Genetics articles within Nature Communications

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  • Article
    | Open Access

    The exosome is responsible for mRNA degradation, which is an important step in the regulation of gene expression. Here the authors report that homozygous missense mutations in the exosome subunit, EXOSC8, may cause neurodegenerative disease in infants through the dysregulation of myelin expression.

    • Veronika Boczonadi
    • , Juliane S. Müller
    •  & Rita Horvath

  • Article |

    The Gag precursor protein recognizes the HIV-1 genomic RNA among hundreds of other viral and cellular RNAs during assembly of viral particles. Here, the authors identify the primary binding site of Gag on the HIV-1 RNA, and show that other RNA regions enhance or inhibit Gag binding.

    • Ekram W. Abd El-Wahab
    • , Redmond P. Smyth
    •  & Roland Marquet

  • Article |

    Overexpression of a drug’s molecular target increases drug resistance in some cases. Here the authors show that overexpressing antibiotic targets in Escherichia colican cause positive and negative changes in drug resistance, depending on whether the drug induces harmful reactions involving its target.

    • Adam C. Palmer
    •  & Roy Kishony

  • Article |

    Imprinted mouse X-chromosome inactivation is controlled by two long non-coding RNAs, Tsix and Xist. Here, Maclary et al. demonstrate that Tsix is dispensable during the initiation and maintenance of X-inactivation in vivo and in vitro, but required to prevent Xist expression as trophectodermal progenitors differentiate.

    • Emily Maclary
    • , Emily Buttigieg
    •  & Sundeep Kalantry

  • Article
    | Open Access

    Fruit colour is a trait that affects the harvesting, and therefore oil yield, of the economically important oil palm. Here, the authors identify a gene that may control fruit colour in the oil palm and suggest that selection for this gene during early development could advance the breeding potential of this important crop.

    • Rajinder Singh
    • , Eng-Ti Leslie Low
    •  & Ravigadevi Sambanthamurthi

  • Article
    | Open Access

    Non-alcoholic fatty liver disease (NAFLD) is characterized by increased hepatic triglyceride content (HTGC) in the absence of high alcohol consumption. Here the authors show that a genetic variant in TM6SF2, which is known to be associated with HTGC, is a clinically relevant modifier of hepatic fibrogenesis and increases the risk of progressive NAFLD.

    • Yang-Lin Liu
    • , Helen L. Reeves
    •  & Quentin M. Anstee

  • Article
    | Open Access

    Nucleocytoplasmic large DNA viruses, NCLDVs, are eukaryotic viruses with large genomes, known to infect animals and diverse unicellular eukaryotes. Here, Maumus et al. find NCLDV-like sequences in two land plants and show that they are transcriptionally inactive and highly methylated.

    • Florian Maumus
    • , Aline Epert
    •  & Guillaume Blanc

  • Article |

    De novocopy number variations are known to occur in somatic cell populations and pluripotent stem cells. Here the authors use single-cell array comparative genomic hybridization to identify copy number variations in individual human somatic and embryonic stem cells.

    • Kurt Jacobs
    • , Afroditi Mertzanidou
    •  & Claudia Spits

  • Article |

    Selecting for varieties of commercial crops with enhanced nutritional quality is important in agriculture. Here, the authors identify alleles of a gene in tomatoes that give rise to increased levels of vitamin E and find that the promoter of the gene is differentially methylated.

    • Leandro Quadrana
    • , Juliana Almeida
    •  & Fernando Carrari

  • Article |

    Hox genes have been implicated in the development and functioning of neural circuits in vertebrates. Here, the authors show that although hox3genes are not required for overall neural circuit development, they do appear to be necessary to prevent the formation of specific aberrant neuronal connections.

    • Leung-Hang Ma
    • , Charlotte L. Grove
    •  & Robert Baker

  • Article |

    Acne vulgarisis a common, inflammatory skin disorder. Here the authors carry out a genome-wide association study and identify three genetic variants that associate with an increased risk of developing acne, which together suggest a mechanistic role for the TGFβ cell signalling pathway in acne development and progression.

    • Alexander A. Navarini
    • , Michael A. Simpson
    •  & Jonathan N. Barker

  • Article |

    Helicobacter pylori chronically infects humans, and this is associated with high mutation and recombination rates in the bacterium. Here the authors provide evidence that genome evolution in H. pyloriduring acute infection of the host is orders of magnitude faster than any previously determined mutation rates in bacteria.

