Transcription articles within Nature Communications

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  • Article |

    Telomere uncapping in senescent cells is accompanied by loss of the TRF2 telomere capping factor and upregulation of the long noncoding RNA TERRA. Here the authors characterize the TERRA transcriptome and show that TERRA upregulation may promote SUV39H1 recruitment, H3K9 trimethylation and telomere end-to-end fusions.

    • Antonio Porro
    • , Sascha Feuerhahn
    •  & Joachim Lingner

  • Article |

    The quantitative relationship between the fluctuation of specific extrinsic and intrinsic factors, and stochastic fluctuations in gene expression - or noise - has not been clearly established. Here, Yang et al.demonstrate that intrinsic noise is independent of - while extrinsic noise scales linearly with - variation in RNA polymerase abundance.

    • Sora Yang
    • , Seunghyeon Kim
    •  & Nam Ki Lee

  • Article |

    Despite numerous previous studies, the nature of the interaction of transcription factors (TF) with their endogenous response elements (REs) has remained unclear. Here the authors characterize the binding of p53 and glucocorticoid receptor to their endogenous REs and find that transcriptionally productive interactions are transient and involve only a small fraction of cellular TF molecules.

    • Tatsuya Morisaki
    • , Waltraud G. Müller
    •  & James G. McNally

  • Article |

    It was suggested that despite the conservation of their components, yeast and human pol II initiation complexes diverged in architecture. Mühlbacher et al.now demonstrate that the yeast and human core complexes are structurally conserved and provide insight into the conformations adopted by TFIIF during initiation.

    • Wolfgang Mühlbacher
    • , Sarah Sainsbury
    •  & Patrick Cramer

  • Article |

    The elongation factors DSIF and NELF have established roles in polymerase pausing, elongation and 3'-end processing of replication-dependent histone mRNAs. Here the authors demonstrate that DSIF and NELF form a complex with Integrator and allow proper 3'-processing of snRNA transcripts by preventing the recruitment of CstF.

    • Junichi Yamamoto
    • , Yuri Hagiwara
    •  & Yuki Yamaguchi

  • Article |

    The process of somatic hypermutation, used by B cells to increase antibody diversity, is catalysed by the activation-induced deaminase (AID), which needs to access single-stranded DNA to mediate its function. Here, the authors propose a mechanism for the generation of single-stranded DNA substrate required for AID activity.

    • Xiaohua Wang
    • , Manxia Fan
    •  & Matthew D. Scharff

  • Article
    | Open Access

    The nexine is a conserved layer of the pollen wall in land plants. The authors show that the AHL family protein TRANSPOSABLE ELEMENT SILENCING VIA AT-HOOK (TEK) is necessary for nexine formation in Arabidopsis, acting downstream of the transcription factor ABORTED MICROSPORES (AMS).

    • Yue Lou
    • , Xiao-Feng Xu
    •  & Zhong-Nan Yang

  • Article
    | Open Access

    The atrioventricular canal partitions the developing vertebrate heart. Here, the authors show that the cardiac transcription factor Gata4 together with histone modification enzymes and localized co-factors binds atrioventricular canal-specific enhancers, thereby repressing gene activity in the cardiac chambers.

    • Sonia Stefanovic
    • , Phil Barnett
    •  & Vincent M. Christoffels

  • Article
    | Open Access

    Cyclin-dependent kinase 12 (Cdk12) phosphorylates the C-terminal domain (CTD) of RNA polymerase II to regulate transcription. Here, the authors solve the crystal structure of the Cdk12 kinase domain and show that Cdk12 has its highest activity on a CTD substrate that carries a serine 7 phosphorylation.

    • Christian A. Bösken
    • , Lucas Farnung
    •  & Matthias Geyer

  • Article
    | Open Access

    Bacterial RNA polymerase (RNAP) is crucial for cellular gene expression and a validated target for antimicrobial drugs. Here, Malinen et al. explore the effects of the CBR class of RNAP inhibitors on the E. coliRNAP transcription cycle and provide detailed mechanistic insight into their antibacterial action.

    • Anssi M. Malinen
    • , Monali NandyMazumdar
    •  & Georgiy A Belogurov

  • Article
    | Open Access

    The thermodynamics of unwinding polynucleotide duplexes can be determined from energy changes for DNA and mRNA interactions. Here the authors show that the ratio between mRNA/DNA and DNA/DNA duplex stability upstream of the 3′- spice sites is a characteristic that can contribute to intron–exon recognition.

