Non-coding RNAs articles within Nature

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  • Article |

    A set of 34 excised introns in Saccharomyces cerevisiae, characterized by having a short distance between the lariat branch point and the 3′ splice site, have a biological function within the TOR growth-signalling network.

    • Jeffrey T. Morgan
    • , Gerald R. Fink
    •  & David P. Bartel

  • 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

  • News & Views |

    Manipulation of host-cell metabolism is an essential aspect of viral replication cycles. Viral co-option of a cellular long non-protein-coding RNA has now been found to be a key step in this process.

    • Nicholas S. Heaton
    •  & Bryan R. Cullen

  • Article |

    A 22-nucleotide fragment of a transfer RNA regulates translation by binding to the mRNA of a ribosomal protein and increasing its expression, and downregulation of the fragment in patient-derived liver tumour cells reduces tumour growth in mice.

    • Hak Kyun Kim
    • , Gabriele Fuchs
    •  & Mark A. Kay

  • News & Views |

    Flies use master lists of DNA sequences from transposons to identify and silence these virus-like, genomic parasites. How the lists themselves escape the fate of their transposon targets has now been solved. See Letter p.54

    • Phillip D. Zamore

  • Article |

    Transcription of Drosophila PIWI-interacting RNA (piRNA) clusters is enforced through RNA polymerase II pre-initiation complex formation within repressive heterochromatin, accomplished through the transcription factor IIA subunit paralogue Moonshiner.

    • Peter Refsing Andersen
    • , Laszlo Tirian
    •  & Julius Brennecke

  • News & Views |

    Ultraviolet light can damage DNA, triggering a general shutdown of gene transcription — yet some genes are activated by UV light. An investigation of this counter-intuitive behaviour reveals a surprising gene-regulation mechanism.

    • Antonio Conconi
    •  & Brendan Bell

  • News & Views |

    It emerges that nascent non-coding RNAs transcribed from regulatory DNA sequences called enhancers bind to the enzyme CBP to promote its activity locally. In turn, the activities of CBP stimulate further enhancer transcription.

    • Karen Adelman
    •  & Emily Egan

  • Technology Feature |

    As researchers open up to the reality of RNA modification, an expanded epitranscriptomics toolbox takes shape.

    • Kelly Rae Chi

  • News & Views |

    Production of the cell's translational apparatus, the ribosome, requires the orchestrated function of hundreds of proteins. A structure of its earliest precursor yields unprecedented insight into ribosome formation.

    • Marlene Oeffinger

  • Letter |

    The activation of lipid X receptors (LXRs) in mouse liver not only promotes cholesterol efflux but also inhibits cholesterol synthesis simultaneously; this is mediated by the lipid-responsive long non-coding RNA LeXis, which is induced by a Western diet and orchestrates crosstalk between LXRs and the cholesterol biosynthetic pathway.

    • Tamer Sallam
    • , Marius C. Jones
    •  & Peter Tontonoz

  • Letter |

    A known oncogene, MITF, resides in a region of chromosome 3 that is amplified in melanomas and associated with poor prognosis; now, a long non-coding RNA gene, SAMMSON, is shown to also lie in this region, to also act as a melanoma-specific survival oncogene, and to be a promising therapeutic target for anti-melanoma therapy.

    • Eleonora Leucci
    • , Roberto Vendramin
    •  & Jean-Christophe Marine

  • 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

  • Article |

    The ability of the DEAD-box RNA helicase DDX5 to interact with master transcription factor RORγt is dependent on binding of the long noncoding RNA Rmrp; the DDX5–RORγt complex coordinates transcription of selective TH17 genes and is required for the pathogenicity of TH17 cells.

    • Wendy Huang
    • , Benjamin Thomas
    •  & Dan R. Littman

  • Article |

    RNA polymerase III (Pol III), the largest eukaryote polymerase yet characterized, transcribes structured small non-coding RNAs; here cryo-electron microscopy structures of budding yeast Pol III allow building of an atomic-level model of the complete 17-subunit complex, both unbound and while elongating RNA.

    • Niklas A. Hoffmann
    • , Arjen J. Jakobi
    •  & Christoph W. Müller

  • News & Views |

    A screen for compounds that block a bacterial biosynthetic pathway has uncovered an antibiotic lead that shuts off pathogen growth by targeting a molecular switch in a regulatory RNA structure. See Article p.672

    • Thomas Hermann

  • Letter |

    This study demonstrates a role for the Integrator complex in the stimulus-dependent induction of eRNAs and their 3′ processing; together with previously known roles of Integrator in transcription elongation and RNA processing, these results indicate that Integrator has broad functions in the regulation of eukaryotic gene expression.

    • Fan Lai
    • , Alessandro Gardini
    •  & Ramin Shiekhattar

  • News Feature |

    Cells contain an ocean of twisting and turning RNA molecules. Now researchers are working out the structures — and how important they could be.

