Epigenetics articles within Nature

Featured

  • 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

    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

    Experiments in mice show that designed epigenome editors that contain domains of transcriptional repressors can enable stable epigenetic silencing of Pcsk9, a gene with a role in cholesterol homeostasis, without inducing DNA breaks.

    • Martino Alfredo Cappelluti
    • , Valeria Mollica Poeta
    •  & Angelo Lombardo
  • 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
  • News & Views |

    A tool that tags individual cells in a tissue with a unique barcode means that the gene-expression profile of each cell can be plotted in its original location. This allows spatial information to be captured at single-cell resolution.

    • Patrik L. Ståhl
  • News & Views Forum |

    In a huge collaborative effort, millions of cells in the mouse brain have been mapped in detail. Two scientists examine the resulting wealth of insights into gene regulation in brain cells, neuronal connections and how our own brains evolved.

    • Maria Antonietta Tosches
    •  & Heather J. Lee
  • 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 describes the molecular basis of sexual development of Toxoplasma gondii entirely in vitro, demonstrating the role and interaction of AP2XII-1 and AP2XI-2 in the developmental program of this protozoan parasite.

    • Ana Vera Antunes
    • , Martina Shahinas
    •  & Mohamed-Ali Hakimi
  • 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

    After loss of MSL2, a class of dosage-sensitive genes transitions from biallelic to monoallelic expression, whereby one allele remains active, retaining active histone modifications and transcription factor binding, and the other allele is silenced, exhibiting loss of promoter–enhancer contacts and the acquisition of DNA methylation.

    • Yidan Sun
    • , Meike Wiese
    •  & Asifa Akhtar
  • 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 |

    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
  • Research Briefing |

    Cells that have been artificially reprogrammed into states similar to embryonic stem cells — known as induced pluripotent stem cells — can bear a memory of their previous history. An innovative method that incorporates a step mimicking early development yields pluripotent cells that more closely resemble those in embryos, both on a molecular and functional level.

  • Article |

    Protein complexes containing RNA polymerase II and immature RNA are associated with active genes immediately after replication, suggesting that transmission of active transcriptional states to daughter cells may not require any additional epigenetic bookmarks.

    • Tyler K. Fenstermaker
    • , Svetlana Petruk
    •  & Alexander Mazo
  • 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
  • Article |

    A high throughput recruitment assay testing the transcriptional activity of more than 100,000 protein fragments tiling across most human chromatin regulators and transcription factors maps the locations and strengths of activation, repression and bifunctional domains, and identifies the sequences necessary for these functions.

    • Nicole DelRosso
    • , Josh Tycko
    •  & Lacramioara Bintu
  • 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