Genetics articles within Nature

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  • News Feature |

    Plant breeders are turning their attention to roots to increase yields without causing environmental damage. Virginia Gewin unearths some promising subterranean strategies.

    • Virginia Gewin

  • Letter |

    These authors performed a large-scale study in which they identified 2,576 somatic mutations across 1,507 coding genes from 441 breast, lung, ovarian and prostate cancer types and subtypes. The study provides an overview of the mutational spectra across major human cancers, implies an expanded role for Gα subunits in multiple cancer types and identifies several potential therapeutic targets.

    • Zhengyan Kan
    • , Bijay S. Jaiswal
    •  & Somasekar Seshagiri

  • Letter |

    Climate change can affect the phenology, population dynamics and morphology of species, but it is difficult to study all these factors and their interactions at once. Using long-term data for individual yellow-bellied marmots, these authors show that climate change has increased the length of the marmot growing season, leading to a gradual increase in individual size. It has simultaneously increased the fitness of large individuals, leading to a rapid increase in population size.

    • Arpat Ozgul
    • , Dylan Z. Childs
    •  & Tim Coulson

  • News |

    How human proteins are made from DNA can be followed in real time.

    • Brendan Borrell

  • Letter |

    Ependymoma is a type of neural tumour that arises throughout the central nervous system. Using comparative transcriptomics in mouse and human tumours, these authors home in on mutations that are specific to individual tumour subgroups. In doing so, they generate the first mouse model of ependymoma and demonstrate the power of interspecific genomic comparisons to interrogate cancer subgroups.

    • Robert A. Johnson
    • , Karen D. Wright
    •  & Richard J. Gilbertson

  • Letter |

    Chronic myelogenous leukaemia (CML) can progress from a chronic to an acute phase. These authors show in mouse models that leukaemia progression is controlled by the cell-fate regulator Musashi2, which in turn regulates Numb, Notch and p53 to block cellular differentiation. Musashi2 expression can be increased by aberrant transcription factors found in leukaemia, is observed during cancer progression in human CML patients and is associated with poorer prognosis.

    • Takahiro Ito
    • , Hyog Young Kwon
    •  & Tannishtha Reya

  • Article |

    The microbial content of the human gut has been the focus of much research interest recently. Now another layer of complexity has been added: the viral content of the gut. Virus-like particles were isolated from faecal samples from four sets of identical twins and their mothers, at three time points over a one-year period. The viromes (metagenomes) of these particles were then sequenced. The results show that there is high interpersonal variation in viromes, but that intrapersonal diversity was very low over this time period.

    • Alejandro Reyes
    • , Matthew Haynes
    •  & Jeffrey I. Gordon

  • 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 |

    PHF8 is a JmjC domain-containing protein, the gene for which has been linked to X-linked mental retardation (XLMR). These authors demonstrate PHF8 to be a histone demethylase with activity against H4K20me1. It has a role in regulating gene expression as well as in neuronal cell survival and craniofacial development in zebrafish. The results suggest there may be a link between histone methylation dynamics and XLMR.

    • Hank H. Qi
    • , Madathia Sarkissian
    •  & Yang Shi

  • Letter |

    These authors show that the JmjC domain-containing protein PHF8 has histone demethylase activity against H4K20me1 and is linked to two distinct events during cell cycle progression. PHF8 is recruited to the promoters of genes involved in the G1–S phase transition, where it removes H4K20me1 and contributes to gene activation, whereas dissociation of PHF8 from chromatin in prophase allows H4K20me1 to accumulate during mitosis.

    • Wen Liu
    • , Bogdan Tanasa
    •  & Michael G. Rosenfeld

  • Letter |

    Birds and mammals have distinct sex chromosomes: in birds, males are ZZ and females ZW; in mammals, males are XY and females XX. By sequencing the chicken Z chromosome and comparing it with the human X chromosome, these authors overturn the currently held view that these chromosomes have diverged little from their autosomal progenitors. The Z and X chromosomes seem to have followed convergent evolutionary trajectories, despite evolving with opposite systems of heterogamety.

    • Daniel W. Bellott
    • , Helen Skaletsky
    •  & David C. Page

  • Letter |

    The methylation of DNA in 5′ promoter regions suppresses gene expression, but what is the role of DNA methylation in the bodies of genes? Here, a map of DNA methylation is generated from human brain tissue; it is found that most methylated CpG islands are within intragenic and intergenic regions, rather than within promoters. It is proposed that intragenic methylation regulates the expression of alternative gene transcripts in different tissues and cell types.

    • Alika K. Maunakea
    • , Raman P. Nagarajan
    •  & Joseph F. Costello

  • News Feature |

    A once-threatened population of African fish is now providing a view of evolution in action. Laura Spinney asks what Lake Victoria cichlids have revealed about speciation.

    • Laura Spinney

  • Letter |

    The insulin/IGF-1 signalling (IIS) pathway is involved in various biological processes, including regulation of longevity. In the worm Caenorhabditis elegans, the transcription factor DAF-16a, one of two isoforms, has a major role in this pathway, regulating longevity, stress response and dauer diapause. These authors describe a new isoform, DAF-16d/f, which is also important in the regulation of lifespan. The DAF-16 isoforms functionally cooperate to fine-tune IIS-mediated processes in the context of a whole organism.

    • Eun-Soo Kwon
    • , Sri Devi Narasimhan
    •  & Heidi A. Tissenbaum

  • Letter |

    The genetic basis of alopecia areata, one of the most common human autoimmune diseases, is largely unknown. This study reports a genome-wide association for this trait that implies the involvement of acquired and innate immunity. Among significant associations are the cytomegalovirus UL16-binding protein genes, which encode activating ligands for the natural killer cell receptor, NKG2D, here implicated for the first time in any autoimmune disease.

