Molecular biology articles within Nature

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  • Article |

    A study details the creation of an Escherichia coli genetically recoded organism that is resistant to viral infection, and describes a further modification that keeps the organism and its genetic information biocontained.

    • Akos Nyerges
    • , Svenja Vinke
    •  & George M. Church

  • Article |

    A technique to detect the release of N-terminal fragments of Drosophila adhesion G-protein-coupled receptors (aGPCRs) provides insight into the dissociation of aGPCRs, and shows that receptor autoproteolysis enables non-cell-autonomous activity of aGPCRs in the brain.

    • Nicole Scholz
    • , Anne-Kristin Dahse
    •  & Tobias Langenhan

  • Article
    | Open Access

    Acute loss of H3K4me3 does not have detectable effects on transcriptional initiation, but leads to a widespread decrease in transcriptional output, an increase in RNA polymerase II pausing and slower elongation

    • Hua Wang
    • , Zheng Fan
    •  & Kristian Helin

  • Article |

    Massively parallel assays reveal a highly conserved sequence motif termed the GYM motif, which potentiates RNA interference by directing Dicer-mediated small RNA processing.

    • Young-Yoon Lee
    • , Haedong Kim
    •  & V. Narry Kim

  • News & Views |

    The enzyme Dicer cleaves a type of RNA called a pre-microRNA to make the mature functional RNA. Structural evidence now sheds light on the catalytic mechanism involved and the role of a newly found RNA sequence termed GYM.

    • Gunter Meister

  • Article |

    The active-state structure of human DICER bound to pre-miRNA reveals the structural basis for the specificity of DICER in how it selects substrates in a sequence dependent manner, and sheds light on DICER-related diseases.

    • Young-Yoon Lee
    • , Hansol Lee
    •  & Soung-Hun Roh

  • News & Views |

    High-resolution structures of the bacterial Rho protein in complex with an RNA polymerase enzyme and partner proteins provide support for the long-held model of how Rho helps to terminate gene transcription.

    • Fahad Rashid
    •  & James Berger

  • Article
    | Open Access

    An analysis of MitCOM—a comprehensive resource for the identification, organization and interaction of mitochondrial machineries and pathways in yeast—identifies a constitutive pathway for the removal of preproteins.

    • Uwe Schulte
    • , Fabian den Brave
    •  & Thomas Becker

  • Research Briefing |

    In egg cells, the ribosomes — the machinery responsible for protein synthesis — are stored in a dormant state that is released later in the developing embryo. An evolutionarily conserved set of proteins has been shown to bind to ribosomes in the egg cells of vertebrates, stabilizing the ribosomes and suppressing their activity.

  • Article |

    Mass spectrometry and structural studies demonstrate the specific changes in protein composition that accompany the transition of ribosomes in zebrafish and Xenopus eggs from a dormant to an active state during early embryogenesis.

    • Friederike Leesch
    • , Laura Lorenzo-Orts
    •  & Andrea Pauli

  • News & Views |

    CRISPR–Cas is a bacterial defence system that can attack invading DNA to protect host cells, or help to insert DNA safely into the genome. Structures of this latter type of CRISPR–Cas system have now been visualized.

    • Orsolya Barabas
    •  & Phoebe A. Rice

  • News & Views |

    Messenger RNA has 64 possible triplet sequences, or codons, three of which usually terminate protein synthesis. But some organisms can use all codons to specify amino acids, thanks in part to a surprising feature of a transfer RNA.

    • Pavel V. Baranov
    •  & John F. Atkins

  • Article |

    Analyses of in-frame stop codons in protein-coding genes of Blastocrithidia nonstop with all three stop codons reassigned reveal a mechanism for UGA reassignment in eukaryotes involving shortening of the tRNA anticodon stem and a mutant eRF1 release factor.

    • Ambar Kachale
    • , Zuzana Pavlíková
    •  & Julius Lukeš

  • Article |

    Structural studies of Escherichia coli transcription intrinsic termination complexes representing distinct intermediates using cryo-electron microscopy provide insights into the steps and mechanism of transcription termination.

    • Linlin You
    • , Expery O. Omollo
    •  & Yu Zhang

  • 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 |

    Structures of the human METTL1–WDR4 complex are revealed, providing molecular insights into substrate recognition, modification and catalytic regulation by the N7-methylguanosine methyltransferase complex.

    • Jiazhi Li
    • , Longfei Wang
    •  & Richard I. Gregory

  • News & Views |

    Radiation-damaged paternal DNA has been found to cause embryos of the second generation of nematode worms, but not the first, to die. The proposed mechanisms help to explain the observed lack of such an effect in humans.

    • Ronald Cutler
    •  & Jan Vijg

  • Research Briefing |

    The mammalian testis is a rapidly evolving organ, in both structural and molecular terms. An investigation of testicular cell nuclei from 11 species has unveiled genes, cell types and evolutionary forces that underlie these changes.

  • Article
    | Open Access

    Evolutionary analyses of single-nucleus transcriptome data for testes from 11 species are reported, illuminating the molecular evolution of spermatogenesis and associated forces, and providing a resource for investigating the testis across mammals.

