Gene regulation articles within Nature

Featured

  • Article
    | Open Access

    In Caenorhabditis tropicalis, selective expression of genetic alleles from one parent but not the other can arise from maternally inherited small transcripts acting via the PIWI-interacting RNA host defence pathway.

    • Pinelopi Pliota
    • , Hana Marvanova
    •  & Alejandro Burga

  • Article |

    Variant-to-gene-to-program is a new approach to building maps of genome function to link risk variants to disease genes and to convergent signalling pathways in an unbiased manner; its strength is demonstrated in coronary artery disease.

    • Gavin R. Schnitzler
    • , Helen Kang
    •  & Jesse M. Engreitz

  • Article
    | Open Access

    Low-affinity transcription factor binding sites are prevalent across the genome, and single nucleotide changes that increase binding affinity even slightly can cause gain-of-function gene expression and phenotypes (such as polydactyly).

    • Fabian Lim
    • , Joe J. Solvason
    •  & Emma K. Farley

  • Article
    | Open Access

    Deep learning models were used to design synthetic cell-type-specific enhancers that work in fruit fly brains and human cell lines, an approach that also provides insights into these gene regulatory elements.

    • Ibrahim I. Taskiran
    • , Katina I. Spanier
    •  & Stein Aerts

  • Article
    | Open Access

     Prophage lysogeny-to-lysis transitions are controlled by regulatory modules consisting of transcription factors and partner small proteins that are activated through DNA-damage-independent pathways, including by quorum sensing, and these modules determine inter-prophage competition outcomes.

    • Justin E. Silpe
    • , Olivia P. Duddy
    •  & Bonnie L. Bassler

  • Article |

    A high throughput recruitment assay testing the transcriptional activity of more than 100,000 protein fragments tiling across most human chromatin regulators and transcription factors maps the locations and strengths of activation, repression and bifunctional domains, and identifies the sequences necessary for these functions.

    • Nicole DelRosso
    • , Josh Tycko
    •  & Lacramioara Bintu

  • Article
    | Open Access

    Frameshift mutations that create arginine-rich basic tails in transcription factors and other proteins can lead to altered phase separation in the nucleolus, which in turn leads to syndromes such as brachyphalangy, polydactyly and tibial aplasia.

    • Martin A. Mensah
    • , Henri Niskanen
    •  & Denes Hnisz

  • Article |

    Results are presented that indicate that alterations to gene regulatory three-dimensional architecture are a critical mechanism that enables structural variant-based oncogene activation in cancer genomes and sheds light on the essential elements for such gene activation events.

    • Zhichao Xu
    • , Dong-Sung Lee
    •  & Jesse R. Dixon

  • Article
    | Open Access

    A non-genetic mechanism of sex determination in the human malaria parasite, Plasmodium falciparum, is described, and the male development 1 gene is identified as a potential target for interventions that block malaria transmission.

    • A. R. Gomes
    • , A. Marin-Menendez
    •  & A. M. Talman

  • Article |

    The systematic categorization of human enhancers by their cofactor dependencies provides a conceptual framework to understand the sequence and chromatin diversity of enhancers and their roles in different gene-regulatory programmes.

    • Christoph Neumayr
    • , Vanja Haberle
    •  & Alexander Stark

  • Article |

    A new high-throughput assay applied to 1,000 enhancers and 1,000 promoters in human cells reveals how different classes of enhancers and promoters control RNA expression.

    • Drew T. Bergman
    • , Thouis R. Jones
    •  & Jesse M. Engreitz

  • Article |

    In Drosophila, there are extensive physical and functional associations of distant paralogous genes, including co-regulation by shared enhancers and co-transcriptional initiation over distances of nearly 250 kilobases.

    • Michal Levo
    • , João Raimundo
    •  & Michael S. Levine

  • Article |

    A chromatin accessibility atlas of 240,919 cells in the adult and developing Drosophila brain reveals 95,000 enhancers, which are integrated in cell-type specific enhancer gene regulatory networks and decoded into combinations of functional transcription factor binding sites using deep learning.

