Gene expression articles within Nature

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  • Letter |

    Epistasis has rarely been shown among natural polymorphisms in human traits; this research using advanced computation and gene expression data reveals many instances of epistasis between common single nucleotide polymorphisms in humans, with epistasis and the direction of its effect replicating in independent cohorts.

    • Gibran Hemani
    • , Konstantin Shakhbazov
    •  & Joseph E. Powell

  • Article |

    Evolutionary study of long noncoding RNA (lncRNA) repertoires and expression patterns in 11 tetrapod species identifies approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have ancient origins; many lncRNAs, particularly ancient ones, are actively regulated and may function mainly in embryonic development.

    • Anamaria Necsulea
    • , Magali Soumillon
    •  & Henrik Kaessmann

  • Letter |

    Exploration of the interacting effect of statin exposure and genetic variation on gene expression identifies a cis-eQTL that is differentially associated with expression of the GATM gene, which encodes a rate-limiting enzyme involved in creatine synthesis, and that is associated with incidence of statin-induced myopathy, the major adverse effect of statin treatment.

    • Lara M. Mangravite
    • , Barbara E. Engelhardt
    •  & Ronald M. Krauss

  • News & Views |

    Tet proteins regulate gene expression by removing methyl groups from DNA bases. This activity may be a facilitating step in turning on the cell-division pathway that produces sperm and egg cells. See Letter p.443

    • Sylvain Guibert
    •  & Michael Weber

  • Article |

    Transient overexpression of the transcription factors NKX2-1 and PAX8 in a murine cell model is shown to direct the differentiation of embryonic stem cells towards a thyroid follicular cell lineage; the resulting three-dimensional thyroid follicles created by subsequent thyrotropin treatment show hallmarks of thyroid function in vitro and rescue thyroid function in vivo when transplanted into athyroid mice, adding to our understanding of the molecular mechanisms underlying thyroid development.

    • Francesco Antonica
    • , Dominika Figini Kasprzyk
    •  & Sabine Costagliola

  • Brief Communications Arising |

    • Pontus Boström
    • , Jun Wu
    •  & Bruce M. Spiegelman

  • Letter |

    APJ is shown to be a bifunctional receptor for both mechanical stretch and the endogenous peptide apelin, a finding that is important for the development of APJ agonists to treat heart failure.

    • Maria Cecilia Scimia
    • , Cecilia Hurtado
    •  & Pilar Ruiz-Lozano

  • News & Views |

    It seems that embryonic stem cells regularly pass through a transient state during which they can generate all the cell types of an animal, including those of the placenta. See Article p.57

    • Azim Surani
    •  & Julia Tischler

  • Letter |

    A genomic map of nearly 300,000 potential cis-regulatory sequences determined from diverse mouse tissues and cell types reveals active promoters, enhancers and CCCTC-binding factor sites encompassing 11% of the mouse genome and significantly expands annotation of mammalian regulatory sequences.

    • Yin Shen
    • , Feng Yue
    •  & Bing Ren

  • News & Views |

    Transcription factors regulate the expression of genes by binding to certain DNA sequences. But the outcome can be markedly different, depending on whether the binding is stable or short-lived. See Letter p.251

    • Tommy Kaplan
    •  & Nir Friedman

  • Letter |

    In a mouse model of mammary carcinoma, loss of deleted in colorectal cancer (DCC) promotes metastasis formation, and in cell cultures derived from p53-deficient mouse mammary tumours DCC expression controls netrin-1-dependent cell survival, supporting the function of DCC as a context-dependent tumour suppressor that limits survival of disseminated tumour cells.

    • Paul Krimpenfort
    • , Ji-Ying Song
    •  & Anton Berns

  • News & Views |

    Separating primary from secondary changes in the autistic brain has long been a research goal. With knowledge of wide-ranging molecular deficits, identification of the best therapeutic targets becomes a priority. See Letter p.380

    • Željka Korade
    •  & Károly Mirnics

  • News & Views |

    Enhancer sequences increase gene transcription with the help of a co-activator complex, the Mediator. Another protein complex — cohesin — seems to work with Mediator to bring together enhancers and promoters. See Article p. 430

    • Rolf Ohlsson

  • Article |

    Gene activation may involve the formation of a DNA loop that connects enhancer-bound transcription factors with the transcription apparatus at the core promoter. But this process is not well understood. Here, two proteins, mediator and cohesin, are shown to connect the enhancers and core promoters of active genes in embryonic stem cells. These proteins seem to generate cell-type-specific DNA loops linked to the gene expression program of each cell.

