Molecular biology articles within Nature

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  • 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

  • News & Views |

    It emerges that strings of nucleotides are added to messenger RNAs that are undergoing silencing in nematode worms. The composition of these nucleotide tails promotes the formation of small RNAs that drive heritable gene regulation.

    • Kailee J. Reed
    •  & Taiowa A. Montgomery

  • Article |

    A human–SARS-CoV-2 protein interaction map highlights cellular processes that are hijacked by the virus and that can be targeted by existing drugs, including inhibitors of mRNA translation and predicted regulators of the sigma receptors.

    • David E. Gordon
    • , Gwendolyn M. Jang
    •  & Nevan J. Krogan

  • Article |

    Cryo-electron microscopy structures of the DNA-binding domains of the pioneer transcription factor SOX2 and its close homologue SOX11 elucidate the role of these factors in initiating chromatin opening and nucleosome remodelling.

    • Svetlana O. Dodonova
    • , Fangjie Zhu
    •  & Patrick Cramer

  • Article |

    The detection of microorganism-associated ligands by plant cells activates a signalling cascade in which the kinase BIK1 is monoubiquinated, released from the FLS2–BAK1 complex, and internalized by endocytosis.

    • Xiyu Ma
    • , Lucas A. N. Claus
    •  & Libo Shan

  • Article |

    The authors provide high-resolution structures of two arenavirus polymerases, revealing that the active site of arenavirus polymerase is inherently switched on, without the requirement for allosteric activation by 5′-viral RNA, and that dimerization facilitates polymerase activity.

    • Ruchao Peng
    • , Xin Xu
    •  & Yi Shi

  • News & Views |

    Chromatin, the complex of DNA and protein in cell nuclei, can be modified by ubiquitin molecules. It emerges that this modification occurs in a molecular reaction chamber formed from an enzyme and a scaffold protein.

    • Nick Gilbert
    •  & Fred van Leeuwen

  • Article |

    Long noncoding RNAs and certain unstable transcripts tend to localize to chromatin, in a process that is shown here to depend on an RNA motif that recognizes the small nuclear ribonuclear protein U1, and to rely on transcription.

    • Yafei Yin
    • , J. Yuyang Lu
    •  & Xiaohua Shen

  • Article |

    The cryo-electron microscopy structure of the 16-subunit yeast SWI/SNF complex RSC in complex with a nucleosome substrate provides insights into the chromatin-remodelling function of this family of protein complexes.

    • Felix R. Wagner
    • , Christian Dienemann
    •  & Patrick Cramer

  • Article |

    The cryo-electron microscopy structure of the yeast SWI/SNF complex bound to a nucleosome substrate provides insights into the chromatin-remodelling function of this family of protein complexes and suggests mechanisms by which the mutated proteins may cause cancer.

    • Yan Han
    • , Alexis A Reyes
    •  & Yuan He

  • Article |

    The yeast E3 ligase Bre1 forms a core–shell condensate with the scaffold protein Lge1, implicating liquid–liquid phase separation as a mechanism in the ubiquitination of histone H2B along gene bodies.

    • Laura D. Gallego
    • , Maren Schneider
    •  & Alwin Köhler

  • Article |

    Cryo-EM structures of the FANCI–FANCD2 complex bound to DNA reveal that monoubiquitination triggers structural changes that enable the complex to function as a sliding DNA clamp and coordinate the repair of DNA interstrand crosslinks.

    • Renjing Wang
    • , Shengliu Wang
    •  & Nikola P. Pavletich

  • News & Views |

    A by-product of alcohol metabolism can damage the genome by crosslinking opposing DNA strands. The discovery of a safe mechanism that reverses such damage might open up avenues of research for drug discovery.

    • Irene Gallina
    •  & Julien P. Duxin

  • Article |

    Single-molecule visualization shows that condensin—a motor protein that extrudes DNA in one direction only—can encounter and pass a second condensin molecule to form a new type of DNA loop that gathers DNA from both sides.

    • Eugene Kim
    • , Jacob Kerssemakers
    •  & Cees Dekker

  • News & Views |

    A key DNA-repair enzyme has a surprising role during the early steps in the assembly of ribosomes — the molecular machines that translate the genetic code into protein.

    • Alan J. Warren

  • Technology Feature |

    A powerful set of molecular tools helps synthetic biologists to assemble DNA of different sizes, from the gene to the chromosome scale.

    • Michael Eisenstein

  • News & Views |

    The first 3D structure of a full-length G-protein-coupled receptor whose natural activator is unknown has been determined, providing insights into an unusual mode of activation and a basis for discovering therapeutics.

    • Brian Krumm
    •  & Bryan L. Roth

  • News & Views |

    The non-coding RNA Xist has been shown to enlist the SPEN protein to recruit a team of protein complexes — initiating the process that prevents transcription of one of the two X chromosomes found in female mammalian cells.

