Molecular biology articles within Nature Cell Biology

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  • News & Views |

    When transcription by RNA polymerase II is stalled by ultraviolet-induced DNA damage, it recruits repair factors, leading to excision of the damaged site and DNA synthesis to fill the gap. Three new studies show that, for aldehyde-induced DNA crosslinks, repair is activated by the same factors, but without base excision and gap filling.

    • Marco Saponaro

  • News & Views |

    Organ morphogenesis begins with proliferation, which results in tissue pressures and site-specific YAP expression, nuclear translocation and signalling. A study now reports the involvement of anisotropy, localized pressure and YAP signalling in organizer-forming cascades, introducing a new chapter of molecular mechanobiology of organogenesis.

    • Qian Xu
    •  & Thomas G. H. Diekwisch

  • News & Views |

    Eukaryotic transcriptional machinery often shows local enrichment in dynamic clusters at sites of high expression. A study of zebrafish embryos shows that such clusters can fine-tune the timing of zygotic genome activation by sequestering a component required for productive transcription, thus limiting its availability to other genes.

    • Natalia Stec
    •  & Adam Klosin

  • Article
    | Open Access

    Ugolini et al. show that transcription bodies regulate gene expression during zygotic genome activation in zebrafish development by sequestering CDK9 to limit the transcription of genes away from transcription bodies.

    • Martino Ugolini
    • , Maciej A. Kerlin
    •  & Nadine L. Vastenhouw

  • News & Views |

    tRNA transcriptome composition and regulation are poorly understood. A study reports tRNA transcriptome reprogramming during human cell differentiation, where the abundance of individual tRNA gene transcripts is drastically changed, but each pool of tRNAs containing the same anticodon remains stable.

    • Yichen Hou
    •  & Tao Pan

  • Article
    | Open Access

    Using modification-induced misincorporation tRNA sequencing, Gao and Behrens find that on differentiation, reduced mTORC1 signalling activates MAF1, which restricts RNA polymerase III to human tRNA housekeeping genes, to ensure that tRNA anticodon pools remain stable.

    • Lexi Gao
    • , Andrew Behrens
    •  & Danny D. Nedialkova

  • Article
    | Open Access

    Munk et al. show that exogenous NAD+, but not its precursors, induces metabolic changes in mitochondria affecting nucleotide metabolism with impacts on genomic DNA synthesis and genome integrity.

    • Sebastian Howen Nesgaard Munk
    • , Joanna Maria Merchut-Maya
    •  & Apolinar Maya-Mendoza

  • News & Views |

    YTHDF family members are ‘readers’ of a common mRNA modification, but their effects on mRNA translation and stability have been disputed. A new study shows that YTHDF1 and YTHDF3 are post-translationally regulated through O-GlcNAcylation, unifying disparate results and pointing to environmental cues that could modulate YTHDF function.

    • Mary W. N. Burns
    •  & Jennifer J. Kohler

  • News & Views |

    How spatial organization in the cell is achieved on the organelle scale is unclear. A new study finds that tethering specific proteins near the surface of micelle-like paraspeckles modifies their properties and determines whether these subnuclear organelles are separate from, adhere to, or are engulfed by nuclear speckles.

    • Jeremy D. Schmit
    •  & Miroslav Dundr

  • News & Views |

    The bacterial pathogen Legionella pneumophila uses effectors — toxins — to facilitate pathogenesis within host cells. A recent study identifies dual mechanisms of the effector SidI as an inhibitor of translation elongation. The N-terminal domain mimics tRNA, whereas the C-terminal domain glycosylates the ribosome.

    • Saori Uematsu
    •  & Shu-Bing Qian

  • Article |

    Kramer, Prakash et al. share genome-wide CRISPR screens for factors that alter the levels of two dual-genome-encoded Complex IV subunits, COX1 and COX4. They identify PREPL and NME6 as genes that connect mitochondrial metabolism to mtDNA expression.

    • Nicholas J. Kramer
    • , Gyan Prakash
    •  & L. Stirling Churchman

  • Article
    | Open Access

    Irie, Lee et al. report a role for DMRT1 in human germline development and show that induction of DMRT1 in primordial germ cell-like cells triggers germline commitment, but suppresses pluripotency genes, thus promoting the onset of gametogenesis.

