RNA articles within Nature

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  • Article
    | Open Access

    Cryo-electron microscopy structures of intermediates formed during the degradation of the 30S ribosomal unit shed light on how the 3′ to 5′ exonuclease ribonuclease R controls the ribosomal degradation process.

    • Lyudmila Dimitrova-Paternoga
    • , Sergo Kasvandik
    •  & Helge Paternoga

  • Article
    | Open Access

    Human LINE-1 ORF2p relies on upstream single-stranded target DNA to position the adjacent duplex in the endonuclease active site for nicking of the longer DNA strand, with a single nick generating a staggered DNA break.

    • Akanksha Thawani
    • , Alfredo Jose Florez Ariza
    •  & Kathleen Collins

  • Article |

    The accuracy of eukaryotic ribosome translocation relies on eukaryote-specific elements of the 80S ribosome, elongation factor 2 and transfer RNAs, all of which contribute to the maintenance of the messenger RNA reading frame.

    • Nemanja Milicevic
    • , Lasse Jenner
    •  & Gulnara Yusupova

  • Article
    | Open Access

    Analysis of the group II intron ribonucleoprotein shows the molecular interactions involved in branchpoint adenosine recognition, lariat formation and exon ligation, providing clues to the evolutionary conservation of structural components and catalytic mechanisms in premessenger RNA splicing.

    • Ling Xu
    • , Tianshuo Liu
    •  & Anna Marie Pyle

  • Article
    | Open Access

    The Bacteroides fragilis type III CRISPR protein Cmr conjugates ATP to S-adenosyl methionine, generating S-adenosyl methionine (SAM)-AMP, a novel second messenger with a role in antiviral signalling.

    • Haotian Chi
    • , Ville Hoikkala
    •  & Malcolm F. White

  • Article
    | Open Access

    The endoribonuclease PUCH, a trimer of Schlafen-like-domain proteins, initiates piRNA processing in the nematode Caenorhabditis elegans through 5′-end piRNA precursor cleavage.

    • Nadezda Podvalnaya
    • , Alfred W. Bronkhorst
    •  & René F. Ketting

  • Article
    | Open Access

    Bacteriophage T4 uses an enzyme known as ADP-ribosyltransferase ModB to modify the translational apparatus of bacteria it infects, not only by ADP-ribosylating proteins, but also by attaching entire RNA chains in a process known as RNAylation.

    • Maik Wolfram-Schauerte
    • , Nadiia Pozhydaieva
    •  & Katharina Höfer

  • Article |

    Cryo-electron microscopy structures and biochemical analyses provide insight into how short prokaryotic Argonaute proteins are assembled and activated, and reveal that oligomerization has a key role in driving catalytic activity.

    • Zhangfei Shen
    • , Xiao-Yuan Yang
    •  & Tian-Min Fu

  • Article |

    Hepatitis C virus utilizes flavin adenine dinucleotide as a non-canonical initiating nucleotide for the viral RNA polymerase, resulting in 5′ capping of viral RNA, which provides protection against the host innate immune response.

    • Anna V. Sherwood
    • , Lizandro R. Rivera-Rangel
    •  & Jeppe Vinther

  • Article
    | Open Access

    Of the two types of Argonaute proteins produced by animals, AGO and PIWI, PIWI proteins can bind RNAs with less complementarity, enabling efficient silencing of transposons without the need to produce new RNA guides.

    • Ildar Gainetdinov
    • , Joel Vega-Badillo
    •  & Phillip D. Zamore

  • Article |

    Systematic alteration of HIV-1 TAR RNA and quantitative determination of its propensity to bind to the Tat protein establish a key role role for a rare and short-lived RNA state in Tat-dependent transactivation in cells.

    • Megan L. Ken
    • , Rohit Roy
    •  & Hashim M. Al-Hashimi

  • Article
    | Open Access

    Structural analysis of Cas12a2, a CRISPR-associated nuclease that nonspecifically cleaves ssRNA, ssDNA and dsDNA, reveals a complete activation pathway involved in the abortive infection system protecting cells against invasion.

    • Jack P. K. Bravo
    • , Thomson Hallmark
    •  & David W. Taylor

  • Article
    | Open Access

    RNA targeting by the Sulfuricurvum type V single-effector nuclease SuCas12a2 drives abortive infection through non-specific cleavage of double-stranded DNA—after recognition of an RNA target through an activating protospacer-flanking sequence, SuCas12a2 efficiently degrades ssRNA, ssDNA and dsDNA.

    • Oleg Dmytrenko
    • , Gina C. Neumann
    •  & Chase L. Beisel

  • Article
    | Open Access

    Reconstitution of the SARS-CoV-2 RNA 5′ cap reveals the unconventional mechanism by which SARS-CoV-2 caps its RNA genome, providing a new target in the development of antiviral agents to treat COVID-19.