    • Bodo Linz
    • , Helen M. Windsor
    •  & Barry J. Marshall

  • Article
    | Open Access

    Tracing the source of malarial infections is an important step towards monitoring and controlling the disease. Here, Preston et al. analyse sequence data from 711 isolates and design a genetic barcode based on combined mitochondrial and apicoplast genomes that is able to distinguish between malaria parasites isolated from different geographical regions.

    • Mark D. Preston
    • , Susana Campino
    •  & Taane G. Clark

  • Article |

    While Hodgkin lymphoma (HL) is a common cancer affecting young adults in Western countries, its genetic basis is poorly understood. Here, the authors carry out a genome-wide association analysis in HL patients and healthy controls; identifying a new HL risk locus and implicating TCF3in the disease aetiology.

    • W. Cozen
    • , M. N. Timofeeva
    •  & J. D. McKay

  • Article
    | Open Access

    Extreme reproductive sex ratios could result in the suppression or elimination of pest populations. Here, the authors design a synthetic sex distortion system in Anopheles gambiaethat gives rise to fertile mosquito strains that produce over 95% male offsprings and could therefore be used to suppress mosquito populations.

    • Roberto Galizi
    • , Lindsey A. Doyle
    •  & Andrea Crisanti

  • Article
    | Open Access

    Wilms tumour (WT) is the most common paediatric kidney cancer and few driver genes related to its development have been identified. Here, the authors identify DROSHAmutations that may contribute to WT tumorigenesis through their effect on primary microRNA processing.

    • Giovana T. Torrezan
    • , Elisa N. Ferreira
    •  & Dirce M. Carraro

  • Article |

    The blind mole rat (BMR), Spalax galili, is perfectly adapted to life underground. Here, the authors sequence the BMR genome and transcriptome and highlight genomic features that may have played a role in adaptation to extreme underground stressors, such as darkness hypercapnia and hypoxia.

    • Xiaodong Fang
    • , Eviatar Nevo
    •  & Jun Wang

  • Article |

    Coffin–Siris syndrome (CSS) is a genetic disorder characterized by growth deficiency, microcephaly, intellectual disability and nail hypoplasia of the fifth digits. Here, the authors identify de novo mutations in the SOX11 gene of CSS patients and show that knockdown of sox11a/bcauses brain abnormalities in zebrafish.

    • Yoshinori Tsurusaki
    • , Eriko Koshimizu
    •  & Naomichi Matsumoto

  • Article |

    Mutations in WD-repeat-containing protein 62 (Wdr62) are associated with microcephaly, a congenital disorder characterized by reduced brain size. The authors show that Wdr62 deficiency in mouse embryos leads to mitotic arrest of neural progenitors and that Wdr62 genetically interacts with Aurora kinase Ato control mitotic progression of neural progenitors.

    • Jian-Fu Chen
    • , Ying Zhang
    •  & Lee Niswander

  • Article
    | Open Access

    Plant colonization of land is an important evolutionary event. Here, the authors sequence the genome of a filamentous terrestrial alga and, through a comparative analysis with related algae and land plant species, provide insight into how aquatic algae adapted to terrestrial environments.

    • Koichi Hori
    • , Fumito Maruyama
    •  & Hiroyuki Ohta

  • Article
    | Open Access

    Brassica oleracea is plant species comprising economically important vegetable crops. Here, the authors report the draft genome sequence of B. oleracea and, through a comparative analysis with the closely related B. rapa, reveal insights into Brassicaevolution and divergence of interspecific genomes and intraspecific subgenomes.

    • Shengyi Liu
    • , Yumei Liu
    •  & Andrew H Paterson

  • Article
    | Open Access

    Horizontal gene transfer occurs in most bacteria, yet it is unclear whether it happens in clonal species. Here, Everitt et al. show widespread within-species recombination, driven by mobile elements, in the genome of the pathogen Staphylococcus aureus, but no recombination between closely related strains.

    • Richard G. Everitt
    • , Xavier Didelot
    •  & Daniel J. Wilson

  • Article
    | Open Access

    Rice false smut, caused by the pathogenic ascomycete fungus Ustilaginoidea virens (Cooke) Takah, has a significant economic impact on crop production. Here, Zhang et al. report the draft genome sequence of U. virensand provide insight into the evolution of genes involved in pathogenicity and adaptation to a biotrophic and floret-infecting lifestyle.