    • Naoko Irie
    • , Sun-Min Lee
    •  & M. Azim Surani

  • News & Views |

    RNA modifications have emerged as key gene regulators. A new study shows that increased levels of reactive oxygen species in cancer induce widespread, sequence-specific modifications of guanines in the seed regions of microRNAs, altering the targets of those miRNAs and influencing tumorigenesis.

    • Marta Montes
    •  & Maite Huarte

  • News & Views |

    Pathways linked to the modification of RNA with N6-methyladenosine (m6A) are known to be involved in initiating and maintaining cancer. But many of the key components of these pathways remain undiscovered. The RBFOX2 protein has now been identified as an m6A reader involved in locus-specific chromatin regulation, with therapeutic implications for myeloid leukaemia.

    • James Russell
    •  & Konstantinos Tzelepis

  • News & Views |

    The interaction of non-immune and immune cells in the tumour microenvironment (TME) determines the quality of the immune attack on nascent tumour cells. A new study in melanoma cells shows that specific histone variants dampen the expression of cytokine genes in cancer-associated fibroblasts, leading to an immunosuppressive TME.

    • David Corujo
    •  & Marcus Buschbeck

  • News & Views |

    The compact state of chromatin induced by the methylation of lysine 9 on histone H3 has long been implicated in a heritable state of transcriptional repression. A study now shows that transient deposition of H3K9me3 helps to stabilize stalled DNA replication forks, while its reversal enables accurate fork restart.

    • Susan M. Gasser

  • Article
    | Open Access

    Han et al. identify the long non-coding RNA LIPTER as a key mediator of lipid droplet transport and metabolism in human cardiomyocytes. LIPTER overexpression mitigates cardiomyopathy and preserves cardiac function in obese and diabetic mouse models.

    • Lei Han
    • , Dayang Huang
    •  & Lei Yang

  • News & Views |

    In cancer, alternative polyadenylation has been shown to lead to altered 3′ UTRs with different regulatory potentials. A study now suggests a mechanism that leads to 3′ UTR lengthening and translational repression of a subset of metastasis-suppressing genes, revealing a new prospective therapeutic vulnerability.

    • Kathleen Watt
    •  & Lynne-Marie Postovit

  • News & Views |

    Coordination of protein quality control processes across organelles is poorly understood. A study now shows that the cytosolic juxtanuclear quality control (JUNQ) and intranuclear quality control (INQ) compartments face each other on opposite sides of the nuclear envelope before their vacuolar degradation, promoting proteostasis.

    • Simon Alberti
    •  & Serena Carra

  • Article
    | Open Access

    Levra Levron et al. report that epidermal injury elicits the priming of distant memory progenitors that have not contributed in the original healing, but acquire enhanced repair abilities, although favouring field cancerization.

    • Chiara Levra Levron
    • , Mika Watanabe
    •  & Giacomo Donati

  • News & Views |

    The house-keeping aminoacyl-tRNA synthetases are increasingly recognized for their regulatory roles beyond protein synthesis. Research now uncovers a function of nuclear arginyl-tRNA synthetase in the regulation of alternative mRNA splicing through SRRM2 in response to inflammation and decreased arginine levels.

    • Jie Chen

  • Comment |

    Alternative splicing of eukaryotic messenger RNA transcripts often leads to the production of several mature RNAs — including linear RNAs and circular RNAs (circRNAs) — from a single gene locus. The names given to circRNAs are often ambiguous and lack consistency across studies. This Comment calls on the community to embrace a common nomenclature for naming circRNAs to ensure clarity and reproducibility.

    • Ling-Ling Chen
    • , Albrecht Bindereif
    •  & Fangqing Zhao

  • News & Views |

    Tight regulation of the activity of EWS–ETS fusion proteins is essential for the growth of Ewing sarcomas. Two new studies show that the transcriptional repressor ETV6 is essential for tumour growth, acting to restrain fusion-protein-mediated gene activation, and revealing the importance of tissue-specific transcription factors to oncogenesis.

    • April A. Apfelbaum
    •  & Elizabeth R. Lawlor

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