Transcription articles within Nature

Featured

  • Article |

    RNA polymerase (Pol) I transcribes ribosomal RNA that is critically required for ribosome assembly, and the enzyme is a major determinant of protein biosynthesis and cell growth; here the crystal structure of the complete 14-subunit Pol I from yeast is determined, providing insights into its unique architecture and the possible functional roles of its components.

    • Carlos Fernández-Tornero
    • , María Moreno-Morcillo
    •  & Christoph W. Müller

  • Letter |

    A novel approach to analyse high-depth Hi-C data provides a comprehensive chromatin interaction map at approximately 5–10 kb resolution in human fibroblasts; this reveals that TNF-α-responsive enhancers are already in contact with target promoters before signalling and that this chromatin looping is a strong predictor of gene induction.

    • Fulai Jin
    • , Yan Li
    •  & Bing Ren

  • Article |

    The ChIP-exo technique is used to map the organization of transcription initiation complexes across the human genome at near-base-pair resolution; most of the transcription initiation complexes give rise to non-coding, non-polyadenylated RNA, indicating that pervasive non-coding transcription arise from specific promoters and is regulated.

    • Bryan J. Venters
    •  & B. Franklin Pugh

  • Letter |

    A study of prostate cancer cells reveals a transcriptional activation role for long non-coding RNAs (PRNCR1 and PCGEM1) that bind to the androgen receptor, and is also observed for the truncated androgen receptor characteristic of many aggressive prostate cancers.

    • Liuqing Yang
    • , Chunru Lin
    •  & Michael G. Rosenfeld

  • Letter |

    Rett syndrome is caused by mutations in MeCP2, and this study identifies a site on MeCP2, T308, whose phosphorylation is regulated by neuronal activity: phosphorylation of T308 blocks the interaction of MeCP2 with the NCoR co-repressor complex, suppressing MeCP2's ability to repress transcription, and mice carrying mutations of MeCP2 T308 show Rett-syndrome-related symptoms.

    • Daniel H. Ebert
    • , Harrison W. Gabel
    •  & Michael E. Greenberg

  • Letter |

    The malaria parasite Plasmodium falciparum escapes immune detection by expressing one of 60 antigenically distinct var genes at any one time during the course of infection: here it is shown that the P. falciparum protein PfSETvs has a key role in var gene silencing through the trimethylation of histone H3K36.

    • Lubin Jiang
    • , Jianbing Mu
    •  & Louis H. Miller

  • Article |

    Cryo-electron microscopy structures of key intermediates during the sequential assembly of the pre-initiation complex are presented; structures of the closed and open-promoter complexes allow insights into the process of promoter melting.

    • Yuan He
    • , Jie Fang
    •  & Eva Nogales

  • Letter |

    The structures of three distinct human transcription factor IID (TFIID) protein assemblies are solved using cryo-electron microscopy; by incorporating TAF8 and TAF10, the key structural changes that remodel TFIID during assembly are determined, particularly the transition from a symmetric core-TFIID to an asymmetric holo-complex.

    • Christoph Bieniossek
    • , Gabor Papai
    •  & Imre Berger

  • Letter |

    Crystal structures of the Pol II–TFIIB complex in free form and bound by the DNA template and a short RNA product are reported; the latter complex represents an initially transcribing complex, a critical transient state in the pathway from transcription initiation to elongation.

    • Sarah Sainsbury
    • , Jürgen Niesser
    •  & Patrick Cramer

  • Letter |

    The pleiotropic transcription factor IRF4 is shown to regulate CD4+ T-cell differentiation and TH17 function through cooperative binding interactions with BATF and JUN family proteins via AP1–IRF4 composite elements (AICEs).

    • Peng Li
    • , Rosanne Spolski
    •  & Warren J. Leonard

  • Article
    | Open Access

    A description is given of the ENCODE effort to provide a complete catalogue of primary and processed RNAs found either in specific subcellular compartments or throughout the cell, revealing that three-quarters of the human genome can be transcribed, and providing a wealth of information on the range and levels of expression, localization, processing fates and modifications of known and previously unannotated RNAs.

    • Sarah Djebali
    • , Carrie A. Davis
    •  & Thomas R. Gingeras

  • Letter |

    Centromere identity is thought to be epigenetically propagated by stable inheritance of nucleosomes containing the histone variant CENP-A; the authors propose a different model here in which germline transcription defines the genomic regions that exclude CENP-A incorporation during embryogenesis in the holocentric worm Caenorhabditis elegans.

    • Reto Gassmann
    • , Andreas Rechtsteiner
    •  & Arshad Desai

  • Article |

    Downregulation of the glucose transporter GLUT4 in adipose tissue occurs early in the development of type 2 diabetes; here GLUT4-mediated glucose uptake is shown to induce a novel form of the transcription factor ChREBP, which regulates de novo lipogenesis and systemic glucose metabolism.

    • Mark A. Herman
    • , Odile D. Peroni
    •  & Barbara B. Kahn

  • News & Views |

    A genome-wide, high-resolution study of DNA-binding sites for proteins that transcribe DNA into RNA reveals details about how this process occurs in vivo. See Article p.295

    • Stephen Buratowski

  • Letter |

    Circadian rhythmicity of cardiac ion-channel expression and of an index of myocardial repolarization is under the control of Klf15, a clock-dependent oscillator that is required for generating transient outward potassium current, and deficiencies or excesses of which cause loss of rhythmic variation in myocardial and abnormal repolarization, and an enhanced susceptibility to ventricular arrhythmias.

