Molecular biology articles within Nature

Featured

  • Article |

    The meiotic proteins Spo11 and Rec8, which ensure meiotic recombination and reductional chromosome segregation, have additional activities that challenge centromere stability by promoting centromeric nucleosome remodelling in both fission yeast and human cells.

    • Haitong Hou
    • , Eftychia Kyriacou
    •  & Julia Promisel Cooper

  • Technology Feature |

    Advances in sequencing technology mean that scientists are on the verge of finally finishing an end-to-end human genome map.

    • Michael Eisenstein

  • News & Views |

    A study reveals that a process called loop extrusion, which is central to the folding and function of chromosomes, also seems to play a key part in the repair of double-strand DNA breaks.

    • Leonid A. Mirny

  • 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 |

    Multiplexed imaging of 3,660 chromosomal loci in individual mouse embryonic stem cells by DNA seqFISH+ with immunofluorescence of 17 chromatin marks and subnuclear structures reveals invariant organization of loci within individual cells, and heterogeneous and long-lived distinct combinatorial chromatin states in cellular subpopulations.

    • Yodai Takei
    • , Jina Yun
    •  & Long Cai

  • Article |

    Binding of METTL3 to chromatin is enriched over IAP family endogenous retroviral elements in mouse embryonic stem cells, helping to ensure the integrity of heterochromatin at these elements.

    • Wenqi Xu
    • , Jiahui Li
    •  & Hongjie Shen

  • Article |

    An ultra-high-throughput multiplex protein–DNA binding assay is used to assess binding of 270 human transcription factors to 95,886 noncoding variants in the human genome, providing data to improve prediction of the effects of noncoding variants on transcription factor binding and thereby increase understanding of molecular pathways involved in diverse human traits and genetic diseases.

    • Jian Yan
    • , Yunjiang Qiu
    •  & Bing Ren

  • News & Views |

    A large-scale, high-resolution cell atlas of gene expression and regulation in human embryos enables innovative investigation of development through multi‑organ and multi‑modal analysis.

    • Felicia Kuperwaser
    •  & Itai Yanai

  • Article |

    Long-distance V(D)J recombination is facilitated by contraction of the Igh locus and linear RAG scanning along chromatin, both driven by cohesin-mediated loop extrusion, which allows recombination of widely separated gene segments to occur.

    • Hai-Qiang Dai
    • , Hongli Hu
    •  & Frederick W. Alt

  • Article |

    A high-throughput, chromosome-wide analysis of DNA looping reveals its contribution to the organization of chromatin, and provides insight into how nucleosomes are deposited and organised de novo.

    • Aakash Basu
    • , Dmitriy G. Bobrovnikov
    •  & Taekjip Ha

  • Article |

    Inhibitors of mitochondrial transcription that target human mitochondrial RNA polymerase provide a chemical biology tool for studying the role of mitochondrial DNA expression in a wide range of pathologies.

    • Nina A. Bonekamp
    • , Bradley Peter
    •  & Nils-Göran Larsson

  • Article |

    Tryptophan depletion in melanoma cells after prolonged treatment with interferon-γ (IFNγ) results in ribosomal frameshifting and the production of aberrant peptides that can be presented to T cells and induce an immune response.

    • Osnat Bartok
    • , Abhijeet Pataskar
    •  & Reuven Agami

  • Article |

    Experiments using a conditional triple-knockout mouse strain show that histone H1 regulates the activity of chromatin domains by controlling chromatin compaction, genome architecture and  histone methylation.

    • Michael A. Willcockson
    • , Sean E. Healton
    •  & Arthur I. Skoultchi

  • Article |

    Mutations in histone H1 induce the remodelling of chromatin architecture to a more relaxed state, which leads to malignant transformation through changes in histone modifications and the expression of stem cell genes.

    • Nevin Yusufova
    • , Andreas Kloetgen
    •  & Ari M. Melnick

  • Article |

    Expression of three Yamanaka transcription factors in mouse retinal ganglion cells restores youthful DNA methylation patterns, promotes axon regeneration after injury, and reverses vision loss in a mouse model of glaucoma and in aged mice, suggesting that mammalian tissues retain a record of youthful epigenetic information that can be accessed to improve tissue function.

    • Yuancheng Lu
    • , Benedikt Brommer
    •  & David A. Sinclair

  • Article |

    Depletion of TRF2—an essential mediator of telomere protection in most mammalian cells—in mouse embryonic stem cells activates a compensatory transcriptional program that renders TRF2 dispensable for their survival and proliferation.

    • Marta Markiewicz-Potoczny
    • , Anastasia Lobanova
    •  & Eros Lazzerini Denchi

  • Article |

    Experiments in mouse pluripotent embryonic and epiblast stem cells show that TRF2 is dispensable for telomere protection specifically specifically in the pluripotent cells that form during early embryonic development, when cells form T-loops independently of this protein.

    • Phil Ruis
    • , David Van Ly
    •  & Simon J. Boulton

  • Article |

    A comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin structure, the methylome and 3D genome organization in the zebrafish (Danio rerio) enables identification of species-specific and evolutionarily conserved regulatory features, and provides a foundation for modelling studies on human disease and development.

    • Hongbo Yang
    • , Yu Luan
    •  & Feng Yue

  • Career Feature |

    Scientists who aren’t virologists or vaccinologists can still make crucial contributions to the global effort to battle SARS-CoV-2.

    • Amy DePaul

  • 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

  • News & Views |

    Mismatches are alterations in DNA that prevent the bases on each strand of the double helix from aligning correctly. It emerges that mismatches can bend DNA into favourable conformations for binding by proteins.

    • Kale Kundert
    •  & James S. Fraser

  • News & Views |

    Homologous recombination is a mechanism for DNA repair that enables the exchange of genetic information between DNA molecules. Structural analysis reveals how the protein RecA orchestrates this process.

    • Upasana Roy
    •  & Eric C. Greene

  • 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 |

    Cryo-electron microscopy structures of the bacterial recombination protein RecA with DNA, and of RecA–D-loop complexes, provide insights into the double-stranded DNA opening, homology search and strand-exchange processes of homologous recombination.

    • Haijuan Yang
    • , Chun Zhou
    •  & Nikola P. Pavletich

  • Article |

    Single-nucleus RNA-sequencing analyses of brain from humans, macaques, marmosets, mice and ferrets reveal diverse ways that interneuron populations have changed during evolution.

    • Fenna M. Krienen
    • , Melissa Goldman
    •  & Steven A. McCarroll

  • 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

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