    • Marina N. Nedelcheva-Veleva
    • , Mihail Sarov
    •  & Stoyno S. Stoynov

  • Article
    | Open Access

    Topoisomerases facilitate the progress of elongating polymerases during transcription. Zomerdijk and colleagues now demonstrate an additional role for this enzyme; their data suggest that Top2 can cleave DNA inducing topological changes at the ribosomal DNA promoter, which assists de novoassembly of the RNA polymerase I pre-initiation complex.

    • Swagat Ray
    • , Tatiana Panova
    •  & Joost C. B. M. Zomerdijk

  • Article |

    Microsporidia are widespread human parasites, but limited genome annotation has hampered efforts to understand their biology. Peyretailladeet al. use sequence motifs upstream of start codons to annotate or re-annotate microsporidian genomes and find new genes potentially involved in interactions with the host.

    • Eric Peyretaillade
    • , Nicolas Parisot
    •  & Pierre Peyret

  • Article |

    The mitochondrial transcription factor A (TFAM) mediates both mitochondrial transcription and DNA compaction, but how it achieves these two functions is unknown. In this study, TFAM is shown to slide along DNA and cause local melting, suggesting a mechanism for how TFAM modulates both transcription and compaction.

    • Géraldine Farge
    • , Niels Laurens
    •  & Gijs J.L. Wuite

  • Article
    | Open Access

    Phosphorylation of the carboxy-terminal domain of RNA polymerase II is important for controlling gene transcription. In this study, the transcription elongation factor Tefb is shown to phosphorylate serine-5 and its activity is enhanced when the polymerase is already phosphorylated on serine-7.

    • Nadine Czudnochowski
    • , Christian A. Bösken
    •  & Matthias Geyer

  • Article
    | Open Access

    Lysine-specific demethylase 1 (LSD1) removes methyl groups from mono-methylated and dimethylated lysine 4 of histone H3 and represses transcription. In this study, a role for LSD1 in the regulation of genes involved in energy expenditure in adipocytes is reportedin vitroand in mice fed on a high-fat diet.

    • Shinjiro Hino
    • , Akihisa Sakamoto
    •  & Mitsuyoshi Nakao

  • Article |

    Whether plants can remember their transcriptional response to stress is unknown. By repeatedly exposingArabidopsisto drought, we show that the plants remember their transcriptional response to stress and that the altered genes retain the epigenetic mark H3K4me3 and stalled phosphorylated polymerase II.

    • Yong Ding
    • , Michael Fromm
    •  & Zoya Avramova

  • Article
    | Open Access

    The super elongation complex, which is involved in transcriptional elongation, contains the Eleven-nineteen Lysine-rich Leukemia protein (ELL). In this study, ELL is shown to stabilize RNA polymerase II prior to recruitment into the super elongation complex, suggesting ELL has a role in early transcription elongation.

    • Jung S. Byun
    • , Temesgen D. Fufa
    •  & Kevin Gardner

  • Article
    | Open Access

    IKK kinases activate nuclear factor-κB, and the activated form of this transcription factor is found in endothelial cells in diseased tissue. In this study, mice lacking IKKβ in the endothelium are generated, and it is shown that defects in endothelial cell function are both IKK kinase activity dependent and independent.

    • Noboru Ashida
    • , Sucharita SenBanerjee
    •  & Anthony Rosenzweig

  • Article
    | Open Access

    Saccharomycesyeasts can produce ethanol from sugars in the presence of oxygen. In this study, the authors demonstrate thatDekkera bruxellensis, a distantly related yeast, can also produce and consume ethanol due to the loss of a cis-regulatory element from the promoters of genes crucial for respiration.

    • Elżbieta Rozpędowska
    • , Linda Hellborg
    •  & Jure Piškur

  • Article
    | Open Access

    Regulatory T cells are characterized by the expression of Foxp3, however, how the expression of this protein is controlled is unclear. Here, the authors show that the nuclear orphan receptor, Nr4a2, is a transcriptional activator of Foxp3, and suggest that it is required for the function of regulatory T cells.

    • Takashi Sekiya
    • , Ikkou Kashiwagi
    •  & Akihiko Yoshimura

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