Genetics articles within Nature Communications

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  • Article |

    Determining the link between gene polymorphisms and phenotypic traits is the subject of intense research in agricultural plant science. In this study, Fu et al. conduct RNA sequencing in maize kernels to determine gene polymorphisms, which may aid future research aiming to improve the nutritional value of maize.

    • Junjie Fu
    • , Yanbing Cheng
    •  & Guoying Wang

  • Article |

    Insulinomas develop from pancreatic β-cells and secrete insulin, but the underlying genetic defects are largely unknown. In this study, Cao et al. identify recurrent T372R mutations in the transcription factor YY1, and validate this hotspot mutation in 30% of insulinomas.

    • Yanan Cao
    • , Zhibo Gao
    •  & Guang Ning

  • Article
    | Open Access

    Mitochondrial ribosomes are uniquely affected by mutations in the mitochondrial genome. By mapping the position of ribosomes on transcripts, the authors here reveal functional differences between mitochondrial and cytosolic ribosomes, and show that mutations in mitochondrial tRNAs induce ribosome stalling.

    • Koos Rooijers
    • , Fabricio Loayza-Puch
    •  & Reuven Agami

  • Article |

    Mutations in the GABA A receptor have been implicated in alcohol dependence in humans. In this study, the authors show that mice with mutations in the beta 1 subunit of the GABA A receptor exhibit spontaneous GABA A channel opening and preferentially consume alcohol, working harder to access it.

    • Quentin M. Anstee
    • , Susanne Knapp
    •  & Howard C. Thomas

  • Article
    | Open Access

    Men and women differ in terms of their neurochemistry, behaviour and susceptibility to disease. Here the authors show that sex differences in gene expression and splicing are widespread in adult human brain, and that sex-biased expression is likely to have functional consequences.

    • Daniah Trabzuni
    • , Adaikalavan Ramasamy
    •  & Mina Ryten

  • Article |

    Little is known about the genes that confer salt tolerance in trees. Here, Ma et al. report the genome sequence of the desert poplar, Populus euphratica, and provide insight into the genetic architecture and adaptation of this salt tolerant desert poplar.

    • Tao Ma
    • , Junyi Wang
    •  & Jianquan Liu

  • Article
    | Open Access

    Schizophrenia and bipolar disorder are important psychiatric disorders with overlapping genetic components. Here, the authors identify and replicate a genome-wide significant risk locus for the two disorders, and suggest a role for NDST3in severe psychiatric disease.

    • Todd Lencz
    • , Saurav Guha
    •  & Ariel Darvasi

  • Article |

    Renal cell carcinoma (RCC) accounts for 80–90% of all kidney cancers, but to date, only five genome-wide significant RCC risk loci have been identified. Here, Gudmundsson et al.identify a new RCC susceptibility locus and provide insight into the genetic basis of the disease.

    • Julius Gudmundsson
    • , Patrick Sulem
    •  & Kari Stefansson

  • Article |

    The Hoppel transposable element mediates heterochromatin formation in Drosophila. Here Savva et al. report that the RNA-editing enzyme, ADAR, edits a long double-stranded RNA generated by the Hoppeltransposon, thereby regulating heterochromatin formation and gene expression.

    • Yiannis A. Savva
    • , James E. C. Jepson
    •  & Robert A. Reenan

  • Article |

    The miR-372-3 cluster has a role in oncogenesis. In this study, by utilizing parthenogenetic induced pluripotent stem cells, that lack the paternal genome, Stelzer et al.report that these miR-372-3 are negatively regulated by a paternally imprinted antisense transcript and that loss of its expression promotes oncogenesis.

    • Yonatan Stelzer
    • , Ido Sagi
    •  & Nissim Benvenisty

  • Article
    | Open Access

    PALB2 is a BRCA1-/BRCA2-interacting protein and heterozygous mutations in PALB2 are associated with hereditary breast cancer predisposition. Here the authors show that human lymphoblastoid cells from heterozygous PALB2mutation carriers display abnormal DNA replication dynamics and DNA damage response.

    • Jenni Nikkilä
    • , Ann Christin Parplys
    •  & Robert Winqvist

  • Article |

    Loss of the tumour suppressor Rb1 alone is thought to be insufficient for tumorigenesis. In this study, Liu et al. demonstrate that cells in which all three Rb1 family members are inactivated can initiate tumour formation, but only if cell survival is ensured by the retention of cell–cell contacts.

    • Yongqing Liu
    • , Ester Sánchez-Tilló
    •  & Douglas C. Dean

  • Article |

    Hodgkin’s lymphoma has a genetic component that is poorly understood. In this study, Frampton et al. perform a genome-wide association study in German patients and combine the results with a previously published UK genome-wide association study to identify susceptibility loci at 3p24.1 and 6q23.3.

