Molecular biology articles within Nature

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  • Article
    | Open Access

    A study demonstrates that nucleotide modifications in mRNA-based therapeutics can lead to +1 ribosomal frameshifting during translation, yielding products that can trigger immune responses.

    • Thomas E. Mulroney
    • , Tuija Pöyry
    •  & Anne E. Willis

  • Article
    | Open Access

    Cryogenic electron microscopy structures of amyloid filaments extracted from patient brains reveal that the protein TAF15 forms filaments that characterize certain cases of frontotemporal lobar degeneration.

    • Stephan Tetter
    • , Diana Arseni
    •  & Benjamin Ryskeldi-Falcon

  • News & Views |

    A transcription factor in immune cells forms an unexpectedly ladder-like complex with two DNA molecules, allowing the expression of genes that these cells need to suppress harmful immune responses.

    • Zhi Liu
    •  & Ye Zheng

  • Article
    | Open Access

    Whole-genome alignment of 239 primate species reveals noncoding regulatory elements that are under selective constraint in primates but not in other placental mammals, that are enriched for variants that affect human gene expression and complex traits in diseases.

    • Lukas F. K. Kuderna
    • , Jacob C. Ulirsch
    •  & Kyle Kai-How Farh

  • 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 |

    The epigenetic modification H3K9me3 is asymmetrically partitioned at long interspersed nuclear element retrotransposons for their silencing in S phase, a newly discovered mechanism that is mediated by the HUSH complex and the DNA polymerase Pol ε.

    • Zhiming Li
    • , Shoufu Duan
    •  & Zhiguo Zhang

  • News & Views |

    Bacteria and archaea are microorganisms that often use RNA-guided defences called CRISPR to destroy the genomes of viruses that infect them. It now emerges that viruses make RNAs that act as mimics to divert such defences.

    • Carolyn Kraus
    •  & Erik J. Sontheimer

  • Article
    | Open Access

    After the production of double-stranded breaks in mammalian cells, ATM drives the formation of the D compartment, which regulates DNA damage-responsive genes, through the clustering of damaged topologically associating domains, with a mechanism that is consistent with polymer–polymer phase separation.

    • Coline Arnould
    • , Vincent Rocher
    •  & Gaëlle Legube

  • Article
    | Open Access

    In response to bacterial CRISPR–Cas immunity, phages and plasmids have evolved small non-coding RNA anti-CRISPRs, known as Racrs, that sequester Cas proteins in abberrant complexes and thereby inhibit immunity.

    • Sarah Camara-Wilpert
    • , David Mayo-Muñoz
    •  & Rafael Pinilla-Redondo

  • Perspective |

    Although the catalogue of human protein-coding genes is nearing completion, the number of non-coding RNA genes remains highly uncertain, and for all genes much work remains to be done to understand their functions.

    • Paulo Amaral
    • , Silvia Carbonell-Sala
    •  & Steven L. Salzberg

  • Article
    | Open Access

    Comparisons of phenotypic and genetic association with protein levels from Icelandic and UK Biobank cohorts show that using multiple analysis platforms and stratifying populations by ancestry improves the detection of associations and allows the refinement of their location within the genome.

    • Grimur Hjorleifsson Eldjarn
    • , Egil Ferkingstad
    •  & Kari Stefansson

  • Article
    | Open Access

    The Pharma Proteomics Project generates the largest open-access plasma proteomics dataset to date, offering insights into trans protein quantitative trait loci across multiple biological domains, and highlighting genetic influences on ligand–receptor interactions and pathway perturbations across a diverse collection of cytokines and complement networks.

    • Benjamin B. Sun
    • , Joshua Chiou
    •  & Christopher D. Whelan

  • News & Views |

    In organisms with X and Y chromosomes, gene expression must be equalized between the sexes. A protein that causes upregulation of gene expression of the X chromosome in male mosquitoes has been discovered.

    • Maggie P. Lauria Sneideman
    •  & Victoria H. Meller

  • Article
    | Open Access

    In situ spatial transcriptomic analysis of more than 1 million cells are used to create a 200-nm-resolution spatial molecular atlas of the adult mouse central nervous system and identify previously unknown tissue architectures.