    • Jasper Janssens
    • , Sara Aibar
    •  & Stein Aerts

  • Article
    | Open Access

    A new technique called immunoGAM, which combines genome architecture mapping (GAM) with immunoselection, enabled the discovery of specialized chromatin conformations linked to gene expression in specific cell populations from mouse brain tissues.

    • Warren Winick-Ng
    • , Alexander Kukalev
    •  & Ana Pombo

  • Article |

    BANP is identified as the transcription factor that binds the CGCG element in a DNA-methylation-dependent manner, opens chromatin and activates a class of essential CpG-island-regulated genes.

    • Ralph S. Grand
    • , Lukas Burger
    •  & Dirk Schübeler

  • Article |

    Micro Capture-C allows physical contacts to be determined at base-pair resolution, revealing that transcription factors have an important role in the maintenance of the contacts between enhancers and promoters.

    • Peng Hua
    • , Mohsin Badat
    •  & James O. J. Davies

  • Article |

    Disruption of a promoter can release its partner enhancer to activate other promoters in the same contact domain, and this process, named ‘enhancer release and retargeting’, can often lead to gene alterations that cause disease.

    • Soohwan Oh
    • , Jiaofang Shao
    •  & Michael G. Rosenfeld

  • Article |

    Mapping enhancer regulation across human cell types and tissues illuminates genome function and provides a resource to connect risk variants for common diseases to their molecular and cellular functions.

    • Joseph Nasser
    • , Drew T. Bergman
    •  & Jesse M. Engreitz

  • Article
    | Open Access

    ChIP–seq and CETCh–seq data are used to analyse binding maps for 208 transcription factors and other chromatin-associated proteins in a single human cell type, providing a comprehensive catalogue of the transcription factor landscape and gene regulatory networks in these cells.

    • E. Christopher Partridge
    • , Surya B. Chhetri
    •  & Eric M. Mendenhall

  • Article |

    Structural cells implement a broad range of immune-regulatory functions beyond their roles as barriers and connective tissues, and they utilize an epigenetically encoded potential for immune gene activation in their rapid response to viral infection.

    • Thomas Krausgruber
    • , Nikolaus Fortelny
    •  & Christoph Bock

  • Article |

    A CRISPR-based screening platform was used to identify previously uncharacterized genes that regulate the regulatory T cell-specific master transcription factor Foxp3, indicating that this screening method may be broadly applicable for the discovery of other genes involved in autoimmunity and immune responses to cancer.

    • Jessica T. Cortez
    • , Elena Montauti
    •  & Deyu Fang

  • Review Article |

    The scientific, technical and ethical aspects of using CRISPR technology for therapeutic applications in humans are discussed, highlighting both opportunities and challenges of this technology to treat, cure and prevent genetic disease.

    • Jennifer A. Doudna

  • Article |

    Gastrointestinal stromal tumours can be initiated by gain-of-function mutations of the KIT or PDGFRA oncogenes but also by loss of the metabolic complex succinate dehydrogenase (SDH), which leads to DNA hypermethylation; this study shows that in SDH-deficient tumours, displacement of CTCF insulators by DNA methylation activates oncogene expression, illustrating how epigenetic alterations can drive oncogenic signalling in the absence of kinase mutations.

    • William A. Flavahan
    • , Yotam Drier
    •  & Bradley E. Bernstein

  • Article |

    Studies of humans, mice and nematodes reveal a conserved role of neural activity and the transcription factor REST in extended longevity.

    • Joseph M. Zullo
    • , Derek Drake
    •  & Bruce A. Yankner

  • Letter |

    A screen of 23 transcriptional cofactors for their ability to activate 72,000 candidate core promoters in Drosophila melanogaster identified distinct compatibility groups, providing insight into mechanisms that underlie the selective activation of transcriptional programs.

    • Vanja Haberle
    • , Cosmas D. Arnold
    •  & Alexander Stark

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