    • Michael H. Kagey
    • , Jamie J. Newman
    •  & Richard A. Young

  • Letter |

    Interleukin-17-producing helper T (TH17) cells are a distinct T-cell subset characterized by its role in autoimmune disease. Here it is shown that the development of TH17 cells requires the transcription factor IκBζ, as well as nuclear receptors of the ROR family. Mice lacking IκBζ have a defect in TH17 development and are resistant to the induction of experimental autoimmune encephalomyelitis. The study points to some new potential molecular targets for drugs to treat autoimmune disease.

    • Kazuo Okamoto
    • , Yoshiko Iwai
    •  & Hiroshi Takayanagi

  • Article |

    Zscan4 is shown to be involved in maintaining telomeres in embryonic stem (ES) cells. Only 5% of ES cells express Zscan4 at a given time, but nearly all ES cells activate Zscan4 at least once within nine passages. The transient Zscan4-positive state is associated with rapid telomere extension by telomere recombination and upregulation of meiosis–specific homologous recombination genes. Knocking down Zscan4 shortens telomeres, increases karyotype abnormalities and spontaneous sister chromatid exchange, and slows down cell proliferation until reaching crisis by eight passages.

    • Michal Zalzman
    • , Geppino Falco
    •  & Minoru S. H. Ko

  • Letter |

    There is much interest in understanding the genetic mechanisms that underlie individual variations in gene expression. Here, RNA sequencing has been used to study gene expression in lymphoblastoid cell lines derived from Nigerian individuals for whom extensive genotype information is known. Numerous genetic determinants of variation in gene expression were identified, including variation in transcription, splicing and allele-specific expression.

    • Joseph K. Pickrell
    • , John C. Marioni
    •  & Jonathan K. Pritchard

  • Letter |

    Here, sequencing has been used to characterize the mRNA fraction of the transcriptome in Caucasian individuals, to provide a fine-scale view of transcriptomes and to identify genetic variants that affect alternative splicing. Measuring allele-specific expression identified rare expression quantitative trait loci (eQTLs) and allelic differences in transcript structure, revealing new properties of genetic effects on the transcriptome.

    • Stephen B. Montgomery
    • , Micha Sammeth
    •  & Emmanouil T. Dermitzakis

  • Letter |

    An understanding of how fat cells (adipocytes) develop will contribute to our understanding of obesity. The differentiation of committed preadipocytes into adipocytes is known to be controlled by PPARγ and several other transcription factors. But what turns a cell into a preadipocyte? Here, the zinc-finger protein Zfp423 is identified as a transcriptional regulator of preadipocyte determination.

    • Rana K. Gupta
    • , Zoltan Arany
    •  & Bruce M. Spiegelman

  • Letter |

    The vertebrate body plan shows marked bilateral symmetry, although this can be disrupted in conditions such as scoliosis. Here, a mutation in Rere is found that leads to the formation of asymmetrical somites in mouse embryos; furthermore, Rere is shown to control retinoic acid signalling, which is required to maintain somite symmetry by interacting with Fgf8. The results provide insight into how bilateral symmetry is maintained.

    • Gonçalo C. Vilhais-Neto
    • , Mitsuji Maruhashi
    •  & Olivier Pourquié

  • Article |

    Even genetically identical organisms in homogeneous environments vary, indicating that randomness in developmental processes such as gene expression may generate phenotypic diversity. Intestinal specification in the nematode Caenorhabditis elegans, in which wild-type cell fate is invariant and controlled by a small transcriptional network, is now studied. The results demonstrate that mutations in developmental networks can expose stochastic variability in gene expression, leading to phenotypic variation.

    • Arjun Raj
    • , Scott A. Rifkin
    •  & Alexander van Oudenaarden

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