    • Yong Zhang
    • , Kang Zhang
    •  & Wenxian Sun

  • Article
    | Open Access

    Although termites are major human pests, they have an important role in maintaining ecosystem function and biodiversity. Here, the authors sequence the genome and transcriptomes of a dampwood termite and highlight genes that may be involved in the mechanisms underlying insect social behaviour.

    • Nicolas Terrapon
    • , Cai Li
    •  & Jürgen Liebig

  • Article |

    Mutations are the source of genetic variation, yet the mechanisms determining the distribution of mutations are unclear. Here, Jones et al.show that gene interactions allow natural selection to shape the distribution of mutations, suggesting that mutations can be a biased source of genetic variation.

    • Adam G. Jones
    • , Reinhard Bürger
    •  & Stevan J. Arnold

  • Article |

    Paclitaxel is effective in the treatment of breast cancer but predicting which patients might respond to this drug is of clinical importance. Here, Jiang et al. show that germline mutations in TEKT4, a protein that associates with microtubules, are associated with resistance to paclitaxel therapy.

    • Yi-Zhou Jiang
    • , Ke-Da Yu
    •  & Zhi-Ming Shao

  • Article
    | Open Access

    Parkinson’s disease can be caused by a rare mutation in the protein VPS35, but the mechanism responsible for this is largely unknown. Here, Zavodszky et al.show that this mutation leads to defects in the recruitment of endosomal protein sorting machinery and consequent inhibition of autophagy in cells.

    • Eszter Zavodszky
    • , Matthew N.J. Seaman
    •  & David C. Rubinsztein

  • Article
    | Open Access

    Common tobacco (Nicotiana tabacum) is a widely cultivated and economically important non-food crop. Here, the authors report the draft genome sequences for three of the most common tobacco varieties and provide insights into the evolution of tobacco through a comparative analysis with closely related species.

    • Nicolas Sierro
    • , James N.D. Battey
    •  & Nikolai V. Ivanov

  • Article
    | Open Access

    The genetic basis of gastric cancer, the fourth most common cancer worldwide, remains poorly understood. Here, the authors sequence and analyse the exomes and transcriptomes of primary gastric tumours and cell lines, and identify a ZAK kinase isoform that may have an oncogenic role in gastric cancer.

    • Jinfeng Liu
    • , Mark McCleland
    •  & Zemin Zhang

  • Article
    | Open Access

    Spiders use self-produced venom and silk for their daily survival. Here, the authors report the assembled genome of the social velvet spider and a draft assembly of the tarantula genome and, together with proteomic data, provide insights into the evolution of genes that affect venom and silk production.

    • Kristian W. Sanggaard
    • , Jesper S. Bechsgaard
    •  & Jun Wang

  • Article |

    Frameshift mutations in the protein polyglutamine tract-binding protein 1 (PQBP1) are believed to cause X-linked mental retardation. Here, Mizuguchi et al.present the crystal structure of a C-terminal fragment of PQBP1 in complex with the spliceosomal protein U5–15kD, and show details of this interaction that can lead to mechanistic insights into the disease.

    • Mineyuki Mizuguchi
    • , Takayuki Obita
    •  & Hitoshi Okazawa

  • Article
    | Open Access

    Bladder cancer is a complex genetic disease and a common cause of death due to malignancy. Here, the authors carry out whole-genome sequencing of 14 bladder cancers to characterize the genomic landscape of the disease and show that mutational burden is associated with tumour progression in these samples.

    • J. -B. Cazier
    • , S. R. Rao
    •  & F. C. Hamdy

  • Article
    | Open Access

    Current methods to identify the geographical origin of humans based on DNA data present limited accuracy. Here, the authors develop a new algorithm, the Genographic Population Structure (GPS), and demonstrate its ability to place worldwide individuals within their country or, in some cases, village of origin.

    • Eran Elhaik
    • , Tatiana Tatarinova
    •  & Janet S. Ziegle

  • Article
    | Open Access

    The factors varying mutation rate at a particular site in a single genotype remain elusive. Here, Krašovec et al. show that mutation rates at sites conferring resistance to rifampicin in Escherichia coli decrease with population density, and that mutation-rate plasticity is controlled by the luxSgene.

    • Rok Krašovec
    • , Roman V. Belavkin
    •  & Christopher G. Knight

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