Epigenetics articles within Nature

  • News & Views |

    There is debate about how epigenetic marks, such as methyl groups on DNA, can be passed down from parent to offspring. A mouse model involving targeted DNA methylation will better equip researchers to study this process.

    • Serge McGraw
    •  & Sarah Kimmins
  • Research Briefing |

    Cells in which the whole genome has been doubled do not upscale protein synthesis to cope with the increase in DNA. Instead, a shortage of proteins that regulate the packing of DNA in the nucleus leads to poor segregation of DNA structures, which eventually contributes to the development of cancer.

  • Research Briefing |

    Gene expression and features of the DNA–protein complex chromatin were mapped together at high spatial resolution in tissue sections of the mouse or human brain. This spatially resolved technology enables the examination of the spatio-temporal dynamics and regulation of gene expression in complex mammalian tissues.

  • 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
  • Obituary |

    Biologist who revolutionized the chromatin and gene-expression field.

    • Sharon Dent
    •  & Shiv Grewal
  • 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
  • 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 |

    It emerges that the SARS-CoV-2 virus has evolved to mimic one of the histone proteins that package DNA in the cell nucleus. This mimicry leads to disrupted gene transcription and a diminished antiviral response.

    • Lisa Thomann
    •  & Volker Thiel
  • News & Views |

    Gene expression is regulated by clusters of regulatory DNA sequences called enhancers. Basic design principles that protect enhancer networks against the harmful effects of genetic mutations have now been elucidated.

    • Ran Elkon
    •  & Reuven Agami
  • 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

    A study shows that the three-dimensional conformation of the human genome influences the positioning of DNA replication initiation zones, highlighting cohesin-mediated loop anchors as essential determinants of their precise location.

    • Daniel J. Emerson
    • , Peiyao A. Zhao
    •  & Jennifer E. Phillips-Cremins
  • News & Views |

    It emerges that high blood sugar deregulates the enzyme TET3 in the eggs of female mice, preventing it from properly modifying sperm-derived DNA when eggs are fertilized. This leads to metabolic defects in adult progeny.

    • Yumiko K. Kawamura
    •  & Antoine H. F. M. Peters
  • News & Views |

    A protein complex called the rixosome helps to degrade RNA transcripts that linger after gene expression ceases. This discovery points to distinct roles for the rixosome in regulating chromatin in different species.

    • Michael Uckelmann
    •  & Chen Davidovich
  • Outlook |

    If biological ageing can be slowed, halted or rewound, are the machine-learning algorithms the best way to measure it? Some experts are unconvinced.

    • Liam Drew
  • Article |

    Following global DNA demethylation, mouse gonadal primordial germ cells undergo remodelling of repressive chromatin modifications, resulting in a sex-specific signature that is required to safeguard the transcriptional program.

    • Tien-Chi Huang
    • , Yi-Fang Wang
    •  & Petra Hajkova
  • Article
    | Open Access

    In Arabidopsis thaliana, downregulation of the floral repressor FLC in response to cold occurs through a mechanism in which the FLC activator FRIGIDA is sequestered into biomolecular condensates away from the FLC promoter.

    • Pan Zhu
    • , Clare Lister
    •  & Caroline Dean
  • Article |

    KDM5B recruits SETDB1 to repress endogenous retroelements such as MMVL30, suppressing anti-tumour immunity, and the depletion of KDM5B induces a robust adaptive immune response and enhances the response to immune checkpoint blockade.

    • Shang-Min Zhang
    • , Wesley L. Cai
    •  & Qin Yan
  • Article
    | Open Access

    A comprehensive survey of the epigenome from 45 regions of the mouse cortex, hippocampus, striatum, pallidum and olfactory areas using single-nucleus DNA methylation sequencing enables identification of 161 cell clusters with distinct locations and projection targets and provides insights into the regulatory landscape underlying neuronal diversity and spatial regulation.

    • Hanqing Liu
    • , Jingtian Zhou
    •  & Joseph R. Ecker
  • News & Views |

    The protein UTX regulates the DNA–protein complex chromatin to suppress tumour growth. Data suggest that the ability of UTX to condense into liquid-like droplets underlies its chromatin-regulating ability.

    • David Lara-Astiaso
    •  & Brian J. P. Huntly
  • Article |

    Phase separation properties are a major determinant of UTX activity in chromatin regulation in tumour suppression, and are dependent on a core intrinsically disordered region of the protein.

    • Bi Shi
    • , Wei Li
    •  & Hao Jiang
  • News & Views |

    A previously unknown subgroup of uterine fibroid tumours is driven by mutations that result in disruption of the DNA–protein complex chromatin. The findings could inform the management of this common condition.

    • Zehra Ordulu
  • Article |

    BANP is identified as the transcription factor that binds the CGCG element in a DNA-methylation-dependent manner, opens chromatin and activates a class of essential CpG-island-regulated genes.

    • Ralph S. Grand
    • , Lukas Burger
    •  & Dirk Schübeler
  • Research Summary |

    Use of chromatin immunoprecipitation with exonuclease treatment (ChIP–exo) determines the positional organization of hundreds of chromosomal proteins throughout the Saccharomyces cerevisiae genome. The resulting ultra-high-resolution map provides insight into the regulation of genes, enhancers, replication origins, centromeres, subtelomeres and transposons.

    • B. Franklin Pugh
  • News & Views |

    Cancer-associated mutations promote the formation of pancreatic tumours after tissue injury, but how this occurs is unclear. Changes to chromatin in injured cells with such mutations explain this predisposition to malignancy.

    • Dane Vassiliadis
    •  & Mark A. Dawson
  • News & Views |

    Two studies show that some cancers are driven by genetic changes in the NSD3 protein that alter its enzymatic activity. Biochemical and structural characterization hints at a route to pharmacological reversal.

    • Martyna W. Sroka
    •  & Christopher R. Vakoc
  • News & Views |

    Neurons progressively deteriorate with age and lose resilience to injury. It emerges that treatment with three transcription factors can re-endow neurons in the mature eye with youthful characteristics and the capacity to regenerate.

    • Andrew D. Huberman
  • 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