Epigenomics articles within Nature

Featured

  • 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

    This study uses epi-retro-seq to link single-cell epigenomes and cell types to long-distance projections for neurons dissected from different regions projecting to different targets across the whole mouse brain.

    • Jingtian Zhou
    • , Zhuzhu Zhang
    •  & Edward M. Callaway

  • 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
    | Open Access

    Computational and machine-learning approaches that integrate genomic and transcriptomic variation from paired primary and metastatic non-small cell lung cancer samples from the TRACERx cohort reveal the role of transcriptional events in tumour evolution.

    • Carlos Martínez-Ruiz
    • , James R. M. Black
    •  & Nicholas McGranahan

  • Article
    | Open Access

    The authors present two technologies for spatially resolved, genome-wide, joint profiling of the epigenome and transcriptome by cosequencing chromatin accessibility and gene expression, or histone modifications and gene expression on the same tissue section at near-single-cell resolution.

    • Di Zhang
    • , Yanxiang Deng
    •  & Rong Fan

  • Article
    | Open Access

    A study maps genetic and epigenetic heterogeneity of primary colorectal adenomas and cancers at single-clone resolution through spatial multi-omic profiling of individual glands and adjacent normal tissue.

    • Timon Heide
    • , Jacob Househam
    •  & Andrea Sottoriva

  • Article
    | Open Access

    Spatial-ATAC-seq—spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing—delineated tissue-region-specific epigenetic landscapes in mouse embryos and identified gene regulators involved in the development of the central nervous system and the lymphoid tissue.

    • Yanxiang Deng
    • , Marek Bartosovic
    •  & Rong Fan

  • 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

  • Article
    | Open Access

    Data on de novo mutations in Arabidopsis thaliana reveal that mutations do not occur randomly; instead, epigenome-associated mutation bias reduces the occurrence of deleterious mutations.

    • J. Grey Monroe
    • , Thanvi Srikant
    •  & Detlef Weigel

  • 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

  • Article
    | Open Access

    Quantitative analysis of the methylation of mouse cortical neurons that project to different cortical and subcortical target regions provides insight into genetic mechanisms that contribute to differences in cell function.

    • Zhuzhu Zhang
    • , Jingtian Zhou
    •  & Edward M. Callaway

  • Article |

    A ChIP–exo method is used to define the genome-wide positional organization of proteins associated with gene transcription, DNA replication, centromeres, subtelomeres and transposons, revealing distinct protein assemblies for constitutive and inducible gene expression.

    • Matthew J. Rossi
    • , Prashant K. Kuntala
    •  & B. Franklin Pugh

  • Article |

    A comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin structure, the methylome and 3D genome organization in the zebrafish (Danio rerio) enables identification of species-specific and evolutionarily conserved regulatory features, and provides a foundation for modelling studies on human disease and development.

    • Hongbo Yang
    • , Yu Luan
    •  & Feng Yue

  • Article |

    Analysis of cis-regulatory chromatin interactions, open chromatin and transcriptomes for different cell types isolated from mid-gestational human cortex samples provides insights into gene regulation during development.

    • Michael Song
    • , Mark-Phillip Pebworth
    •  & Yin Shen

  • Perspective |

    The authors summarize the history of the ENCODE Project, the achievements of ENCODE 1 and ENCODE 2, and how the new data generated and analysed in ENCODE 3 complement the previous phases.

    • Federico Abascal
    • , Reyes Acosta
    •  & Richard M. Myers

  • Article
    | Open Access

    ChIP–seq and CETCh–seq data are used to analyse binding maps for 208 transcription factors and other chromatin-associated proteins in a single human cell type, providing a comprehensive catalogue of the transcription factor landscape and gene regulatory networks in these cells.

    • E. Christopher Partridge
    • , Surya B. Chhetri
    •  & Eric M. Mendenhall

  • Article |

    An experimental and analytical pipeline is used to assess, at the single-cell level, complex transcriptional and morphological mutant phenotypes that occur in mouse embryos during gastrulation.

    • Stefanie Grosswendt
    • , Helene Kretzmer
    •  & Alexander Meissner

  • Article |

    Structural cells implement a broad range of immune-regulatory functions beyond their roles as barriers and connective tissues, and they utilize an epigenetically encoded potential for immune gene activation in their rapid response to viral infection.

    • Thomas Krausgruber
    • , Nikolaus Fortelny
    •  & Christoph Bock

  • 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 |

    A single-cell approach is used to follow the heritable stochastic changes to DNA methylation that occur in primary chronic lymphocytic leukaemia and healthy B cells, allowing the tracing of cell lineage histories and evolution during treatment with ibrutinib.

    • Federico Gaiti
    • , Ronan Chaligne
    •  & Dan A. Landau

  • Letter |

    A strategy using droplet-based and barcode-linked sequencing captures multiplex chromatin interactions at single-molecule precision, and here provides topological insight into chromatin structures and transcription in Drosophila.

    • Meizhen Zheng
    • , Simon Zhongyuan Tian
    •  & Yijun Ruan

  • Letter |

    Gonadal germline epigenetic reprogramming involves an interplay between DNA methylation, the polycomb complex and Tet1 in both DNA methylation dependent and independent roles, to ensure the activation of a specific subset of genes critical for progression of gametogenesis.

    • Peter W. S. Hill
    • , Harry G. Leitch
    •  & Petra Hajkova

  • Perspective |

    The 4D Nucleome Network aims to map the spatial and dynamic organization of the human and mouse genomes to gain insight into the structure and biological functions of the nucleus.

    • Job Dekker
    • , Andrew S. Belmont
    •  & Sheng Zhong

  • Article |

    A technique called genome architecture mapping (GAM) involves sequencing DNA from a large number of thin nuclear cryosections to develop a map of genome organization without the limitations of existing 3C-based methods.

    • Robert A. Beagrie
    • , Antonio Scialdone
    •  & Ana Pombo

  • Letter |

    Three papers in this issue of Nature use highly sensitive ChIP–seq assays to describe the dynamic patterns of histone modifications during early mouse embryogenesis, showing that oocytes have a distinctive epigenome and providing insights into how the maternal gene expression program transitions to the zygotic program.

    • Bingjie Zhang
    • , Hui Zheng
    •  & Wei Xie

  • Article |

    An improved ATAC-seq approach is used to describe a genome-wide view of accessible chromatin and cis-regulatory elements in mouse preimplantation embryos, allowing construction of a regulatory network of early development that helps to identify key modulators of lineage specification.

    • Jingyi Wu
    • , Bo Huang
    •  & Wei Xie

  • Article |

    The prevalence of N6-adenine DNA methylation in mammals was previously unknown; this study reveals that N6-methyladenine can be found in mouse embryonic stem cells, especially at subfamilies of young (<1.5 million years old) LINE-1 transposons.

    • Tao P. Wu
    • , Tao Wang
    •  & Andrew Z. Xiao

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