    • Lynn Petukhova
    • , Madeleine Duvic
    •  & Angela M. Christiano

  • News & Views |

    Interpreting truly ancient fossils is an especially tricky business. The conclusion that 2.1-billion-year-old structures from Gabon are the remains of large colonial organisms will get palaeobiologists talking.

    • Philip C. J. Donoghue
    •  & Jonathan B. Antcliffe

  • Letter |

    Plants or animals with identical genomes in a given species can develop into wildly differing forms, depending on environmental conditions, a phenomenon that is widespread in nature yet rarely described in genetic and molecular terms. These authors show that the formation of additional teeth-like structures in the mouth of the nematode Pristionchus pacificus in response to overcrowding is mediated by the same endocrine system that controls dauer larva formation.

    • Gilberto Bento
    • , Akira Ogawa
    •  & Ralf J. Sommer

  • 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

  • Article |

    Ultraviolet radiation causes damage to DNA in skin cells, blocking DNA replication and causing mutations that can lead to cancer. One way in which the cell deals with such damage involves specialized DNA polymerases, such as Polη, that can bypass lesions. Here the crystal structure is presented of Pol? in complex with a thymine–thymine dimer and with undamaged DNA. The bulky thymine dimer is accommodated in an atypically large active site, and stabilized by interactions not found in other polymerases.

    • Timothy D. Silverstein
    • , Robert E. Johnson
    •  & Aneel K. Aggarwal

  • Article |

    The canonical role of messenger RNA (mRNA) is in protein coding and synthesis. But could mRNAs also have a role that is related to their ability to compete for microRNA binding? Here, the functional relationship between the mRNAs produced by the PTEN tumour suppressor gene and its pseudogene PTENP1 is investigated. The results suggest that pseudogenes have a biological function, in sequestering microRNAs and so affecting their regulation of gene expression.

    • Laura Poliseno
    • , Leonardo Salmena
    •  & Pier Paolo Pandolfi

  • 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

  • Feature |

    The publishing of the first Trypanosoma cruzi genome sequence was hailed as “a huge intellectual triumph”, but what has it delivered?

    • Julie Clayton

  • News & Views |

    Pseudogenes are considered to be defunct relatives of known genes. But there is some surprising news: pseudogenes are functional and could have a role in the control of cancer1. Two experts discuss the significance of these findings for understanding the regulation of gene expression and cancer biology.

    • Isidore Rigoutsos
    •  & Frank Furnari

  • News |

    Body-louse genome offers a glimpse into the genetic legacy of life as a permanent parasite.

    • Heidi Ledford

  • News |

    The genetic basis of common traits may be buried deeper than researchers had thought.

    • Alla Katsnelson

  • Editorial |

    Taking personal genetic testing into the classroom brings ethical and legal sensitivities to the fore.

  • News & Views |

    The groundwork for analysing the human microbiome — sequencing the collective genome of all our resident microorganisms — is now done. This work is of significance for understanding both human health and disease.

    • Liping Zhao

  • Letter |

    Sialic acid acetylesterase (SIAE) is an enzyme that is involved in B-cell activation and is required to maintain immunological tolerance in mice. It is shown here that rare, inherited and functionally defective SIAE variants are associated with a variety of autoimmune diseases in humans. The study provides one of the first examples of the importance of rare genetic variants in complex diseases, such as those involving autoimmunity.

    • Ira Surolia
    • , Stephan P. Pirnie
    •  & Shiv Pillai

  • Letter |

    Small regulatory RNAs function both in the cytoplasm, inhibiting expression from messenger RNAs, and in the nucleus, silencing heterochromatin and preventing genome rearrangement. Now a new protein involved in RNA interference in the nucleus has been characterized. This protein, NRDE-2, associates with NRDE-3 and short interfering RNAs on nascent transcripts. This association prevents elongation of the transcripts by RNA polymerase II, making this a co-transcriptional form of gene silencing.

    • Shouhong Guang
    • , Aaron F. Bochner
    •  & Scott Kennedy

  • Letter |

    Down's syndrome is caused by trisomy of chromosome 21, and it is known that the growth of certain tumours is reduced in this genetic disorder. Using a mouse model of Down's syndrome, several individual genes on chromosome 21 are now being proposed to mediate the effect on tumour growth and angiogenesis.

    • Louise E. Reynolds
    • , Alan R. Watson
    •  & Kairbaan M. Hodivala-Dilke

  • Editorial |

    Biomedical research continues to use many more male subjects than females in both animal studies and human clinical trials. The unintended effect is to short-change women's health care.

  • Letter |

    Genomic data from 14 Jewish Diaspora communities are here compared with data from 69 Old World non-Jewish populations, to investigate the demographic history of the Jewish people. Analyses shed new light on relationships between communities, reveal unappreciated genetic substructure within the Middle East, and trace the origins of most Jewish Diaspora communities to the Levant.

    • Doron M. Behar
    • , Bayazit Yunusbayev
    •  & Richard Villems

  • Letter |

    The autistic spectrum disorders (ASDs) are highly heritable, yet the underlying genetic determinants remain largely unknown. Here, a genome-wide analysis of rare copy number variants (CNVs) has been carried out, revealing that ASD sufferers carry a higher load of rare, genic CNVs than do controls. Many of these CNVs are de novo and inherited. The results implicate several novel genes in ASDs, and point to the importance of cellular proliferation, projection and motility, as well as specific signalling pathways, in these disorders.

    • Dalila Pinto
    • , Alistair T. Pagnamenta
    •  & Catalina Betancur

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