    • Matthew Frampton
    • , Miguel Inacio da Silva Filho
    •  & Richard S. Houlston

  • Article
    | Open Access

    The kiwifruit is an economically and nutritionally important fruit crop with high vitamin C content. Here, the authors report the draft genome sequence of a heterozygous kiwifruit and through comparative genomic analysis provide valuable insight into kiwifruit evolution.

    • Shengxiong Huang
    • , Jian Ding
    •  & Yongsheng Liu

  • Article
    | Open Access

    Scorpions have maintained the primary anatomical features of their Paleozoic arthropod ancestors. Here, the authors report the genome sequence of Mesobuthus martensiiand highlight evidence of genetic and morphological evolution that represents a unique adaptation model of arthropods.

    • Zhijian Cao
    • , Yao Yu
    •  & Wenxin Li

  • Article
    | Open Access

    Tumour biopsies contain contaminating normal cells and these can influence the analysis of tumour samples. In this study, Yoshihara et al.develop an algorithm based on gene expression profiles from The Cancer Genome Atlas to estimate the number of contaminating normal cells in tumour samples.

    • Kosuke Yoshihara
    • , Maria Shahmoradgoli
    •  & Roel G.W. Verhaak

  • Article
    | Open Access

    Ashkenazi mitochondrial DNA variation has four major founders whose sources are difficult to trace due to the rarity of Ashkenazi Jews in the general population. Here, the authors provide evidence that all four major founders originated from Europe and provide a genealogical record of the Ashkenazi.

    • Marta D. Costa
    • , Joana B. Pereira
    •  & Martin B. Richards

  • Article
    | Open Access

    Viruses contribute to the pathogenesis of certain cancers. Using massively parallel sequencing data from The Cancer Genome Atlas to analyse viral expression in 19 tumour types, Tang et al. both confirm and reject previously described viral associations and present new information on viral integration and host interaction.

    • Ka-Wei Tang
    • , Babak Alaei-Mahabadi
    •  & Erik Larsson

  • Article |

    MicroRNAs are thought to confer robustness to biological processes, but clear experimental evidence is still needed. Here, Siciliano et al. construct a toggle-switch in mammalian cells to show that microRNAs buffer fluctuations in protein levels, thereby providing phenotypic robustness to gene regulatory networks.

    • Velia Siciliano
    • , Immacolata Garzilli
    •  & Diego di Bernardo

  • Article |

    Topoisomerase 2α (Top2α) has essential roles during DNA replication, whereas its isoform Top2β is implicated in gene expression. Thakurela et al.show that Top2α is also required for stem-cell transcriptome regulation and primes developmental genes for activation by Top2β upon terminal differentiation.

    • Sudhir Thakurela
    • , Angela Garding
    •  & Vijay K. Tiwari

  • Article |

    Mutations in the gene that encodes the endosomal cation/proton antiporter NHE9 are implicated in neuropsychiatric disorders. In this study, the authors screen autism-associated variants in the human population and identify specific variants of NHE9 that are characterized by a loss of function in astrocytes.

    • Kalyan C. Kondapalli
    • , Anniesha Hack
    •  & Rajini Rao

  • Article |

    Cre recombinase is widely used to precisely manipulate genes and chromosomes, but it often displays off-target activity. Here, the authors improve the accuracy of Cre-mediated recombination by introducing specific mutations in the enzyme’s dimerization surface.

    • Nikolai Eroshenko
    •  & George M. Church

  • Article
    | Open Access

    Mulberry trees are the primary food source for silkworms, which are reared for the production of silk. In this study, He et al. present the draft genome sequence of Morus notabilisand find that it evolved significantly faster than other plants in the Rosales order.

    • Ningjia He
    • , Chi Zhang
    •  & Zhonghuai Xiang

  • Article
    | Open Access

    Tigers are an endangered species and therefore understanding their genetic architecture could aid conservation efforts. Here, the authors report the first genome sequence of the Amur tiger and, through close species comparative genomic analysis, provide insight into the genome organization, evolutionary divergence and diversity of big cats.

    • Yun Sung Cho
    • , Li Hu
    •  & Jong Bhak

  • Article
    | Open Access

    FGFR2 gene variation is associated with breast cancer risk but the molecular mechanism is unknown. Fletcher et al. provide a link between FGFR2 signalling and breast cancer susceptibility by demonstrating that FGFR2 signalling activates the ERa transcriptional network, which drives transcription of risk genes.

