Genomics articles within Nature

Featured

  • Letter
    | Open Access

    The genome of the southeast Asian orang-utan has been sequenced. The draft assembly of a Sumatran individual alongside sequence data from five Sumatran and five Bornean orang-utan genomes is presented. The resources and analyses described offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.

    • Devin P. Locke
    • , LaDeana W. Hillier
    •  & Richard K. Wilson

  • Outlook |

    The pioneers of nutrition research determined the energy content of food and also helped to overturn misconceptions about various diseases that plagued humankind.

    • Ned Stafford

  • Outlook |

    Genetic studies of people conceived during famine reveals that prenatal malnutrition lingers long after the event.

    • Farooq Ahmed

  • Outlook |

    Health biomarkers, smart technology and social networks are hastening an era of nutrition tailored to your individual needs but relying on information generated by the crowd.

    • Arran Frood

  • News & Views |

    Analysis of ancient nuclear DNA, recovered from 40,000-year-old remains in the Denisova Cave, Siberia, hints at the multifaceted interaction of human populations following their migration out of Africa. See Article p.1053

    • Carlos D. Bustamante
    •  & Brenna M. Henn

  • Outlook |

    Diet-related illnesses are some of the biggest killers today. Can we tailor our food intake to prevent these diseases? Large international projects are underway to find out.

    • Farooq Ahmed

  • Article |

    As part of the modENCODE initiative, which aims to characterize functional DNA elements in D. melanogaster and C. elegans, this study uses RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages of the fruitfly. Among the results are scores of new genes, coding and non-coding transcripts, as well as splicing and editing events.

    • Brenton R. Graveley
    • , Angela N. Brooks
    •  & Susan E. Celniker

  • Article |

    As part of the modENCODE initiative, which aims to characterize functional DNA elements in D. melanogaster and C. elegans, this study presents a genome-wide chromatin landscape of the fruitfly, based on 18 histone modifications. Nine prevalent chromatin states are described. Integrating these analyses with other data types reveals individual characteristics of different genomic elements. The work provides a resource of unprecedented scale for future experimental investigations.

    • Peter V. Kharchenko
    • , Artyom A. Alekseyenko
    •  & Peter J. Park

  • Article
    | Open Access

    Using DNA from a finger bone, the genome of an archaic hominin from southern Siberia has been sequenced to about 1.9-fold coverage. The group to which this individual belonged shares a common origin with Neanderthals, and although it was not involved in the putative gene flow from Neanderthals into Eurasians, it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. A tooth whose mitochondrial genome is very similar to that of the finger bone further suggests that these hominins are evolutionarily distinct from Neanderthals and modern humans.

    • David Reich
    • , Richard E. Green
    •  & Svante Pääbo

  • News & Views |

    Comparative genomics studies reveal molecular signatures of the controversial 'phylotypic' stage — a time when embryos of members of an animal phylum all look more alike than at other embryonic stages. See Letters p.811 & p.815

    • Benjamin Prud'homme
    •  & Nicolas Gompel

  • Letter |

    These authors describe a molecular pathway by which endothelial cells sustain liver regeneration after surgical resection. Activation of vascular endothelial growth factor-A receptor-2 in a defined subpopulation of liver endothelial cells leads to the upregulation of the endothelial-specific transcription factor Id1, which in turn induces Wnt2 and hepatocyte growth factor, which are secreted from the endothelial cells and trigger hepatocyte proliferation.

    • Bi-Sen Ding
    • , Daniel J. Nolan
    •  & Shahin Rafii

  • News Feature |

    Behind the walls of the J. Craig Venter Institute, Ham Smith and Clyde Hutchison quietly worked to bring a synthetic cell to life.

    • Roberta Kwok

  • 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

  • Letter |

    To facilitate their proper segregation, duplicated meiotic chromosomes are physically joined by crossovers. Crossover formation begins with the introduction of meiosis-specific double-strand breaks. These authors identify a new gene in Caenorhabditis elegans, xnd-1, that is required for crossover distribution on both the X and the autosomal chromosomes. Preliminary data suggest that xnd-1 does this by regulating acetylation of histone H2A on lysine 5.

    • Cynthia R. Wagner
    • , Lynnette Kuervers
    •  & Judith L. Yanowitz

  • News |

    Major release of maps charting non-genetic modifications goes beyond DNA in a bid to beat complex human disease.

    • Alla Katsnelson

  • Letter |

    This very large genome-wide association study identifies hundreds of new genetic variants influencing adult height in at least 180 loci enriched for genes involved in skeletal growth defects. The results show that the likely causal gene is often located near the most strongly associated variant, that many loci have multiple independently associated variants and that associated variants are enriched for likely functional effects on genes.

