Molecular biology articles within Nature

Featured

  • Article |

    The PARP2–HPF1 histone-modifying complex bridges two nucleosomes to align broken DNA ends for ligation, initiating conformational changes that activate PARP2 and enable DNA damage repair.

    • Silvija Bilokapic
    • , Marcin J. Suskiewicz
    •  & Mario Halic

  • 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 |

    A high-resolution map of coding regions in the SARS-CoV-2 genome enables the identification of 23 unannotated open reading frames and quantification of the expression of canonical viral open reading frames.

    • Yaara Finkel
    • , Orel Mizrahi
    •  & Noam Stern-Ginossar

  • 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 |

    Fission yeast grown in sublethal levels of caffeine develop heterochromatin-dependent epimutations conferring unstable heritable gene silencing that conveys resistance to caffeine, while remaining genetically wild type.

    • Sito Torres-Garcia
    • , Imtiyaz Yaseen
    •  & Robin C. Allshire

  • Article |

    Single-cell RNA-sequencing analysis of embryogenesis and X chromosome inactivation in the opossum (Monodelphis domestica) resolves the developmental trajectory of a marsupial, and sheds light on the evolution of embryogenesis in mammals.

    • Shantha K. Mahadevaiah
    • , Mahesh N. Sangrithi
    •  & James M. A. Turner

  • Article |

    Structural studies of the dimerization quality control E3 ubiquitin ligase SCF–FBXL17 indicate that its selectivity for aberrant complex formation is based on recognizing both shape and complementarity of interacting domains.

    • Elijah L. Mena
    • , Predrag Jevtić
    •  & Michael Rape

  • Article |

    During the activation of mouse macrophages by lipopolysaccharides, histone deacetylase 3 controls inflammatory responses by both repressing and activating gene transcription depending on its differential association with transcription factors.

    • Hoang C. B. Nguyen
    • , Marine Adlanmerini
    •  & Mitchell A. Lazar

  • 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

  • Perspective |

    The authors summarize the history of the ENCODE Project, the achievements of ENCODE 1 and ENCODE 2, and how the new data generated and analysed in ENCODE 3 complement the previous phases.

    • Federico Abascal
    • , Reyes Acosta
    •  & Richard M. Myers

  • Article
    | Open Access

    A map of cohesin-mediated chromatin loops in 24 types of human cells identifies loops that show cell-type-specific variation, indicating that chromatin loops may help to specify cell-specific gene expression programs and functions.

    • Fabian Grubert
    • , Rohith Srivas
    •  & Michael Snyder

  • Article |

    The chromatin protein MeCP2 is a component of dynamic, liquid-like heterochromatin condensates, and the ability of MeCP2 to form condensates is disrupted by mutations in the MECP2 gene that occur in the neurodevelopmental disorder Rett syndrome.

    • Charles H. Li
    • , Eliot L. Coffey
    •  & Richard A. Young

  • Article |

    The histone variant H3.3 is phosphorylated at Ser31 in induced genes, and this selective mark stimulates the histone methyltransferase SETD2 and ejects the ZMYND11 repressor, thus revealing a role for histone phosphorylation in amplifying de novo transcription.

    • Anja Armache
    • , Shuang Yang
    •  & Steven Z. Josefowicz

  • Article |

    Bulk RNA sequencing of organs and plasma proteomics at different ages across the mouse lifespan is integrated with data from the Tabula Muris Senis, a transcriptomic atlas of ageing mouse tissues, to describe organ-specific changes in gene expression during ageing.

    • Nicholas Schaum
    • , Benoit Lehallier
    •  & Tony Wyss-Coray

  • Article |

    RNA polymerase II has an unexpected function in the nucleolus, helping to drive the expression of ribosomal RNA and to protect nucleolar structure through a mechanism involving triplex R-loop structures.

    • Karan J. Abraham
    • , Negin Khosraviani
    •  & Karim Mekhail

  • Article |

    The DNA modification N6-methyladenine regulates gene expression during mouse trophoblast development by depositing at the boundaries of active chromatin and preventing its spread by antagonizing the chromatin organizer SATB1.

    • Zheng Li
    • , Shuai Zhao
    •  & Andrew Z. Xiao

  • 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 |

    Single-molecule fluorescence resonance energy transfer and real-time confocal laser tracking with fluorescence correlation spectroscopy together characterize how individual lac repressor molecules bypass operator sites while exploring the DNA surface at microsecond timescales.

    • Emil Marklund
    • , Brad van Oosten
    •  & Sebastian Deindl

  • Article |

    Mutagenic lesions such as those that give rise to cancer frequently segregate—unrepaired—during cell division, resulting in phasing of multiple alleles across generations of daughter cells and consequent tumour heterogeneity.

    • Sarah J. Aitken
    • , Craig J. Anderson
    •  & Martin S. Taylor

  • Article |

    Single-molecule fluorescence in situ hybridization and live-cell imaging are used to study the contribution of transcriptional noise to stem cell heterogeneity, revealing that stochastic transcription dynamics are conducive to concomitant stem-cell maintenance and tissue homeostasis.

    • Justin C. Wheat
    • , Yehonatan Sella
    •  & Ulrich Steidl

  • Outlook |

    RNA is now known to travel outside cells to tissues around the body. Researchers are working out whether they can exploit this extracellular RNA to detect and treat disease.

    • Herb Brody

  • Outlook |

    Kenneth Witwer says that RNA in food could have profound effects on the human digestive system and on health more generally.

    • Kenneth Witwer

  • Outlook |

    Some studies have suggested that plants and fungi exchange RNA through extracellular vesicles. This has led some scientists to develop crop sprays that contain RNA.

    • Roxanne Khamsi

  • Article |

    A method termed ac4C-seq is introduced for the transcriptome-wide mapping of the RNA modification N4-acetylcytidine, revealing widespread temperature-dependent acetylation that facilitates thermoadaptation in hyperthermophilic archaea.

    • Aldema Sas-Chen
    • , Justin M. Thomas
    •  & Schraga Schwartz

  • Article
    | Open Access

    Single-cell RNA sequencing identifies the pattern of gene expression during lineage progression in endosymbiotic cells of the fast-growing soft coral Xenia, revealing principles that underlie uptake and maintenance of endosymbionts by this coral.

    • Minjie Hu
    • , Xiaobin Zheng
    •  & Yixian Zheng

  • Article |

    The cryo-EM structure of human U2 small nuclear ribonucleoprotein (snRNP) offers insights into what rearrangements are required for this snRNP to be stably incorporated into the spliceosome, and the role that the DEAD-box ATPase PRP5 may have in these rearrangements.

    • Zhenwei Zhang
    • , Cindy L. Will
    •  & Holger Stark

  • News & Views |

    Sex chromosomes must exchange genetic information at a short region during meiotic cell division. Molecular factors have now been found that alter sex-chromosome structure and enhance this exchange process.

    • Ericka Humphrey
    •  & Francesca Cole

  • 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

Browse broader subjects

Browse narrower subjects

Browse Molecular biology across other nature.com journals