    • Michael N. C. Fletcher
    • , Mauro A. A. Castro
    •  & Kerstin B. Meyer

  • Article |

    Mutually exclusive splicing of genes is a mechanism for generating proteome diversity. Here Kollmar et al. determine the mutually exclusive spliced exome of Drosophila melanogaster and reveal insights into its evolutionary history within the Drosophilagroup.

    • Klas Hatje
    •  & Martin Kollmar

  • Article |

    The metabolic reaction catalysed by the isocitrate dehydrogenase 1 (IDH1) enzyme is commonly perturbed in some glioma subtypes due to gain-of-function mutations in the IDH1 gene. Here, Chaumeil et al.present a method that detects mutant IDH1 activity by measuring the levels of different hyperpolarized metabolites produced by wild-type and mutant IDH1.

    • Myriam M. Chaumeil
    • , Peder E. Z. Larson
    •  & Sabrina M. Ronen

  • Article
    | Open Access

    It is still not clear when the introduction of animal domestication in northwestern Europe occurred. Here the authors provide evidence that Mesolithic hunter-gatherers in Northern Germany already possessed domestic pigs, and pigs were present in the region ~500 years earlier than previously thought.

    • Ben Krause-Kyora
    • , Cheryl Makarewicz
    •  & Almut Nebel

  • Article
    | Open Access

    Turnover of sediment organic matter contributes to global carbon cycling, yet the microorganisms involved are largely unknown. Castelleet al.reveal that an aquifer sediment core hosts a ‘zoo’ of organisms, including representatives of a previously undescribed phylum (Zixibacteria).

    • Cindy J. Castelle
    • , Laura A. Hug
    •  & Jillian F. Banfield

  • Article |

    The distance that individuals disperse to between birth and first breeding determines the dynamics and genetic composition of natural populations. Here the authors show that in great tits (Parus major), the distance of local dispersal is genetically coupled with exploratory behaviour measured in the lab.

    • Peter Korsten
    • , Thijs van Overveld
    •  & Erik Matthysen

  • Article
    | Open Access

    Horizontal gene transfer of mobile genetic elements contributes to bacterial evolution and emergence of new pathogens. Here the authors demonstrate that the highly diverse structure of wall teichoic acid polymers governs horizontal gene transfer among Gram-positive pathogens, even across long phylogenetic distances.

    • Volker Winstel
    • , Chunguang Liang
    •  & Guoqing Xia

  • Article |

    MADS-box genes regulate flowering plant development, but their evolutionary origins are unclear. Here, Ruelens et al.show that three major, apparently flowering plant-specific, MADS-box gene clades are derived from a single ancestral tandem duplication, and identify FLOWERING LOCUS C-like genes in cereals.

    • Philip Ruelens
    • , Ruud A. de Maagd
    •  & Kerstin Kaufmann

  • Article
    | Open Access

    The date palm is one of the most economically important plants of the palm family. Here, the authors present a high-quality genome assembly of the date palm Phoenix dactylifera, and reveal insights into the unique sugar metabolism underlying fruit ripening.

    • Ibrahim S. Al-Mssallem
    • , Songnian Hu
    •  & Jun Yu

  • Article |

    Uncovering the factors that influence the generation of copy number variation (CNV) across the genome may increase our understanding of the role of CNVs in disease. Here, Makino et al.provide insights into the mechanisms underlying CNV formation and suggest a method for identifying disease-associated CNVs.

    • Takashi Makino
    • , Aoife McLysaght
    •  & Masakado Kawata

  • Article |

    Clinical trials of γ-secretase inhibitors to treat Alzheimer’s disease show that side effects occur from their non-selective action. Dimitrov et al.show that improved second generation γ-secretase modulators spare cleavage sites of substrate proteins that are implicated in the side effects.

    • Mitko Dimitrov
    • , Jean-René Alattia
    •  & Patrick C. Fraering

  • Article |

    Genetic effects on gene expression by variants at expression quantitative trait loci (eQTLs), can contribute to human genetic diseases. Here, Liet al. present a method to study eQTLs with effects on protein translation on a transcriptome-wide scale.

    • Quan Li
    • , Angeliki Makri
    •  & Hui-Qi Qu

  • Article
    | Open Access

    Telomerase reverse-trancriptase promoter mutations have been recently found in human melanomas. Here, Nault et al.identify telomerase reverse-trancriptase promoter mutations as the most frequent somatic genetic alterations in hepatocellular carcinomas and as the first mutation identified in cirrhotic preneoplastic lesions.

    • Jean Charles Nault
    • , Maxime Mallet
    •  & Jessica Zucman-Rossi

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