    • Hana Lango Allen
    • , Karol Estrada
    •  & Joel N. Hirschhorn

  • Letter |

    Until now, studies of evolution in the laboratory have primarily been carried out in asexual systems with small genomes, such as bacteria and yeast. Here, however, whole-genome resequencing data are presented from fruitfly populations that have experienced over 600 generations of laboratory selection for accelerated development. The results suggest that unconditionally advantageous alleles rarely arise, are associated with small net fitness gains, or cannot fix because selection coefficients change over time.

    • Molly K. Burke
    • , Joseph P. Dunham
    •  & Anthony D. Long

  • Article |

    Here, the analysis of 'HapMap 3' is reported — a public data set of genomic variants in human populations. The resource integrates common and rare single nucleotide polymorphisms (SNPs) and copy number polymorphisms (CNPs) from 11 global populations, providing insights into population-specific differences among variants. It also demonstrates the feasibility of imputing newly discovered rare SNPs and CNPs.

    • David M. Altshuler
    • , Richard A. Gibbs
    •  & Jean E. McEwen

  • News Feature |

    Stymied in the search for genes underlying human neuropsychiatric diseases, some researchers are looking to dogs instead. David Cyranoski meets the geneticist's new best friend.

    • David Cyranoski

  • Letter |

    Mapping disease loci that underlie putative Mendelian forms of malformations of cortical development is complicated by genetic heterogeneity, small family sizes and diagnostic classifications that may not reflect molecular pathogenesis. These authors use whole-exome sequencing to identify recessive mutations in WDR62 as the cause of a wide spectrum of severe cerebral cortical malformations. WDR62's nuclear localization to germinal neuroepithelia indicates that cortical malformations can be caused by events during progenitor proliferation and neurogenesis.

    • Kaya Bilgüvar
    • , Ali Kemal Öztürk
    •  & Murat Günel

  • Letter |

    A diploid organism has two copies of each gene, one inherited from each parent. The expression levels of the two alleles can be biased by dominant/recessive relationships. In Brassica, self-incompatibility in pollen is determined by dominance relationships between the two alleles of the gene SP11; the recessive allele is methylated and hence silenced. Here it is shown that such methylation is controlled by a small non-coding RNA encoded in the flanking region of the dominant allele.

    • Yoshiaki Tarutani
    • , Hiroshi Shiba
    •  & Seiji Takayama

  • Books & Arts |

    A bold attempt to tell the complicated story behind the human DNA sequence highlights that social change is needed before personalized medicine can take off, finds Jan Witkowski.

    • Jan Witkowski

  • Letter |

    During haematopoiesis, multipotent progenitors differentiate into progressively restricted myeloid or lymphoid progenitors. A comprehensive genome-wide DNA methylation analysis of haematopoietic cell populations with well-characterized differentiation potentials reveals remarkable epigenetic plasticity during lymphoid and myeloid restriction.

    • Hong Ji
    • , Lauren I. R. Ehrlich
    •  & Andrew P. Feinberg

  • Article |

    MicroRNAs are known to affect the levels of both messenger RNA (mRNA) and protein. But as protein production is dependent on the presence of mRNA, it was not clear what the relative contributions of microRNA-mediated mRNA cleavage and translational repression were. These authors have parsed out the two mechanisms, and unexpectedly find that microRNAs function primarily by affecting mRNA levels rather than their translation. This suggests a reassessment of many previous conclusions is necessary.

    • Huili Guo
    • , Nicholas T. Ingolia
    •  & David P. Bartel

  • Letter |

    The ability of retrotransposons to mobilize and insert into genes presents a challenge to a cell needing to maintain its genomic integrity. These authors have studied retrotransposition in embryonic carcinoma-derived cells. On insertion into DNA, the retrotransposon is quickly silenced, but the retrotransposon-specificity of this process implies that multiple silencing mechanisms may exist. Once cells differentiate, the ability to silence newly introduced retrotransposons is lost but previously inactivated retrotransposons remain inactive.

    • Jose L. Garcia-Perez
    • , Maria Morell
    •  & John V. Moran

  • Article
    | Open Access

    These authors report and analyse the draft genome sequence of the demosponge Amphimedon queenslandica. Sponges lie on the earliest branching lineage in the animal kingdom and thus have been important in studies of the origins of multicellularity. Comparative genomic analyses presented here provide significant insights into evolutionary origins of genes and pathways related to the hallmarks of metazoan multicellularity and to cancer biology.

    • Mansi Srivastava
    • , Oleg Simakov
    •  & Daniel S. Rokhsar

  • 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 |

    In the course of characterizing short RNAs from human cells using single-molecule high-throughput sequencing, these authors identify a new short RNA species. The presence of non-genomically encoded poly(U) residues at their 5' ends implies the existence of an unknown RNA copying mechanism in human cells.

    • Philipp Kapranov
    • , Fatih Ozsolak
    •  & Patrice M. Milos

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