RNAi

  • Article |

    The RNA polymerase from the crAss-like bacteriophage phi14:2, which is translocated into the host cell with phage DNA and transcribes early phage genes, is structurally most similar to eukaryotic RNA interference polymerases, suggesting that the latter have a phage origin.

    • Arina V. Drobysheva
    • , Sofia A. Panafidina
    •  & Maria L. Sokolova
  • Article |

    Exposing Caenorhabditis elegans to non-coding small RNAs from pathogenic Pseudomonas aeruginosa induces avoidance behaviours in treated worms and their progeny, which reveals how C. elegans discriminates between bacterial species in its microbial environment.

    • Rachel Kaletsky
    • , Rebecca S. Moore
    •  & Coleen T. Murphy
  • Article |

    Argonaute protein from the bacterium C. butyricum targets multicopy genetic elements and functions in the suppression of plasmid and phage propagation, and there appears to be a DNA-mediated immunity pathway in prokaryotes.

    • Anton Kuzmenko
    • , Anastasiya Oguienko
    •  & Andrey Kulbachinskiy
  • Article |

    Repression of a messenger RNA by a cognate microRNA depends not only on complementary base pairing, but also on the rearrangement of a single base pair, producing a conformation that fits better within the human Ago2 protein.

    • Lorenzo Baronti
    • , Ileana Guzzetti
    •  & Katja Petzold
  • Article |

    In Caenorhabditis elegans, the ribonucleotidyltransferase RDE-3 adds alternating uridine and guanosine ribonucleotides to the 3′ termini of RNAs, a key step in RNA interference and thus epigenetic inheritance in the C. elegans germline.

    • Aditi Shukla
    • , Jenny Yan
    •  & Scott Kennedy
  • Article |

    ZNFX-1 and WAGO-4 localize to germ granules in early Caenorhabditis elegans embryogenesis and later separate to form independent liquid-like droplets, and the temporal and spatial ordering of these droplets may help cells to organize complex RNA processing pathways.

    • Gang Wan
    • , Brandon D. Fields
    •  & Scott Kennedy
  • Letter |

    An in vivo RNA interference screening strategy in glioblastoma enabled the identification of a host of epigenetic targets required for glioblastoma cell survival that were not identified by parallel standard screening in cell culture, including the transcription pause–release factor JMJD6, and could be a powerful tool to uncover new therapeutic targets in cancer.

    • Tyler E. Miller
    • , Brian B. Liau
    •  & Jeremy N. Rich
  • Article |

    The application of genome-wide CRISPR–Cas9 screening coupled with a fluorescent reporter to interrogate the microRNA pathway reveals that continual transient phosphorylation of Argonaute 2 is required to maintain the global efficiency of microRNA-mediated repression.

    • Ryan J. Golden
    • , Beibei Chen
    •  & Joshua T. Mendell
  • Letter |

    Drosophila have two pathways for PIWI-interacting RNA (piRNA) 3′-end formation—depending on which pathway is used, piRNA biogenesis is directed towards either cytoplasmic or nuclear PIWI protein effectors, which balances post-transcriptional versus transcriptional transposon silencing.

    • Rippei Hayashi
    • , Jakob Schnabl
    •  & Julius Brennecke
  • Letter |

    Maternal mRNAs are tethered within the Drosophila germ plasm via base-pairing interactions between mRNAs and piRNPs containing the Aub Piwi protein; the preference for certain mRNAs to be tethered appears to be related to their longer length, which provides more potential piRNP-binding sites, and the results suggest a new role for piRNAs in germ-cell specification independent of their role in transposon silencing.

    • Anastassios Vourekas
    • , Panagiotis Alexiou
    •  & Zissimos Mourelatos
  • Letter |

    Splicing factors such as BUD31 are identified in a synthetic-lethal screen with cells overexpressing the transcription factor MYC; oncogenic MYC leads to an increase in pre-mRNA synthesis, and spliceosome inhibition impairs the growth and tumorigenicity of MYC-dependent breast cancers, suggesting that spliceosome components may be potential therapeutic targets for MYC-driven cancers.

    • Tiffany Y.-T. Hsu
    • , Lukas M. Simon
    •  & Thomas F. Westbrook
  • Letter |

    The assembly of single Drosophila RNA-induced silencing complexes (RISCs) is reconstituted using seven purified proteins, revealing that chaperones help stabilize the interaction of the protein heterodimer Dicer-2–R2D2 bound to the short interfering RNA with Ago2.

    • Shintaro Iwasaki
    • , Hiroshi M. Sasaki
    •  & Yukihide Tomari
  • Letter |

    The fission yeast is shown to have a mechanism to prevent small RNAs from inducing heterochromatin and epigenetic gene silencing; this protective model involves the highly conserved Paf1 complex, which is known to promote transcription and processing of pre-mRNA, and protects protein-coding genes from unwanted silencing by spurious transcripts.

    • Katarzyna Maria Kowalik
    • , Yukiko Shimada
    •  & Marc Bühler
  • Letter |

    The structure of mouse Dis3l2 bound to an oligoU substrate shows a funnel-like substrate-binding site with the RNA being fed into the active site along a path that is distinct from that seen in the related catalytic subunit of the exosome — 12 uracils of the oligoU-tailed RNA are recognized in a complex network of interactions, suggesting the basis for target specificity.

    • Christopher R. Faehnle
    • , Jack Walleshauser
    •  & Leemor Joshua-Tor
  • Letter |

    The human fungal pathogen Mucor circinelloides develops spontaneous resistance to an antifungal drug both through mutation and through a newly identified epigenetic RNA-mediated pathway; RNA interference is spontaneously triggered to silence the fkbA gene, giving rise to drug-resistant epimutants that revert to being drug-sensitive once again when grown in the absence of drug.

