line.

    • Kelly Rae Chi

  • News & Views |

    The question of whether or not all life on Earth has an ultimate common origin is a subtle one, complicated by the phenomenon of lateral gene transfer. It has now been tackled with a formal statistical analysis.

    • Mike Steel
    •  & David Penny

  • News |

    A technology that simultaneously reads a DNA sequence and its crucial modifications makes its debut.

    • Alla Katsnelson

  • Article |

    The coding capacity of the genome is greatly expanded by the process of alternative splicing, which enables a single gene to produce more than one distinct protein. Can the expression of these different proteins be predicted from sequence data? Here, modelling based on information theory has been used to develop a 'splicing code', which can predict, with good accuracy, tissue-dependent changes in alternative splicing.

    • Yoseph Barash
    • , John A. Calarco
    •  & Brendan J. Frey

  • News & Views |

    Diverse messenger RNAs, and thus proteins, can be generated from a single piece of DNA. A computational approach is helping to uncover complex combinatorial rules by which specific gene instructions are selected.

    • J. Ramón Tejedor
    •  & Juan Valcárcel

  • Column |

    Our genome won't win any design awards and doesn't speak well of the intelligence of its 'designer', as Philip Ball explains.

    • Philip Ball

  • Letter |

    The topologies of, and spatial relationships between, chromosomes are important but poorly understood. Here, a high-throughput method is used to study intra- and inter-chromosomal interactions in Saccharomyces cerevisiae. A map of the haploid genome is generated at kilobase resolution, and is used to construct a three-dimensional model of the yeast genome. The findings provide a glimpse of the interface between the form and function of a eukaryotic genome.

    • Zhijun Duan
    • , Mirela Andronescu
    •  & William S. Noble

  • Letter |

    Polycomb group (PcG) proteins are transcriptional repressors that modify chromatin and regulate important developmental genes. One PcG-associated, chromatin-modifying activity is an enzyme that ubiquitinates histone H2A of chromatin. Here, a fruitfly PcG complex that is associated with H2A deubiquitination, and thereby with gene repression, is identified. PcG-mediated gene silencing might thus involve a dynamic balance between ubiquitination and deubiquitination of H2A.

    • Johanna C. Scheuermann
    • , Andrés Gaytán de Ayala Alonso
    •  & Jürg Müller

  • Letter |

    Amyotrophic lateral sclerosis (ALS) is a disorder characterized by the degeneration of motor neurons. About 10% of cases are familial, but the mutations identified in these families account for only 20–30% of such cases. Here a new set of mutations in familial ALS is found — in the gene encoding optineurin. Given the effect of optineurin mutations on the NF-κB protein, it is suggested that inhibiting NF-κB might be useful in treating ALS.

    • Hirofumi Maruyama
    • , Hiroyuki Morino
    •  & Hideshi Kawakami

  • Letter |

    DNA methylation is an important epigenetic mark in many eukaryotes. In Arabidopsis plants, small interfering RNAs bound to the Argonaute 4 (AGO4) protein can direct de novo DNA methylation and consequent gene silencing. Here, a new regulator of RNA-directed DNA methylation has been discovered. This protein, RDM1, is proposed to bind to methylated DNA and to function in the AGO4 effector complex.

    • Zhihuan Gao
    • , Hai-Liang Liu
    •  & Jian-Kang Zhu

  • News |

    Worldwide census ups diversity estimates for marine microbes one-hundred-fold.

    • Jane Qiu

  • 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

  • Letter |

    Primary cilia are tiny hair-like structures expressed on the surface of eukaryotic cells. They participate in a range of processes, such as sensing the extracellular environment and regulating signalling pathways during development. Here, a functional genomic screen is presented that used RNA interference to identify human genes involved in controlling ciliogenesis. Several positive and negative ciliogenesis modulators with broad-ranging functions were found.

    • Joon Kim
    • , Ji Eun Lee
    •  & Joseph G. Gleeson

  • Letter |

    Hereditary hypotrichosis simplex is a rare form of hereditary hair loss in humans, where the hair follicle is miniaturized. Now, the gene involved has been identified, using genetic linkage analysis in three affected families. The gene, APCDD1, is expressed in human hair follicles. It encodes a previously unknown membrane-bound glycoprotein that inhibits signalling through the Wnt protein and functions upstream of β-catenin.

    • Yutaka Shimomura
    • , Dritan Agalliu
    •  & Angela M. Christiano

  • Letter |

    Complex heritable traits — such as human height and many human diseases — are caused by multiple genetic loci, each with small effects. It is hard to identify such loci, however, because of a lack of statistical power. Now, a method has been developed to overcome this problem. The method has been applied to chemical resistance traits and mitochondrial function in yeast, and has identified loci for each of these phenotypes.

    • Ian M. Ehrenreich
    • , Noorossadat Torabi
    •  & Leonid Kruglyak

  • Editorial |

    A surprising US court decision highlights the need to modernize gene-patenting practices if patients are to benefit from advances in genetic research.

  • 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

  • News & Views |

    Cancer cells that invade other parts of the body do so by accumulating genomic aberrations. Analysis of the genomic differences between primary and metastatic tumours should aid the understanding of this process.

    • Joe Gray

  • 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

  • Article |

    Regulatory proteins bind non-coding DNA either at promoters (near to a gene's transcription start site) or at enhancers (far away). Binding at enhancers helps to bring the transcription enzyme RNA polymerase to promoters. Here, studies of some 12,000 enhancers that respond to electrical activity in neurons show that binding to enhancers also brings the polymerase to the enhancers themselves, where it transcribes a novel class of non-coding RNAs. Enhancers may thus be more similar to promoters than hitherto appreciated.

    • Tae-Kyung Kim
    • , Martin Hemberg
    •  & Michael E. Greenberg

  • 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

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