Transcription articles within Nature

Featured

  • Article
    | Open Access

    Cryo-electron microscopy structures of the human Integrator complex in three different functional states shed light on how Integrator terminates RNA polymerase II (Pol II) transcription by disengaging Pol II from the DNA template.

    • Isaac Fianu
    • , Moritz Ochmann
    •  & Patrick Cramer

  • Article
    | Open Access

    Introduction of a long synthetic DNA into yeast genomic loci results in high default transcriptional activity in yeast but low activity in mouse, suggesting distinct default levels of genomic activity in these organisms.

    • Brendan R. Camellato
    • , Ran Brosh
    •  & Jef D. Boeke

  • Article
    | Open Access

    Translation actively dislodges stalled transcription elongation complexes (ECs) from damaged DNA, which enables lesion repair and restoration of transcription activity, and coupled ribosomes discriminate between active ECs and stalled ECs, ensuring destruction of only the latter.

    • Jason Woodgate
    • , Hamed Mosaei
    •  & Nikolay Zenkin

  • 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

    Whole-genome alignment of 239 primate species reveals noncoding regulatory elements that are under selective constraint in primates but not in other placental mammals, that are enriched for variants that affect human gene expression and complex traits in diseases.

    • Lukas F. K. Kuderna
    • , Jacob C. Ulirsch
    •  & Kyle Kai-How Farh

  • Perspective |

    Although the catalogue of human protein-coding genes is nearing completion, the number of non-coding RNA genes remains highly uncertain, and for all genes much work remains to be done to understand their functions.

    • Paulo Amaral
    • , Silvia Carbonell-Sala
    •  & Steven L. Salzberg

  • Article
    | Open Access

    A collection of RNA polymerase mutants spanning all possible substitutions of the rifampicin binding site is generated and characterized, increasing our understanding of antibiotic mechanisms and bacterial physiology.

    • Kevin B. Yang
    • , Maria Cameranesi
    •  & Evgeny Nudler

  • Article
    | Open Access

    Cryo-EM structures and analysis provide insight into the mechanisms by which basic helix–loop–helix transcription factors access E-box DNA sequences that are embedded within nucleosomes, and cooperate with other transcription factors.

    • Alicia K. Michael
    • , Lisa Stoos
    •  & Nicolas H. Thomä

  • Article
    | Open Access

    Binding of the human pioneer transcription factor OCT4 to nucleosomes containing endogenous DNA sequences causes changes to the nucleosome structure and facilitates the cooperative assembly of multiple pioneer transcription factors, a property that can be affected by histone modifications.

    • Kalyan K. Sinha
    • , Silvija Bilokapic
    •  & Mario Halic

  • Article |

    The switch from glucose- to fatty acid-dependent metabolism in cardiomyocytes of newborn mice is governed by γ-linolenic acid in maternal milk, which binds to retinoid X receptors, thereby causing a transcription-dependent metabolic transition.

    • Ana Paredes
    • , Raquel Justo-Méndez
    •  & Mercedes Ricote

  • Article |

    Subunits of SWI/SNF act as mitotic bookmarks to safeguard cell identity during cell division.

    • Zhexin Zhu
    • , Xiaolong Chen
    •  & Charles W. M. Roberts

  • 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

    Acute loss of H3K4me3 does not have detectable effects on transcriptional initiation, but leads to a widespread decrease in transcriptional output, an increase in RNA polymerase II pausing and slower elongation

    • Hua Wang
    • , Zheng Fan
    •  & Kristian Helin

  • Article |

    Structural studies of Escherichia coli transcription intrinsic termination complexes representing distinct intermediates using cryo-electron microscopy provide insights into the steps and mechanism of transcription termination.

    • Linlin You
    • , Expery O. Omollo
    •  & Yu Zhang

  • 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 |

    RNA sensing-mediated payload expression provides a specific, versatile, simple and generalizable means of detecting and manipulating animal cells with broad potential applications.

    • Yongjun Qian
    • , Jiayun Li
    •  & Z. Josh Huang

  • Article |

    The nuclear mitotic apparatus protein NuMA helps to protect genes from oxidative damage by occupying regions around transcription start sites, binding DNA repair factors and promoting transcription following damage.

    • Swagat Ray
    • , Arwa A. Abugable
    •  & Sherif F. El-Khamisy

  • Article |

    CDK11 associates with SF3B1 and phosphorylates threonine residues at the N terminus of SF3B1 during spliceosome activation, and the inhibition of CDK11 blocks the activation and leads to widespread intron retention and the accumulation of non-functional spliceosomes on pre-mRNAs and chromatin.

    • Milan Hluchý
    • , Pavla Gajdušková
    •  & Dalibor Blazek

  • 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 |

    Characterization of Gibbin, encoded by AHDC1, offers insights into the epidermal and mesodermal patterning phenotypes seen in Xia–Gibbs and related syndromes in humans, which derive from abnormal mesoderm maturation as a result of gene-specific DNA methylation decisions.

    • Ann Collier
    • , Angela Liu
    •  & Anthony E. Oro

  • 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
    | Open Access

    A study maps neuronal genomic targets of oestrogen receptor-α and shows how they coordinate brain sexual differentiation, concluding that the genome remains responsive to hormonal changes after structural dimorphisms have been established.

    • B. Gegenhuber
    • , M. V. Wu
    •  & J. Tollkuhn

  • Article
    | Open Access

    The transcriptional effect of an enhancer depends on its contact probabilities with the promoter through a nonlinear relationship, and enhancer strength determines absolute transcription levels as well as the sensitivity of a promoter to CTCF-mediated transcriptional insulation.

    • Jessica Zuin
    • , Gregory Roth
    •  & Luca Giorgetti

  • Article |

    Integrated structure–function studies show that transcription-coupled DNA repair (TCR)—rather than global genomic repair—is responsible for most chromosomal repair events in bacteria, and that TCR mainly occurs independently of the Mfd translocase.

    • Binod K. Bharati
    • , Manjunath Gowder
    •  & Evgeny Nudler

  • Article
    | Open Access

    The authors resolve the structure of five complexes containing RNA polymerase II and the CSA and CSB proteins, offering insight into how the repair of DNA lesions is coupled to transcription.

    • Goran Kokic
    • , Felix R. Wagner
    •  & Patrick Cramer

  • 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 |

    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 |

    A ChIP–exo method is used to define the genome-wide positional organization of proteins associated with gene transcription, DNA replication, centromeres, subtelomeres and transposons, revealing distinct protein assemblies for constitutive and inducible gene expression.

    • Matthew J. Rossi
    • , Prashant K. Kuntala
    •  & B. Franklin Pugh

  • Article |

    An ultra-high-throughput multiplex protein–DNA binding assay is used to assess binding of 270 human transcription factors to 95,886 noncoding variants in the human genome, providing data to improve prediction of the effects of noncoding variants on transcription factor binding and thereby increase understanding of molecular pathways involved in diverse human traits and genetic diseases.

    • Jian Yan
    • , Yunjiang Qiu
    •  & Bing Ren

  • Article |

    Inhibitors of mitochondrial transcription that target human mitochondrial RNA polymerase provide a chemical biology tool for studying the role of mitochondrial DNA expression in a wide range of pathologies.

    • Nina A. Bonekamp
    • , Bradley Peter
    •  & Nils-Göran Larsson

Browse broader subjects

Browse narrower subjects

Browse Transcription across other nature.com journals