Volume 19 Issue 3, March 2012

Volume 19 Issue 3

Soutoglou and colleagues investigate how DNA double strand breaks (DSBs) affect transcription elongation. The introduction of a single DSB within transcribed genes stalls RNAPII and inhibits transcription elongation and reinitiation, in a manner dependent on DNAPK and the proteasome. Image by David Chadwick from iStockphoto. pp 276–282

News and Views

  • News & Views |

    Finding biologically relevant targets is a prerequisite for understanding the function of any trans regulator of gene expression, but this can be particularly challenging with microRNAs (miRNAs). A study in this issue addresses the problem by identifying a novel mode of miRNA target recognition.

    • Giovanni Stefani
    •  & Frank J Slack

Research Highlights

Articles

  • Article |

    The 20S particle, which is composed of NSF, SNAP and the SNARE complex, is important in fusion events. Single-particle cryo-EM and negative stain EM studies of the 20S particle and of NSF in its different nucleotide states suggest how nucleotide-dependent conformational changes in NSF may generate a force via ATP hydrolysis, providing insight into disassembly of SNARE by NSF.

    • Lei-Fu Chang
    • , Song Chen
    • , Cui-Cui Liu
    • , Xijiang Pan
    • , Jiansen Jiang
    • , Xiao-Chen Bai
    • , Xin Xie
    • , Hong-Wei Wang
    •  & Sen-Fang Sui
  • Article |

    DNA double-strand breaks (DSBs) can affect many cellular processes, including transcription. Now the dynamics of RNA polymerase II is studied, following the induction of a single DSB within transcribed genes in human cell lines. The results reveal that the DSB causes inhibition of transcription elongation and reinitiation, in a manner that is dependent on the activity of DNA protein kinase and the proteasome.

    • Tibor Pankotai
    • , Céline Bonhomme
    • , David Chen
    •  & Evi Soutoglou
  • Article |

    Krüppel-like factor 4 (Klf4) promotes the self-renewal of embryonic stem cells, but how Klf4 itself is regulated is unclear. ERK1 and ERK2 are now found to phosphorylate Klf4, targeting it for degradation via the ubiquitin-proteasome pathway and promoting cellular differentiation.

    • Myoung Ok Kim
    • , Sung-Hyun Kim
    • , Yong-Yeon Cho
    • , Janos Nadas
    • , Chul-Ho Jeong
    • , Ke Yao
    • , Dong Joon Kim
    • , Dong-Hoon Yu
    • , Young-Sam Keum
    • , Kun-Yeong Lee
    • , Zunnan Huang
    • , Ann M Bode
    •  & Zigang Dong
  • Article |

    The bacterial nucleotide excision repair pathway starts with the sensor complex UvrA–UvrB scanning the genome and undergoing conformational change when DNA lesions are detected. Now crystal structures of a UvrA dimer and the UvrA–UvrB complex, along with biochemical analyses, provide insight into these early nucleotide excision repair events.

    • Danaya Pakotiprapha
    • , Martin Samuels
    • , Koning Shen
    • , Johnny H Hu
    •  & David Jeruzalmi
  • Article |

    To maintain efficient force generation, myosins must couple the ATPase cycle with actin binding and lever movement, but the mechanism for this coupling and actin activation of myosin has remained elusive. Now, a conserved actin-binding loop is found to be responsible for activating the ATPase by acceleration of the lever swing, increasing the ratio of mechanically productive to futile actomyosin cycles.

    • Boglárka H Várkuti
    • , Zhenhui Yang
    • , Bálint Kintses
    • , Péter Erdélyi
    • , Irén Bárdos-Nagy
    • , Attila L Kovács
    • , Péter Hári
    • , Miklós Kellermayer
    • , Tibor Vellai
    •  & András Málnási-Csizmadia
  • Article |

    How yeast telomeres avoid triggering DNA damage checkpoints is studied by creating de novo telomere ends with different amounts of telomeric repeats. Rif1 and Rif2 protect short telomere tracts through different mechanisms and by blocking the accumulation of proteins that can activate checkpoint kinase Mec1. Moreover, long telomere tracts can perturb DNA end processing on neighboring short tracts and hence dampen checkpoint activation.

    • Cyril Ribeyre
    •  & David Shore
  • Article |

    The Elongator complex has been associated with a wide range of cellular processes, including post-transcriptional modification of tRNAs. Structural and biochemical analyses of Elongator proteins 4, 5 and 6 now show that they form a RecA-like hexameric ring that binds tRNAs in a manner regulated by ATP hydrolysis.

    • Sebastian Glatt
    • , Juliette Létoquart
    • , Céline Faux
    • , Nicholas M I Taylor
    • , Bertrand Séraphin
    •  & Christoph W Müller
  • Article |

    MicroRNAs are thought to repress mRNA targets through perfect pairing with their seed region, but a sizeable number of miRNA interaction sites are orphans, without a perfect canonical miRNA partner. Now a large number of miRNAs are found to use an alternative binding mode that involves the bulging out of an unpaired mRNA nucleotide, leading to a functional mRNA-miRNA interaction.

    • Sung Wook Chi
    • , Gregory J Hannon
    •  & Robert B Darnell
  • Article |

    The AKAP79 scaffold protein couples plasma membrane Ca2+ influx in neurons to activation of calcineurin, which in turn activates NFAT. Analysis of this interaction shows that AKAP79 and NFAT bind the same interface on calcineurin, but the affinity of the calcineurin-AKAP79 interaction is finely balanced to promote calcineurin recruitment to the scaffold while still allowing calcineurin release for NFAT activation.

    • Huiming Li
    • , Matthew D Pink
    • , Jonathan G Murphy
    • , Alexander Stein
    • , Mark L Dell'Acqua
    •  & Patrick G Hogan
  • Article |

    Alternative splicing of the pyruvate kinase M (PKM) pre-mRNA, resulting in the exclusion of either exon 9 or 10, requires a small set of splicing factors, hnRNPA1, hnRNPA2 and PTB. A new study reveals that these general splicing factors function through a concentration-dependent mechanism, coupled with nonsense-mediated decay, to determine the outcome of PKM pre-mRNA splicing.

    • Mo Chen
    • , Charles J David
    •  & James L Manley

Brief Communications

  • Brief Communication |

    Glutamate transporters couple the uptake of glutamate to the transport of cations. A new crystal structure of an archaeal trimeric glutamate transporter homolog, GltPh, captured in an intermediate conformation between the outward and inward facing states, provides insights into the transport mechanism.

    • Grégory Verdon
    •  & Olga Boudker
  • Brief Communication |

    Some bacterial pathogens can obtain iron from the human host by extracting it from transferrin via two bacterial surface proteins, TfbA and TfbB. Now the crystal structures of Neisseria meningitidis TfbB in its apo state and bound to human transferrin reveal how TfbB sequesters transferrin and initiates iron release.

    • Charles Calmettes
    • , Joenel Alcantara
    • , Rong-Hua Yu
    • , Anthony B Schryvers
    •  & Trevor F Moraes
  • Brief Communication |

    Numerous methylated residues exist on histone tails, the functional significance of which remains unknown. New studies in budding yeast now identify monomethylation of histone H4 lysine residues 5, 8 and 12 as functionally important marks that regulate cell growth and stress responses and are catalyzed by the first known H4 methyltransferase in budding yeast, Set5.

    • Erin M Green
    • , Gloria Mas
    • , Nicolas L Young
    • , Benjamin A Garcia
    •  & Or Gozani

Errata

Corrigenda