    • Hailing Shi
    • , Yichun He
    •  & Xiao Wang

  • 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 |

    Cellular lysine residues can be both methylated and acetylated on the same sidechain to form Nε-acetyl-Nε-methyllysine (Kacme), which is found on histone H4 across a range of species and across mammalian tissues and is associated with active chromatin.

    • William J. Lu-Culligan
    • , Leah J. Connor
    •  & Matthew D. Simon

  • Article
    | Open Access

    An in vivo single-cell CRISPR screening method identifies transcriptional phenotypes of 22q11.2 deletion syndrome associated with a broad dysregulation of a class of disease susceptibility genes that are important for RNA processing and synaptic function.

    • Antonio J. Santinha
    • , Esther Klingler
    •  & Randall J. Platt

  • News & Views |

    During translation, messenger RNA guides protein production, and certain conditions can favour particular proteins. Helicase enzymes and mRNA structure control translation during defence responses in plants.

    • Yizhu Lin
    •  & Stephen N. Floor

  • Article
    | Open Access

    Double-stranded RNA structures downstream of start codons play a role in translation initiation by regulating start-codon selection in plant immune responses, and also contribute to translational reprogramming in mammalian systems.

    • Yezi Xiang
    • , Wenze Huang
    •  & Xinnian Dong

  • Article
    | Open Access

    A collection of RNA polymerase mutants spanning all possible substitutions of the rifampicin binding site is generated and characterized, increasing our understanding of antibiotic mechanisms and bacterial physiology.

    • Kevin B. Yang
    • , Maria Cameranesi
    •  & Evgeny Nudler

  • Article |

    We present the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference.

    • Arang Rhie
    • , Sergey Nurk
    •  & Adam M. Phillippy

  • Article
    | Open Access

    Single-cell transcriptomics and in vivo challenge models establish a key role for the aryl hydrocarbon receptor in regulating the function of enteric endothelial cells in response to environmental cues.

    • Benjamin G. Wiggins
    • , Yi-Fang Wang
    •  & Chris Schiering

  • 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
    | Open Access

    Cryo-electron microscopy structures and mass spectrometry analyses show that TAR DNA-binding protein 43 (TDP-43) forms amyloid filaments with a distinct fold in type A frontotemporal lobar degeneration with TDP-43 pathology (FTLD-TDP) compared with TDP-43 filaments in type B FTLD-TDP and amyotrophic lateral sclerosis.

    • Diana Arseni
    • , Renren Chen
    •  & Benjamin Ryskeldi-Falcon

  • Article |

    Rapid activation of protein synthesis in the axolotl highlights the unanticipated impact of a translatome on orchestrating the early steps of wound healing and provides a missing link in our understanding of vertebrate regenerative potential.

    • Olena Zhulyn
    • , Hannah D. Rosenblatt
    •  & Maria Barna

  • Article
    | Open Access

    Structural and biochemical studies of the Saccharomyces cerevisiae Rpd3 small complex in free and H3K36me3 nucleosome-bound states reveal multiple nucleosome-binding modes and provide insights into mechanisms underlying epigenetic regulation by histone modification.

    • Haipeng Guan
    • , Pei Wang
    •  & Haitao Li

  • News & Views |

    Activation of gene transcription is precisely regulated in early embryos. The identification of key transcription factors now shows how the transcription machinery is guided to the right place at the right time in mice.

    • Edlyn Wu
    •  & Nadine L. Vastenhouw

  • Research Briefing |

    Retrotransposons are sequences of DNA in animal genomes that can replicate and reinsert themselves back into the genome. Experiments in flies and other model systems reveal that retrotransposons ‘hijack’ a DNA-repair pathway in host cells to produce circular DNA, enabling their replication and subsequent reinsertion into the genome.

  • Article
    | Open Access

    Single-cell and spatial transcriptomic analysis of eight human heart tissues reveals the cellular profiles and tissue architecture of niches including the cardiac conduction system, and a new tool, drug2cell, identifies drug target expression.

    • Kazumasa Kanemaru
    • , James Cranley
    •  & Sarah A. Teichmann

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