Molecular biology articles within Nature

Featured

  • Article
    | Open Access

    Studies on the µ-opioid receptor using fluorescent labelling of intracellular residues and energy transfer experiments in the presence of different ligands with or without G-protein binding reveals conformational changes that correlate to ligand efficacy.

    • Jiawei Zhao
    • , Matthias Elgeti
    •  & Chunlai Chen

  • Article
    | Open Access

    A comparison of two complete sets of human centromeres reveals that the centromeres show at least a 4.1-fold increase in single-nucleotide variation compared with their unique flanks, and up to 3-fold variation in size, resulting from an accelerated mutation rate.

    • Glennis A. Logsdon
    • , Allison N. Rozanski
    •  & Evan E. Eichler

  • Article
    | Open Access

    Cryo-electron microscopy structures of the human Integrator complex in three different functional states shed light on how Integrator terminates RNA polymerase II (Pol II) transcription by disengaging Pol II from the DNA template.

    • Isaac Fianu
    • , Moritz Ochmann
    •  & Patrick Cramer

  • Article
    | Open Access

    Learning results in persistent double-stranded DNA breaks, nuclear rupture and release of DNA fragments and histones within hippocampal CA1 neurons that, following TLR9-mediated DNA damage repair, results in their recruitment to memory circuits.

    • Vladimir Jovasevic
    • , Elizabeth M. Wood
    •  & Jelena Radulovic

  • Article
    | Open Access

    Poly(ADP-ribose) polymerase 1 (PARP1) functions together with TIMELESS and TIPIN to protect the replisome in early S phase from transcription–replication conflicts, and inhibiting PARP1 enzymatic activity may suffice for treatment efficacy in homologous recombination-deficient settings.

    • Michalis Petropoulos
    • , Angeliki Karamichali
    •  & Thanos D. Halazonetis

  • News & Views |

    In experiments dubbed the Random Genome Project, researchers have integrated DNA strands with random sequences into yeast and mouse cells to find the default transcriptional state of their genomes.

    • Sean R. Eddy

  • Article
    | Open Access

    A multidimensional proteomics analysis of the interactions between around 2,000 nuclear proteins and over 80 modified dinucleosomes representing promoter, enhancer and heterochromatin states provides insights into how chromatin states are decoded by chromatin readers.

    • Saulius Lukauskas
    • , Andrey Tvardovskiy
    •  & Till Bartke

  • Article
    | Open Access

    Introduction of a long synthetic DNA into yeast genomic loci results in high default transcriptional activity in yeast but low activity in mouse, suggesting distinct default levels of genomic activity in these organisms.

    • Brendan R. Camellato
    • , Ran Brosh
    •  & Jef D. Boeke

  • Article |

    Structures of the yeast replisome associated with the FACT complex and an evicted histone hexamer offer insights into the mechanism of replication-coupled histone recycling for maintaining epigenetic inheritance.

    • Ningning Li
    • , Yuan Gao
    •  & Yuanliang Zhai

  • Article
    | Open Access

    In Caenorhabditis tropicalis, selective expression of genetic alleles from one parent but not the other can arise from maternally inherited small transcripts acting via the PIWI-interacting RNA host defence pathway.

    • Pinelopi Pliota
    • , Hana Marvanova
    •  & Alejandro Burga

  • Article
    | Open Access

    The demethylase KDM5C, mutations in which often lead to intellectual disability, is identified as a crucial player in regulating the precise timing of neurodevelopment together with the WNT signalling pathway.

    • Violetta Karwacki-Neisius
    • , Ahram Jang
    •  & Yang Shi

  • Article
    | Open Access

    SAFB proteins protect genome integrity by preventing retrotransposition of L1 elements yet maintaining splicing integrity, via prevention of the exonization of previously integrated transposable elements, a major constituent of human genes.

    • İbrahim Avşar Ilık
    • , Petar Glažar
    •  & Tuğçe Aktaş

  • Article |

    In neutrophil progenitor cells, stopping the process of loop extrusion by depleting nipped-B-like protein (NIPBL) results in the assembly of polymorphonuclear structures and the activation of a neutrophil-specific gene program.

    • Indumathi Patta
    • , Maryam Zand
    •  & Cornelis Murre

  • Article
    | Open Access

    A study identifies a new bacterial ribosome hibernation factor, Balon, and describes its association with EF-Tu and its initiation of mRNA-independent hibernation during protein synthesis.

    • Karla Helena-Bueno
    • , Mariia Yu. Rybak
    •  & Sergey V. Melnikov

  • Article |

    Circular RNAs are exported from the nucleus by Ran-GTP, exportin-2 and IGF2BP1 in a mechanism analogous to protein export rather than mRNA export.

    • Linh H. Ngo
    • , Andrew G. Bert
    •  & Vihandha O. Wickramasinghe

  • Article
    | Open Access

    Translation actively dislodges stalled transcription elongation complexes (ECs) from damaged DNA, which enables lesion repair and restoration of transcription activity, and coupled ribosomes discriminate between active ECs and stalled ECs, ensuring destruction of only the latter.