    • Darwin Jeyaraj
    • , Saptarsi M. Haldar
    •  & Mukesh K. Jain

  • Letter |

    Different organisms use a variety of mechanisms to compensate for X chromosome dosage imbalance between the sexes. In Drosophila, the MSL complex increases transcription on the single X chromosome of males and is thought to regulate transcription elongation, although mechanistic details have been unclear. Here, a global run-on sequencing technique is used to reveal that the MSL complex seems to enhance transcription by facilitating the progression of RNA polymerase II across the bodies of active X linked genes. In this way, MSL can impose dosage compensation on diverse genes with a wide range of transcription levels along the X chromosome.

    • Erica Larschan
    • , Eric P. Bishop
    •  & Mitzi I. Kuroda

  • Letter |

    During gene transcription, RNA polymerase (Pol) II moves forward along DNA and synthesizes mRNA. However, Pol II can also move backwards and stall, which is important for regulatory purposes or when the polymerase hits an obstacle such as a nucleosome. This arrested state is reactivated by the transcription factor TFIIS. Here, a crystal structure is presented of a backtracked yeast Pol II complex in which the backtracked RNA can be observed, plus a structure of a backtracked complex that contains TFIIS. A model is presented for Pol II backtracking, arrest and reactivation during transcription elongation.

    • Alan C. M. Cheung
    •  & Patrick Cramer

  • News & Views |

    Oscillations in gene transcription that occur in response to biological daily clocks coordinate the physiological workings of living organisms. But turnover in cellular energy may be sufficient to make the clock tick. See Article p.498 & Letter p.554

    • Joseph Bass
    •  & Joseph S. Takahashi

  • Article |

    A novel technique called native elongating transcript sequencing (NET-seq) is described, which can quantify transcription with single nucleotide resolution. It is based on sequencing nascent transcripts associated with RNA polymerase II that are captured directly from live cells, and is used to gain insights into polymerase pausing and backtracking and the directionality of transcription.

    • L. Stirling Churchman
    •  & Jonathan S. Weissman

  • Letter |

    Ubiquitination of histone H2A has been implicated in polycomb-mediated transcriptional silencing, but its precise functions are unclear. Here, ZRF1 is shown to be recruited to ubiquitinated H2A and to function in displacing polycomb-repressive complex 1 (PRC1) from chromatin to facilitate transcriptional activation.

    • Holger Richly
    • , Luciana Rocha-Viegas
    •  & Luciano Di Croce

  • 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

  • Letter |

    In the course of characterizing short RNAs from human cells using single-molecule high-throughput sequencing, these authors identify a new short RNA species. The presence of non-genomically encoded poly(U) residues at their 5' ends implies the existence of an unknown RNA copying mechanism in human cells.

    • Philipp Kapranov
    • , Fatih Ozsolak
    •  & Patrice M. Milos

  • 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 |

    Transcriptional enhancers are segments of regulatory DNA located some distance from the coding region of a gene, and several of them may sometimes serve apparently redundant functions. These authors demonstrate in Drosophila that such 'redundant' enhancers, by contributing higher overall levels of transcription, ensure robustness of phenotypes against both genetic and environmental perturbations, for example mutations in other genes or temperature changes that would otherwise lead to aberrant development.

    • Nicolás Frankel
    • , Gregory K. Davis
    •  & David L. Stern

  • News & Views |

    Genomes don't just encode protein-coding RNAs. They also give rise to various groups of RNAs that can regulate gene expression. Short RNAs that form from enhancer sequences might be one such class of regulatory RNA.

    • Bing Ren

  • Article |

    Regulatory proteins bind non-coding DNA either at promoters (near to a gene's transcription start site) or at enhancers (far away). Binding at enhancers helps to bring the transcription enzyme RNA polymerase to promoters. Here, studies of some 12,000 enhancers that respond to electrical activity in neurons show that binding to enhancers also brings the polymerase to the enhancers themselves, where it transcribes a novel class of non-coding RNAs. Enhancers may thus be more similar to promoters than hitherto appreciated.

    • Tae-Kyung Kim
    • , Martin Hemberg
    •  & Michael E. Greenberg

  • Letter |

    In response to oncogenic stress, the tumour suppressor ARF activates the p53 protein. ARF protein is highly stable in most human cell lines, so it has been thought that ARF activation occurs mainly at the level of transcription. Here, however, ARF is shown to be unstable in normal human cells but stable in cancer cells, through a transcription-independent mechanism. A ubiquitin ligase for ARF is identified and shown to promote ARF degradation in normal cells. This activity is prevented in cancer cells, stabilizing ARF.

    • Delin Chen
    • , Jing Shan
    •  & Wei Gu

  • 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 |

    Although cyclin D1 is frequently overexpressed in human cancers, the full range of its functions in normal development and oncogenesis is unclear. Here, tagged cyclin D1 knock-in mouse strains are developed to allow a search for cyclin D1-binding proteins in different mouse organs using high-throughput mass spectrometry. The results show that, in addition to its established cell cycle roles, cyclin D1 has an in vivo transcriptional function in mouse development.

    • Frédéric Bienvenu
    • , Siwanon Jirawatnotai
    •  & Piotr Sicinski

  • Letter |

    Rho is a general transcription termination factor in bacteria, but the mechanism by which it disrupts the RNA polymerase (RNAP) elongation complex is unknown. Here, Rho is shown to bind tightly to the RNAP throughout the transcription cycle, with the formation of the RNAP–Rho complex being crucial for termination. Furthermore, RNAP is proposed to have an active role in Rho termination through an allosteric mechanism.

    • Vitaly Epshtein
    • , Dipak Dutta
    •  & Evgeny Nudler

Browse broader subjects

Browse narrower subjects

Browse Transcription across other nature.com journals