    • Gina J. Park
    • , Adam Osinski
    •  & Vincent S. Tagliabracci

  • Article
    | Open Access

    The evolutionarily conserved RNA-binding protein GTSF1 and its homologues interact with members of the PIWI class of Argonaute proteins, increasing the efficiency of the RNA-cleaving activity of PIWI proteins, an essential function across the animal kingdom.

    • Amena Arif
    • , Shannon Bailey
    •  & Phillip D. Zamore

  • Article
    | Open Access

    Structures of the Dcr-2–Loqs-PD complex while it is processing a double-stranded RNA (dsRNA) substrate elucidate the interactions between Dcr-2 and Loqs-PD, and show that Dcr-2 undergoes substantial conformational changes during a dsRNA-processing cycle.

    • Shichen Su
    • , Jia Wang
    •  & Jinbiao Ma

  • Article
    | Open Access

    Cryo-electron microscopy structures of Drosophila Dicer-2–R2D2 complexes with and without small interfering RNA reveal how the RNA is presented to Argonaute in the correct orientation for viral gene silencing.

    • Sonomi Yamaguchi
    • , Masahiro Naganuma
    •  & Osamu Nureki

  • Article |

    Single-molecule spectroscopy and structural studies were used to examine the dynamics of association of eIF1A and eIF5B with the human translation initiation complex and their role in presenting tRNA to the complex to initiate translation.

    • Christopher P. Lapointe
    • , Rosslyn Grosely
    •  & Joseph D. Puglisi

  • Article |

    Herpesvirus microRNAs interfere directly with host cell microRNA processing, thereby disrupting mitochondrial architecture, evading intrinsic host defences and driving the switch from latent to lytic infection.

    • Thomas Hennig
    • , Archana B. Prusty
    •  & Bhupesh K. Prusty

  • Article |

    A high-resolution structure of human telomerase bound to telomeric DNA reveals details of telomerase assembly and its active site, and sheds light on how mutations alter telomerase function.

    • George E. Ghanim
    • , Adam J. Fountain
    •  & Thi Hoang Duong Nguyen

  • Article |

    Time-resolved RNA–protein cross-linking with a pulsed femtosecond ultraviolet laser, followed by immunoprecipitation and high-throughput sequencing, enables the determination of binding and dissociation kinetics of the RNA-binding protein DAZL within cells.

    • Deepak Sharma
    • , Leah L. Zagore
    •  & Eckhard Jankowsky

  • Article |

    Single-stranded, DNA-damage-associated small RNAs generated by a BRCA1–RNA-interference complex promote PALB2–RAD52-mediated DNA repair at transcriptional termination pause sites that contain R-loops and are rich in single-stranded DNA breaks in both quiescent and proliferating cells.

    • Elodie Hatchi
    • , Liana Goehring
    •  & David M. Livingston

  • Article |

    A methyltransferase ribozyme, along with the small-molecule cofactor O6-methylguanine, is shown to catalyse the site-specific installation of 1-methyladenosine in various RNAs, providing insights into the catalytic abilities of RNA.

    • Carolin P. M. Scheitl
    • , Mohammad Ghaem Maghami
    •  & Claudia Höbartner

  • Article |

    Telomeric-repeat-containing RNA is recruited to telomeres by a mechanism that involves the DNA recombinase RAD51 and the formation of DNA–RNA hybrids, or R-loops—a process similar to that involved in homology-directed DNA repair.

    • Marianna Feretzaki
    • , Michaela Pospisilova
    •  & Joachim Lingner

  • Article |

    A protein condensate formed by multivalent interactions between the long non-coding RNA Xist and specific RNA-binding proteins drives the compartmentalization required to perpetuate gene silencing on the inactive X chromosome.

    • Amy Pandya-Jones
    • , Yolanda Markaki
    •  & Kathrin Plath

  • Article |

    Time-resolved cryogenic electron microscopy structures of a ribosome during the delivery of aminoacyl-tRNA by EF-Tu•GTP capture 33 ribosomal states, enabling visualization of the initial selection, proofreading and peptidyl transfer stages.

    • Anna B. Loveland
    • , Gabriel Demo
    •  & Andrei A. Korostelev

  • 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 |

    A cryo-electron microscopy structure of the RNA-dependent RNA polymerase of SARS-CoV-2 sheds light on coronavirus replication and enables the analysis of the inhibitory mechanisms of candidate antiviral drugs.

    • Hauke S. Hillen
    • , Goran Kokic
    •  & Patrick Cramer

  • Article |

    Analyses of mouse models of inflammation suggest some chronic inflammatory conditions may result from Z-DNA-binding protein 1 sensing endogenous Z-form nucleic acids—such as those of endogenous retroelements—through its Zα domains.

    • Huipeng Jiao
    • , Laurens Wachsmuth
    •  & Manolis Pasparakis

  • Article |

    A silkworm model recapitulates key steps of Zucchini-mediated cleavage of pre-pre-piRNA and provides insights into Zucchini-mediated and -independent pathways that generate pre-piRNAs, which converge to a common piRNA maturation step.

    • Natsuko Izumi
    • , Keisuke Shoji
    •  & Yukihide Tomari

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