Volume 19 Issue 8, August 2012

Volume 19 Issue 8

The cover image of an Escherichia coli colony stochastically expressing single fluorescent protein molecules that are visualized as individual spots on the cell membrane highlights the heterogeneity of gene expression in different cells and emphasizes the necessity for cells to control noise in gene expression, a topic examined in detail by Wang, Xiao and colleagues. Image created by Zach Hensel. pp 797–802

News and Views

  • News & Views |

    The recent mapping and modeling of protein-protein interfaces between general transcription factors TFIIE, TFIIH and Pol II have provided new insights into TFIIH-mediated melting of the transcription start site to form an open Pol II preinitiation complex and the stabilization of the complex by TFIIE, leading to a new mechanistic model for open-complex formation.

    • Michael Carey
  • News & Views |

    The search for the holy replicator has been revitalized through ultradeep sequencing of small RNA–primed single-stranded DNA. Saturation sequencing provides an explanation for the lack of overlap in prior data sets, suggests that frequency of origin usage but not site selection is developmentally regulated, and uncovers a complex four-stranded DNA structure associated with most origins.

    • David M Gilbert

Research Highlights

Articles

  • Article |

    During the final stages of yeast ribosome synthesis, immature translation-incompetent pre-40S particles that contain 20S pre-rRNA are converted to the mature translation-competent subunits containing 18S rRNA. In vitro and in vivo data now demonstrate that processing of 20S pre-rRNA is stimulated by translation initiation factor Fun12, and that its interaction with 60S ribosomal subunits is required for efficient 20S pre-rRNA processing.

    • Simon Lebaron
    • , Claudia Schneider
    • , Robert W van Nues
    • , Agata Swiatkowska
    • , Dietrich Walsh
    • , Bettina Böttcher
    • , Sander Granneman
    • , Nicholas J Watkins
    •  & David Tollervey
  • Article |

    Human JAK2 tyrosine kinase mediates signaling through numerous cytokine receptors. The JAK2 JH2 pseudokinase domain negatively regulates the activity of the JH1 kinase domain. The structures of wild-type JH2 and of the dominant V617F mutant provide a solid foundation for discerning the mechanism of action of the JH2 domain in normal JAK signaling and in dysregulated signaling that causes disease.

    • Rajintha M Bandaranayake
    • , Daniela Ungureanu
    • , Yibing Shan
    • , David E Shaw
    • , Olli Silvennoinen
    •  & Stevan R Hubbard
  • Article |

    The Drosha–DGCR8, or Microprocessor, complex, is required for microRNA biogenesis. DGCR8 recognizes the RNA substrates, whereas Drosha functions as an endonuclease. High-throughput sequencing and cross-linking immunoprecipitation (HITS-CLIP) analyses reveal many other RNA targets of DGCR8 besides microRNAs, including snoRNAs, which are processed in a Drosha-independent manner, as well as long noncoding RNAs and mRNAs of protein-coding genes.

    • Sara Macias
    • , Mireya Plass
    • , Agata Stajuda
    • , Gracjan Michlewski
    • , Eduardo Eyras
    •  & Javier F Cáceres
  • Article |

    The subtilisin-like domain of PatG can catalyze the macrocyclization of linear peptide. The crystal structure of the PatG macrocyclase domain, along with mutagenesis and functional analyses, reveals how the enzyme recognizes its substrate and enforces macrocyclization over hydrolysis of the acyl-enzyme intermediate. This information is also used to engineer variants with altered specificity and enhanced catalytic activity.

    • Jesko Koehnke
    • , Andrew Bent
    • , Wael E Houssen
    • , David Zollman
    • , Falk Morawitz
    • , Sally Shirran
    • , Jeremie Vendome
    • , Ada F Nneoyiegbe
    • , Laurent Trembleau
    • , Catherine H Botting
    • , Margaret C M Smith
    • , Marcel Jaspars
    •  & James H Naismith
  • Article |

    Piwi proteins bind a class of small germline RNAs, called piRNAs, whose biogenesis and functions are largely unknown. High-throughput sequencing after cross-linking and immunoprecipitation (HITS-CLIP) analysis in combination with RNA sequencing to analyze the genome-wide RNA target repertoire of mouse Piwi (Miwi) proteins in testis uncovers the in vivo piRNA biogenesis pathway and demonstrates that Miwi binds spermiogenic RNAs directly without using piRNAs as guides.

    • Anastassios Vourekas
    • , Qi Zheng
    • , Panagiotis Alexiou
    • , Manolis Maragkakis
    • , Yohei Kirino
    • , Brian D Gregory
    •  & Zissimos Mourelatos
  • Article |

    The post-transcriptional addition of uridyl ribonucleotides by terminal uridyltransferases (TUTases) to the ′A ends of various cytoplasmic RNAs, including microRNAs, has been implicated in regulating their stability, biogenesis or activity. The crystal structure of Schizosaccharomyces pombe TUTase Cid1 in its apo form and bound to UTP provides insight into the enzyme's active site, UTP selectivity and RNA-binding mechanism.

    • Luke A Yates
    • , Sophie Fleurdépine
    • , Olivia S Rissland
    • , Luigi De Colibus
    • , Karl Harlos
    • , Chris J Norbury
    •  & Robert J C Gilbert
  • Article |

    The general transcription factors TFIIE and TFIIH subunit Ssl2/XPB function in the transition of the preinitiation complex (PIC) to the open polymerase II (Pol II) complex. Efforts to localize TFIIE and Ssl2 in the yeast PIC now reveal crucial roles for the three TFIIE winged-helix domains and for Ssl2 in promoting DNA strand separation.