    • Jackson B. Trotman
    •  & J. Mauro Calabrese

  • News Feature |

    Making changes to the molecular messengers that create proteins might offer flexible therapies for cancer, pain or high cholesterol, in addition to genetic disorders.

    • Sara Reardon

  • Article |

    A combination of optical tweezers and fluorescent-particle tracking is used to dissect the dynamics of the Hsp100 disaggregase ClpB, and show that the processive extrusion of polypeptide loops is the mechanistic basis of its activity.

    • Mario J. Avellaneda
    • , Kamila B. Franke
    •  & Sander J. Tans

  • 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

  • Article |

    Structural studies on the yeast transcription coactivator complex SAGA (Spt–Ada–Gcn5–acetyltransferase) provide insights into the mechanism of initiation of regulated transcription by this multiprotein complex, which is conserved among eukaryotes.

    • Haibo Wang
    • , Christian Dienemann
    •  & Patrick Cramer

  • Article |

    The topoisomerase Top2 and the chromatin-binding protein Hmo1 maintain under-wound and over-wound DNA at different regions within a gene and thereby modulate the topology of genes.

    • Yathish Jagadheesh Achar
    • , Mohamood Adhil
    •  & Marco Foiani

  • Article |

    Structural studies on the yeast transcription coactivator complex SAGA (Spt–Ada–Gcn5–acetyltransferase) provide insights into the mechanism of initiation of regulated transcription by this multiprotein complex, which is conserved among eukaryotes.

    • Gabor Papai
    • , Alexandre Frechard
    •  & Adam Ben-Shem

  • Article |

    Mycobacterium tuberculosis suppresses the production of inflammatory cytokines by host cells through the host-mediated ubiquitination of a mycobacterial protein, enhancing the interaction of a host signalling inhibitor with another signalling molecule.

    • Lin Wang
    • , Juehui Wu
    •  & Baoxue Ge

  • Article |

    The crystal structure of the SA2–SCC1 subunits of human cohesin in complex with CTCF reveals the molecular basis of the cohesin–CTCF interaction that enables the dynamic regulation of chromatin folding.

    • Yan Li
    • , Judith H. I. Haarhuis
    •  & Daniel Panne

  • Article |

    DNA replication in eukaryotes requires the histone variant H2A.Z, which binds the enzyme SUV420H1 to promote the dimethylation of histone H4, in turn recruiting the origin-recognition complex to activate early replication origins.

    • Haizhen Long
    • , Liwei Zhang
    •  & Guohong Li

  • Article |

    Cryo-electron microscopy structures of the TniQ–Cascade complex encoded by the Vibrio cholerae Tn6677 transposon reveal the mechanistic basis of the functional association of CRISPR- and transposon-associated machineries.

    • Tyler S. Halpin-Healy
    • , Sanne E. Klompe
    •  & Israel S. Fernández

  • Article |

    Single-cell mapping of chromatin accessibility, DNA methylation and RNA expression during gastrulation in mouse embryos shows characteristic epigenetic changes that accompany formation of the primary germ layers.

    • Ricard Argelaguet
    • , Stephen J. Clark
    •  & Wolf Reik

  • Obituary |

    Biochemist whose discoveries led to faster, more-accurate DNA testing.

    • Jesús Avila
    • , Federico Mayor
    •  & Lourdes Ruiz-Desviat

  • Article |

    Analyses of primary and relapse samples of embryonal tumours with multilayered rosettes provide insights into the molecular mechanisms that underlie the development and opportunities for the treatment of this deadly disease.

    • Sander Lambo
    • , Susanne N. Gröbner
    •  & Marcel Kool

  • Article |

    Chaperones interact with a canonical motif in α-synuclein, which can be prevented by phosphorylation of α-synuclein at Tyr39, whereas inhibition of this interaction leads to the localization of α-synuclein to the mitochondria and aggregate formation.

    • Björn M. Burmann
    • , Juan A. Gerez
    •  & Sebastian Hiller

  • Article |

    A subpopulation of Caenorhabditis elegans, in which there is a naturally occurring transient increase in reactive oxygen species during early development, exhibits increased stress resistance, improved redox homeostasis and prolonged lifespan, which are linked to a global decrease in level of the histone mark H3K4me3.

    • Daphne Bazopoulou
    • , Daniela Knoefler
    •  & Ursula Jakob

  • Article |

    Two cryo-electron-microscopy images of the histone chaperone FACT interacting with components of nucleosomes shed light on how FACT manipulates nucleosomes to promote transcription, DNA repair and DNA replication.

    • Yang Liu
    • , Keda Zhou
    •  & Karolin Luger

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