    • Florent Murat
    • , Noe Mbengue
    •  & Henrik Kaessmann

  • Article |

    RibosomeST—a ribosome with a specialized nascent polypeptide exit tunnel—cotranslationally regulates the folding of a subset of male germ-cell-specific proteins that are essential for the formation of sperm.

    • Huiling Li
    • , Yangao Huo
    •  & Jiahao Sha

  • Article |

    Results are presented that indicate that alterations to gene regulatory three-dimensional architecture are a critical mechanism that enables structural variant-based oncogene activation in cancer genomes and sheds light on the essential elements for such gene activation events.

    • Zhichao Xu
    • , Dong-Sung Lee
    •  & Jesse R. Dixon

  • Article
    | Open Access

    A non-genetic mechanism of sex determination in the human malaria parasite, Plasmodium falciparum, is described, and the male development 1 gene is identified as a potential target for interventions that block malaria transmission.

    • A. R. Gomes
    • , A. Marin-Menendez
    •  & A. M. Talman

  • Article |

    Provora is an ancient supergroup of microbial predators that are genetically, morphologically and behaviourally distinct from other eukaryotes, and comprise two divergent clades of predators—Nebulidia and Nibbleridia—that differ fundamentally in ultrastructure, behaviour and gene content.

    • Denis V. Tikhonenkov
    • , Kirill V. Mikhailov
    •  & Patrick J. Keeling

  • Article
    | Open Access

    Structural studies of the CRISPR-associated transposon comprising Cas12k, TnsC, TnsB and TniQ from Scytonema hofmannii using cryo-electron microscopy reveal insights into the architecture and mechanism of RNA-guided DNA transposition.

    • Jung-Un Park
    • , Amy Wei-Lun Tsai
    •  & Elizabeth H. Kellogg

  • Research Briefing |

    It has not been clear how sperm DNA is compacted in the pollen of flowering plants. Research has now revealed that sperm chromatin, which is a complex of DNA and proteins, is packaged by a special histone protein that spontaneously aggregates in a phenomenon known as phase separation.

  • News & Views |

    Two groups have visualized actin — the protein polymer that gives cells their shape — at high resolution. The structures provide in-depth views of the polymer as it adopts fleeting states and undergoes conformational changes.

    • Pilar Cossio
    •  & Glen M. Hocky

  • Article
    | Open Access

    The cryogenic-electron microscopy structure of the D. thermocuniculi IsrB protein in complex with its cognate ωRNA and a target DNA shows that the RNA-dominant IsrB effector complex shares a common scaffold with the protein-dominant Cas9 effector complex.

    • Seiichi Hirano
    • , Kalli Kappel
    •  & Feng Zhang

  • Article |

    RNA sensing-mediated payload expression provides a specific, versatile, simple and generalizable means of detecting and manipulating animal cells with broad potential applications.

    • Yongjun Qian
    • , Jiayun Li
    •  & Z. Josh Huang

  • Article |

    The cryo-electron microscopy structure of NuA4 from Saccharomyces cerevisiae bound to the nucleosome illustrates how NuA4 is assembled and provides mechanistic insights into nucleosome recognition and transcription co-activation by a histone acetyltransferase.

    • Keke Qu
    • , Kangjing Chen
    •  & Zhucheng Chen

  • Article |

    The nuclear mitotic apparatus protein NuMA helps to protect genes from oxidative damage by occupying regions around transcription start sites, binding DNA repair factors and promoting transcription following damage.

    • Swagat Ray
    • , Arwa A. Abugable
    •  & Sherif F. El-Khamisy

  • Article
    | Open Access

    Cryo-electron tomography is used to reveal the structural dynamics and functional diversity of translating ribosomes in Mycoplasma pneumoniae, providing insight into the translation elongation cycle inside cells and how it is reshaped by antibiotics.

    • Liang Xue
    • , Swantje Lenz
    •  & Julia Mahamid

  • Article |

    CDK11 associates with SF3B1 and phosphorylates threonine residues at the N terminus of SF3B1 during spliceosome activation, and the inhibition of CDK11 blocks the activation and leads to widespread intron retention and the accumulation of non-functional spliceosomes on pre-mRNAs and chromatin.

    • Milan Hluchý
    • , Pavla Gajdušková
    •  & Dalibor Blazek

  • Article |

    Cryogenic electron microscopy analyses reveal a new, compact structure of telomeric chromatin, providing mechanistic insight into telomere maintenance and function.

    • Aghil Soman
    • , Sook Yi Wong
    •  & Lars Nordenskiöld

  • Article
    | Open Access

    The structures of single COOLAIR RNA isoforms change in abundance and shape in response to external conditions; structural mutation of these isoforms altered FLC expression and flowering time, consistent with a regulatory role of the COOLAIR structure in FLC transcription.

    • Minglei Yang
    • , Pan Zhu
    •  & Yiliang Ding

  • Article
    | Open Access

    Live-seq, a single-cell transcriptome profiling approach that preserves cell viability during RNA extraction using fluidic force microscopy, can address a range of biological questions by transforming scRNA-seq from an end-point to a temporal analysis approach.

    • Wanze Chen
    • , Orane Guillaume-Gentil
    •  & Bart Deplancke

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