    • Silvia Calo
    • , Cecelia Shertz-Wall
    •  & Joseph Heitman
  • Article |

    The molecular basis for mating-type determination in the ciliate Paramecium has been elucidated, revealing a novel function for a class of small RNAs — these scnRNAs are typically involved in reprogramming the Paramecium genome during sexual reproduction by recognizing and excising transposable elements, but they are now found to be co-opted to switch off expression of the newly identified mating-type gene mtA by excising its promoter, and to mediate epigenetic inheritance of mating types across sexual generations.

    • Deepankar Pratap Singh
    • , Baptiste Saudemont
    •  & Eric Meyer
  • Letter |

    A mouse model of T-cell leukaemia is used to test whether PTEN loss is required for tumour maintenance as well as initiation; although it had little effect on tumour load in haematopoietic organs, PTEN reactivation reduced the CCR9-dependent tumour dissemination to the intestine that was amplified on PTEN loss, exposing the importance of tumour microenvironment in PTEN-deficient settings.

    • Cornelius Miething
    • , Claudio Scuoppo
    •  & Scott W. Lowe
  • Letter |

    Here, Argonaute from the prokaryote Thermus thermophilus is shown to use small DNA guides to interfere directly with invading foreign DNA, rather than being involved in RNA-guided RNA interference, as observed in eukaryotes.

    • Daan C. Swarts
    • , Matthijs M. Jore
    •  & John van der Oost
  • Article |

    Here, the first genome-wide in vivo RNA interference screens in a mammalian animal model are reported: genes involved in normal and abnormal epithelial cell growth are studied in developing skin tissue in mouse embryos, and among the findings, β-catenin is shown to act as an antagonist to normal epithelial cell growth as well as promoting oncogene-driven growth.

    • Slobodan Beronja
    • , Peter Janki
    •  & Elaine Fuchs
  • Letter |

    The CRISPR/Cas system known to aid bacterial defences by targeting invading DNA can also act to evade eukaryotic defences through a different class of small RNAs downregulating an endogenous immunogenic bacterial lipoprotein.

    • Timothy R. Sampson
    • , Sunil D. Saroj
    •  & David S. Weiss
  • Letter |

    In the fission yeast Schizosaccharomyces pombe RNA interference (RNAi) machinery promotes heterochromatin assembly and silencing of centromeric repeats; here it is shown that RNAi participates in silencing other genomic regions, such as sexual differentiation genes and retrotransposons, and this process is regulated by developmental and environmental signals.

    • Soichiro Yamanaka
    • , Sameet Mehta
    •  & Shiv I. S. Grewal
  • Letter |

    Double-stranded RNA interference (RNAi) in Caenorhabditis elegans is heritable; here a genetic screen for factors required for RNAi inheritance identifies the nuclear-localized Argonaute gene hrde-1, which acts in the germ cells of progeny to promote multigenerational inheritance of silencing and, also, germline immortality.

    • Bethany A. Buckley
    • , Kirk B. Burkhart
    •  & Scott Kennedy
  • Article |

    Argonaute proteins are an essential part of the guide-RNA–protein complex that carries out RNA-induced gene silencing; structure–function studies of the yeast complex reveal conserved features of the eukaryotic complex, which underlie formation of the catalytically active conformation.

    • Kotaro Nakanishi
    • , David E. Weinberg
    •  & Dinshaw J. Patel
  • Letter |

    Five current human African trypanosomiasis drugs are used for genome-scale RNA interference target sequencing screens in Trypanosoma brucei, and reveal the transporters, organelles, enzymes and metabolic pathways that function to facilitate antitrypanosomal drug action.

    • Sam Alsford
    • , Sabine Eckert
    •  & David Horn
  • Letter |

    Realizing the full potential of human embryonic stem cells (hESCs) in research and clinical applications requires a detailed understanding of the genetic network that governs their unique properties. A genome-wide RNA interference screen identifies a wealth of new regulators of self-renewal and pluripotency properties in hESCs. The transcription factor PRDM14, for example, is required for the maintenance of hESC identity and reprogramming of somatic cells to pluripotency.

    • Na-Yu Chia
    • , Yun-Shen Chan
    •  & Huck-Hui Ng
  • Article |

    The uptake of calcium by mitochondria has a central role in cell physiology, and an imbalance can trigger cell death. Now the first protein that is localized to the mitochondrion and is specifically required for calcium uptake has been identified. This protein, mitochondrial calcium uptake 1 (MICU1), represents the founding member of a set of proteins required for high-capacity calcium uptake. Its discovery should aid in the full molecular characterization of the mitochondrial calcium uptake pathways.

    • Fabiana Perocchi
    • , Vishal M. Gohil
    •  & Vamsi K. Mootha
  • Letter |

    Primary cilia are tiny hair-like structures expressed on the surface of eukaryotic cells. They participate in a range of processes, such as sensing the extracellular environment and regulating signalling pathways during development. Here, a functional genomic screen is presented that used RNA interference to identify human genes involved in controlling ciliogenesis. Several positive and negative ciliogenesis modulators with broad-ranging functions were found.

    • Joon Kim
    • , Ji Eun Lee
    •  & Joseph G. Gleeson
  • Letter |

    High mutation rates in the influenza A virus facilitate the generation of viral escape mutants, rendering vaccines and drugs potentially ineffective, but targeting host cell determinants could prevent viral escape. Here, 287 human host cell genes influencing influenza A virus replication are found using a genome-wide RNA interference screen. An independent assay is then used to investigate overlap between genes necessary for different viral strains.

    • Alexander Karlas
    • , Nikolaus Machuy
    •  & Thomas F. Meyer