    • Sebastian Grünberg
    • , Linda Warfield
    •  & Steven Hahn
  • Article |

    How intrinsic stochasticity of gene expression is controlled is not well understood. A quantitative single-molecule analysis of transcription factor expression dynamics based on a new strategy (cotranslational activation by cleavage, or CoTrAC), sheds light on the mechanisms that cells use to control noise in gene regulatory networks.

    • Zach Hensel
    • , Haidong Feng
    • , Bo Han
    • , Christine Hatem
    • , Jin Wang
    •  & Jie Xiao
  • Article |

    LEDGF (p75) is a chromatin-binding protein implicated in cancer, autoimmune disease and HIV-1 pathogenesis, but its cellular function was still unclear. Now LEDGF is found to have a role in the repair of DNA double-stranded breaks via homologous recombination, promoting end resection by CtIP.

    • Mads Daugaard
    • , Annika Baude
    • , Kasper Fugger
    • , Lou Klitgaard Povlsen
    • , Halfdan Beck
    • , Claus Storgaard Sørensen
    • , Nikolaj H T Petersen
    • , Poul H B Sorensen
    • , Claudia Lukas
    • , Jiri Bartek
    • , Jiri Lukas
    • , Mikkel Rohde
    •  & Marja Jäättelä
  • Article |

    In Mycobacterium tuberculosis, the activity of a protein lysine acetyltransferase (PAT) is allosterically regulated by cAMP binding to a domain fused to the catalytic domain. Now the crystal structures of the autoinhibited and cAMP-activated PAT, along with biochemical analysis, reveal how allosteric regulation between independent protein domains can evolve.

    • Ho Jun Lee
    • , P Therese Lang
    • , Sarah M Fortune
    • , Christopher M Sassetti
    •  & Tom Alber
  • Article |

    Phosphorylation of residues in the N-terminal tail of histone H3 signals different biological outcomes. High-resolution NMR analyses now reveal a mechanistic hierarchy of H3 phosphorylation events, whereby phosphorylation of Ser10 impedes the phosphorylation of Thr6 and Thr11 by PKC and Chk1, respectively. Because both enzymes also target Ser10, this establishes an autoinhibitory feedback loop on H3 tails.

    • Stamatios Liokatis
    • , Alexandra Stützer
    • , Simon J Elsässer
    • , Francois-Xavier Theillet
    • , Rebecca Klingberg
    • , Barth van Rossum
    • , Dirk Schwarzer
    • , C David Allis
    • , Wolfgang Fischle
    •  & Philipp Selenko
  • Article |

    While the conserved translin–TRAX complex (also known as C3PO) functions as an endoribonuclease that promotes RNA interference (RNAi) in animal cells, new research shows that C3PO is not involved in RNAi in Neurospora crassa but instead functions as a ribonuclease that removes the 5′ pre-tRNA fragments after processing of pre-tRNAs by RNase P. This function may be conserved in mammals.

    • Liande Li
    • , Weifeng Gu
    • , Chunyang Liang
    • , Qinghua Liu
    • , Craig C Mello
    •  & Yi Liu

Brief Communications

  • Brief Communication |

    A systematic in vitro analysis of five different forms of cytosine in mammalian and yeast RNA polymerase II (Pol II) transcription demonstrates that Pol II can read and distinguish subtle differences in modified cytosines and process them differently, suggesting a putative functional interplay between cytosine modification status and transcription.

    • Matthew W Kellinger
    • , Chun-Xiao Song
    • , Jenny Chong
    • , Xing-Yu Lu
    • , Chuan He
    •  & Dong Wang
  • Brief Communication |

    The assembly of diverse immunoglobulin genes results in part from Rag protein–mediated DNA double-strand breaks at the edges of immunoglobulin gene segments, followed by the combinatorial reassembly of these segments. A transposase from the insect Helicoverpa zea is now shown to be active in vitro, and its breakage and joining activities resemble those of Rag, suggesting a common progenitor.

    • Cary G Hencken
    • , Xianghong Li
    •  & Nancy L Craig

Resources

  • Resource |

    How metazoans determine where to initiate DNA replication remains mysterious. Now deep sequencing of short nascent strands in different human cell types provides an extensive map of replication origins, identifying cell type–specific signatures and a putative consensus motif with the potential to form G-quadruplex structures.

    • Emilie Besnard
    • , Amélie Babled
    • , Laure Lapasset
    • , Ollivier Milhavet
    • , Hugues Parrinello
    • , Christelle Dantec
    • , Jean-Michel Marin
    •  & Jean-Marc Lemaitre
  • Resource |

    RNA 3′-end formation is thought to be crucial in controlling gene expression. Direct RNA sequencing was used to analyze the 3′ ends of Arabidopsis thaliana RNA in unprecedented detail, revealing extreme heterogeneity of RNA 3′ ends, patterns of cleavage and polyadenylation, and previously unrecognized noncoding RNAs.

    • Alexander Sherstnev
    • , Céline Duc
    • , Christian Cole
    • , Vasiliki Zacharaki
    • , Csaba Hornyik
    • , Fatih Ozsolak
    • , Patrice M Milos
    • , Geoffrey J Barton
    •  & Gordon G Simpson