    • Jason Woodgate
    • , Hamed Mosaei
    •  & Nikolay Zenkin

  • Article
    | Open Access

    Cryo-electron microscopy structures of intermediates formed during the degradation of the 30S ribosomal unit shed light on how the 3′ to 5′ exonuclease ribonuclease R controls the ribosomal degradation process.

    • Lyudmila Dimitrova-Paternoga
    • , Sergo Kasvandik
    •  & Helge Paternoga

  • Article
    | Open Access

    Spatial and single-cell transcriptomic analyses of the mouse basolateral amygdala reveal transcriptomic signatures, spatial resolution and interactions of cells that constitute the memory engram, including crucial neuron–astrocyte interactions.

    • Wenfei Sun
    • , Zhihui Liu
    •  & Stephen R. Quake

  • Article |

    We study the interplay between cohesin and replication by reconstituting a functional replisome using purified proteins, showing how cohesin initially responds to replication and providing a molecular model for the establishment of sister chromatid cohesion.

    • Yasuto Murayama
    • , Shizuko Endo
    •  & Hiroyuki Araki

  • Article
    | Open Access

    Dissection of the nuclear pore complex provides a model in which the HIV capsid enters the nucleus through karyopherin mimicry, a mechanism likely to be conserved across other viruses.

    • C. F. Dickson
    • , S. Hertel
    •  & D. A. Jacques

  • Article
    | Open Access

    Low-affinity transcription factor binding sites are prevalent across the genome, and single nucleotide changes that increase binding affinity even slightly can cause gain-of-function gene expression and phenotypes (such as polydactyly).

    • Fabian Lim
    • , Joe J. Solvason
    •  & Emma K. Farley

  • News & Views |

    LINE-1 DNA elements self-duplicate, inserting the copy into new regions of the genome — a key process in chromosome evolution. Structures of the machinery that performs this process in humans are now reported.

    • Gael Cristofari

  • Article
    | Open Access

    tRNA display enables the direct selection of orthogonal aminoacyl-tRNA synthetases that acylate orthogonal tRNAs with non-canonical monomers, enabling in vivo synthesis of proteins that include these monomers and expanding the repertoire of the genetic code.

    • Daniel L. Dunkelmann
    • , Carlos Piedrafita
    •  & Jason W. Chin

  • News Feature |

    Scientists are attempting to rapidly domesticate wild plant species by editing specific genes, but they face major technical challenges — and concerns about exploitation of Indigenous knowledge.

    • Michael Marshall

  • Article
    | Open Access

    Messenger RNAs transcribed from olfactory-receptor genes may have non-coding functions that include recruitment of transcriptional enhancers and inhibition of potentially thousands of competing alleles to ensure stable transcription of a single allele.

    • Ariel D. Pourmorady
    • , Elizaveta V. Bashkirova
    •  & Stavros Lomvardas

  • Article
    | Open Access

    Genome-wide replication timing maps of mouse embryos from the zygote to the blastocyst stage were generated using single-cell Repli-seq, shedding light on the establishment of the epigenome at the beginning of mammalian development.

    • Tsunetoshi Nakatani
    • , Tamas Schauer
    •  & Maria-Elena Torres-Padilla

  • Article
    | Open Access

    X-ray crystallography, cryo-electron microscopy, structural modelling, biochemistry, cell biology, and evolutionary analysis enable characterization of ORF2p, the reverse transcriptase of the ancient ‘parasitic’ LINE-1 retrotransposon that has written around one-third of the human genome.

    • Eric T. Baldwin
    • , Trevor van Eeuwen
    •  & Martin S. Taylor

  • Article
    | Open Access

    Human LINE-1 ORF2p relies on upstream single-stranded target DNA to position the adjacent duplex in the endonuclease active site for nicking of the longer DNA strand, with a single nick generating a staggered DNA break.

    • Akanksha Thawani
    • , Alfredo Jose Florez Ariza
    •  & Kathleen Collins

  • Article
    | Open Access

    Methylome-based clustering and cross-modality integration with companion datasets from the BRAIN Initiative Cell Census Network enabled the construction of a 3D multi-omic genome atlas of the adult mouse brain featuring thousands of cell-type-specific profiles.

    • Hanqing Liu
    • , Qiurui Zeng
    •  & Joseph R. Ecker

  • Article
    | Open Access

    A single-cell multiomics analysis of over 200,000 cells of the primary motor cortex of human, macaque, marmoset and mouse shows that divergence of transcription factor expression corresponds to species-specific epigenome landscapes, and conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome.

    • Nathan R. Zemke
    • , Ethan J. Armand
    •  & Bing Ren

  • 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

Browse broader subjects

Browse narrower subjects

Browse Molecular biology across other nature.com journals