Epigenetic memory articles within Nature

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  • Article
    | Open Access

    Disturbances in the gut microbiota of male mice manifest as fitness defects in their offspring by affecting plancenta function, revealing a paternal gut–germline axis.

    • Ayele Argaw-Denboba
    • , Thomas S. B. Schmidt
    •  & Jamie A. Hackett

  • Article |

    The DNA modification N6-methyladenine regulates gene expression during mouse trophoblast development by depositing at the boundaries of active chromatin and preventing its spread by antagonizing the chromatin organizer SATB1.

    • Zheng Li
    • , Shuai Zhao
    •  & Andrew Z. Xiao

  • Article |

    In Caenorhabditis elegans, the ribonucleotidyltransferase RDE-3 adds alternating uridine and guanosine ribonucleotides to the 3′ termini of RNAs, a key step in RNA interference and thus epigenetic inheritance in the C. elegans germline.

    • Aditi Shukla
    • , Jenny Yan
    •  & Scott Kennedy

  • Article |

    Single-cell allelic HiC analysis, combined with allelic gene expression and chromatin states, reveals parent-of-origin-specific dynamics of chromosome organization and gene expression during mouse preimplantation development.

    • Samuel Collombet
    • , Noémie Ranisavljevic
    •  & Edith Heard

  • Article |

    Single-cell mapping of chromatin accessibility, DNA methylation and RNA expression during gastrulation in mouse embryos shows characteristic epigenetic changes that accompany formation of the primary germ layers.

    • Ricard Argelaguet
    • , Stephen J. Clark
    •  & Wolf Reik

  • Letter |

    The effect of vitamin C deprivation on mouse germline development is analysed, revealing that maternal vitamin C is required for proper DNA demethylation and the development of fetal oocytes, whereas the lack of vitamin C during pregnancy leads to reduced female fecundity in the offspring.

    • Stephanie P. DiTroia
    • , Michelle Percharde
    •  & Miguel Ramalho-Santos

  • Letter |

    Spatial genome organization into lamina-associated domains is first established in the mouse zygote immediately after fertilization without inheritance from the maternal germline—with the paternal and maternal pronucleus exhibiting different organization, which subsequently converges prior to implantation of the embryo.

    • Máté Borsos
    • , Sara M. Perricone
    •  & Jop Kind

  • Letter |

    By applying an optimized ATAC-seq protocol to human early embryos, distinct accessible chromatin landscapes are found before and after zygotic genome activation, revealing a marked epigenetic transition during zygotic genome activation and putative regulatory elements wiring human early development.

    • Jingyi Wu
    • , Jiawei Xu
    •  & Yingpu Sun

  • Analysis
    | Open Access

    Investing in adolescents as the parents of the next generation is important for the wellbeing of current and future generations.

    • George C. Patton
    • , Craig A. Olsson
    •  & Susan M. Sawyer

  • Article |

    Analysis of parental allele-specific chromatin accessibility genome-wide in mouse zygotes and morula embryos, and investigation of the epigenetic mechanisms underlying these allelic sites, identifying maternal H3K27me3 as a DNA methylation-independent mechanism for genomic imprinting.

    • Azusa Inoue
    • , Lan Jiang
    •  & Yi Zhang

  • Letter |

    An analysis of mouse skin reveals that super-enhancers are critical to identity, lineage commitment and plasticity of adult stem cells; dynamic super-enhancer remodelling in new niches is dependent on the levels of pioneer transcription factor SOX9, which is identified as a key regulator of super-enhancer chromatin for hair follicle stem cells.

    • Rene C. Adam
    • , Hanseul Yang
    •  & Elaine Fuchs

  • Article |

    This study uses single-cell expression profiling of pluripotent stem cells after various perturbations, and uncovers a high degree of variability that can be inherited through cell divisions—modulating microRNA or external signalling pathways induces a ground state with reduced gene expression heterogeneity and a distinct chromatin profile.

    • Roshan M. Kumar
    • , Patrick Cahan
    •  & James J. Collins

  • Letter |

    The Arabidopsis thaliana floral repressor FLC is epigenetically silenced by prolonged cold in a process called vernalization and then is reactivated before the completion of seed development; a histone demethylase, ELF6, is now shown to be involved in reactivating FLC in reproductive tissues, allowing the resetting of FLC expression and thus the requirement for vernalization in each generation.

    • Pedro Crevillén
    • , Hongchun Yang
    •  & Caroline Dean

  • Letter |

    Genome-scale DNA methylation maps over early human embryogenesis and embryonic stem cell derivation provide insights into shared and unique modes of regulation when compared to the mouse model, including relationships to gene expression, transposable element activity, and maternal-specific methylation.

    • Zachary D. Smith
    • , Michelle M. Chan
    •  & Alexander Meissner

  • Letter |

    Using a new method to estimate DNA methylation turnover rate, embryonic stem cells are shown to lack clonal transmission of methylation but still maintain a stable epigenetic state, whereas somatic cells transmit methylation clonally but lose epigenetic state coherence owing to the persistence of accumulated methylation errors.

    • Zohar Shipony
    • , Zohar Mukamel
    •  & Amos Tanay

  • Article |

    Genome-wide analysis of matched human IVF embryonic stem cells (IVF ES cells), induced pluripotent stem cells (iPS cells) and nuclear transfer ES cells (NT ES cells) derived by somatic cell nuclear transfer (SCNT) reveals that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT; NT ES cells and iPS cells derived from the same somatic cells contain comparable numbers of de novo copy number variations, but whereas DNA methylation and transcriptome profiles of NT ES cells and IVF ES cells are similar, iPS cells have residual patterns typical of parental somatic cells.

    • Hong Ma
    • , Robert Morey
    •  & Shoukhrat Mitalipov

  • Article |

    The molecular basis for mating-type determination in the ciliate Paramecium has been elucidated, revealing a novel function for a class of small RNAs — these scnRNAs are typically involved in reprogramming the Paramecium genome during sexual reproduction by recognizing and excising transposable elements, but they are now found to be co-opted to switch off expression of the newly identified mating-type gene mtA by excising its promoter, and to mediate epigenetic inheritance of mating types across sexual generations.

    • Deepankar Pratap Singh
    • , Baptiste Saudemont
    •  & Eric Meyer

  • Article |

    Pluripotent stem cells can be generated in the laboratory through somatic cell nuclear transfer (generating nuclear transfer embryonic stem cells, ntESCs) or transcription-factor-based reprogramming (producing induced pluripotent stem cells, iPSCs). These methods reset the methylation signature of the genome — but to what extent? Here it is found that mouse iPSCs 'remember' the methylation status of their tissue of origin, but the methylation of ntESCs is more similar to that of naturally produced ES cells.

    • K. Kim
    • , A. Doi
    •  & G. Q. Daley

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