    • Elie Dolgin

  • News & Views |

    Two new techniques identify proteins that directly interact with a non-protein-coding RNA called Xist to mediate inactivation of one X chromosome in female mammals. See Letter p.232

    • Anna Roth
    •  & Sven Diederichs

  • Letter |

    The mechanisms by which Xist, a long non-coding RNA, silences one X chromosome in female mammals are unknown; here a mass spectrometry-based approach is developed to identify several proteins that interact directly with Xist, including the transcriptional repressor SHARP that is required for transcriptional silencing through the histone deacetylase HDAC3.

    • Colleen A. McHugh
    • , Chun-Kan Chen
    •  & Mitchell Guttman

  • News & Views |

    The discovery of peptides encoded by what were thought to be non-coding – or 'junk' – regions of precursors to microRNA sequences reveals a new layer of gene regulation. These sequences may not be junk, after all. See Letter p.90

    • Peter M. Waterhouse
    •  & Roger P. Hellens

  • Letter |

    Plant primary microRNA (miRNA) transcripts (pri-miRNAs) are not just a source of miRNAs but can also encode regulatory peptides (miPEPs) that enhance the accumulation, and so the effect, of the corresponding mature miRNAs—an observation that may have agronomical applications.

    • Dominique Lauressergues
    • , Jean-Malo Couzigou
    •  & Jean-Philippe Combier

  • Letter |

    The addition of the N6-methyladenosine (m6A) mark to primary microRNAs by METTL3 in mammalian cells is found to promote the recognition of these microRNA precursors by DGCR8, a component of the microprocessor complex.

    • Claudio R. Alarcón
    • , Hyeseung Lee
    •  & Sohail F. Tavazoie

  • Letter |

    A eukaryotic viral internal ribosome entry site (IRES) element is described that binds both bacterial and eukaryotic ribosomes and initiates translation in both, demonstrating that RNA structure-based initiation can occur in both these domains of life, although in bacteria the element uses a mechanism that differs from that in eukaryotes.

    • Timothy M. Colussi
    • , David A. Costantino
    •  & Jeffrey S. Kieft

  • Letter |

    A newly developed method, NAD captureSeq, has been used to show that bacteria cap the 5′-ends of some RNAs to protect against degradation, much as happens with eukaryotic messenger RNAs, although with a different modification: nicotinamide adenine dinucleotide.

    • Hana Cahová
    • , Marie-Luise Winz
    •  & Andres Jäschke

  • Letter |

    DEAD-box RNA helicase DDX21 is involved in both the transcription and RNA processing of ribosomal genes in human cells, sensing the transcriptional status of both RNA polymerase I and RNA polymerase II and associating with non-coding RNAs involved in ribonucleoprotein formation, possibly allowing for coordinated regulation of protein synthesis.

    • Eliezer Calo
    • , Ryan A. Flynn
    •  & Joanna Wysocka

  • Letter |

    The transcriptions of frq sense and antisense RNAs are mutually inhibitory and form a double negative feedback loop required for robust and sustained circadian rhythmicity: antisense transcription inhibits sense expression by causing chromatin modifications and premature transcription termination.

    • Zhihong Xue
    • , Qiaohong Ye
    •  & Yi Liu

  • Letter |

    The CRISPR/Cas system is an RNA-guided bacterial protection system against foreign nucleic acids of bacterial and archaeal origin; here a high-resolution crystal structure of the CRIPSR RNA–Cas complex shows that the CRIPSR RNA plays an essential role not only in target recognition but also in complex assembly.

    • Hongtu Zhao
    • , Gang Sheng
    •  & Yanli Wang

  • Letter |

    Here, a long noncoding RNA, termed Mhrt, is identified in the loci of myosin heavy chain (Myh) genes in mice and shown to be capable of suppressing cardiomyopathy in the animals, as well as being repressed in diseased human hearts.

    • Pei Han
    • , Wei Li
    •  & Ching-Pin Chang

  • Letter |

    The 11-subunit RNA exosome is thought to regulate the mammalian noncoding transcriptome; here, a mouse model is generated in which the essential Exosc3 subunit of the RNA exosome in B cells is conditionally deleted, revealing a link between sites of genomic RNA exosome function and AID-mediated chromosomal translocations.

    • Evangelos Pefanis
    • , Jiguang Wang
    •  & Uttiya Basu

  • Letter |

    Crystal structure of the RNA-guided endonuclease Cas9 bound to a guide RNA and a target DNA duplex reveals how base-specific recognition of a short motif known as PAM in the DNA target results in localized strand separation in the DNA immediately upstream of the PAM, allowing the target DNA strand to hybridize to the guide RNA.

    • Carolin Anders
    • , Ole Niewoehner
    •  & Martin Jinek

  • Article |

    Programmed −1 ribosomal frameshifting (−1 PRF) is a process by which a signal in a messenger RNA causes a translating ribosome to shift by one nucleotide, thus changing the reading frame; here −1 PRF in the mRNA for the co-receptor for HIV-1, CCR5, is stimulated by two microRNAs and leads to degradation of the transcript by nonsense-mediated decay and at least one other decay pathway.

    • Ashton Trey Belew
    • , Arturas Meskauskas
    •  & Jonathan D. Dinman

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