Chromatin

  • 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
  • Article |

    The cryo-electron microscopy structure of NuA4 from Saccharomyces cerevisiae bound to the nucleosome illustrates how NuA4 is assembled and provides mechanistic insights into nucleosome recognition and transcription co-activation by a histone acetyltransferase.

    • Keke Qu
    • , Kangjing Chen
    •  & Zhucheng Chen
  • 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

    The transcriptional effect of an enhancer depends on its contact probabilities with the promoter through a nonlinear relationship, and enhancer strength determines absolute transcription levels as well as the sensitivity of a promoter to CTCF-mediated transcriptional insulation.

    • Jessica Zuin
    • , Gregory Roth
    •  & Luca Giorgetti
  • Article
    | Open Access

    PROTAC degrader–induced SWI/SNF inactivation abolishes DNA accessibility at enhancer elements of oncogenes and also tempers supra-physiologic expression of driver transcription factors, resulting in potent inhibition of tumour growth in mouse models.

    • Lanbo Xiao
    • , Abhijit Parolia
    •  & Arul M. Chinnaiyan
  • 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 |

    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
  • 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
  • Article |

    Micro Capture-C allows physical contacts to be determined at base-pair resolution, revealing that transcription factors have an important role in the maintenance of the contacts between enhancers and promoters.

    • Peng Hua
    • , Mohsin Badat
    •  & James O. J. Davies
  • 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 |

    The meiotic proteins Spo11 and Rec8, which ensure meiotic recombination and reductional chromosome segregation, have additional activities that challenge centromere stability by promoting centromeric nucleosome remodelling in both fission yeast and human cells.

    • Haitong Hou
    • , Eftychia Kyriacou
    •  & Julia Promisel Cooper
  • Article |

    Multiplexed imaging of 3,660 chromosomal loci in individual mouse embryonic stem cells by DNA seqFISH+ with immunofluorescence of 17 chromatin marks and subnuclear structures reveals invariant organization of loci within individual cells, and heterogeneous and long-lived distinct combinatorial chromatin states in cellular subpopulations.

    • Yodai Takei
    • , Jina Yun
    •  & Long Cai
  • Article |

    Binding of METTL3 to chromatin is enriched over IAP family endogenous retroviral elements in mouse embryonic stem cells, helping to ensure the integrity of heterochromatin at these elements.

    • Wenqi Xu
    • , Jiahui Li
    •  & Hongjie Shen
  • Article |

    A high-throughput, chromosome-wide analysis of DNA looping reveals its contribution to the organization of chromatin, and provides insight into how nucleosomes are deposited and organised de novo.

    • Aakash Basu
    • , Dmitriy G. Bobrovnikov
    •  & Taekjip Ha
  • Article |

    Experiments using a conditional triple-knockout mouse strain show that histone H1 regulates the activity of chromatin domains by controlling chromatin compaction, genome architecture and  histone methylation.

    • Michael A. Willcockson
    • , Sean E. Healton
    •  & Arthur I. Skoultchi
  • Article |

    Mutations in histone H1 induce the remodelling of chromatin architecture to a more relaxed state, which leads to malignant transformation through changes in histone modifications and the expression of stem cell genes.

    • Nevin Yusufova
    • , Andreas Kloetgen
    •  & Ari M. Melnick
  • 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 |

    Fission yeast grown in sublethal levels of caffeine develop heterochromatin-dependent epimutations conferring unstable heritable gene silencing that conveys resistance to caffeine, while remaining genetically wild type.

    • Sito Torres-Garcia
    • , Imtiyaz Yaseen
    •  & Robin C. Allshire
  • Article |

    During the activation of mouse macrophages by lipopolysaccharides, histone deacetylase 3 controls inflammatory responses by both repressing and activating gene transcription depending on its differential association with transcription factors.

    • Hoang C. B. Nguyen
    • , Marine Adlanmerini
    •  & Mitchell A. Lazar
  • Article
    | Open Access

    A map of cohesin-mediated chromatin loops in 24 types of human cells identifies loops that show cell-type-specific variation, indicating that chromatin loops may help to specify cell-specific gene expression programs and functions.

    • Fabian Grubert
    • , Rohith Srivas
    •  & Michael Snyder
  • Article |

    The histone variant H3.3 is phosphorylated at Ser31 in induced genes, and this selective mark stimulates the histone methyltransferase SETD2 and ejects the ZMYND11 repressor, thus revealing a role for histone phosphorylation in amplifying de novo transcription.

    • Anja Armache
    • , Shuang Yang
    •  & Steven Z. Josefowicz
  • Article |

    Cryo-electron microscopy structures of the DNA-binding domains of the pioneer transcription factor SOX2 and its close homologue SOX11 elucidate the role of these factors in initiating chromatin opening and nucleosome remodelling.

    • Svetlana O. Dodonova
    • , Fangjie Zhu
    •  & Patrick Cramer
  • Article |

    The cryo-electron microscopy structure of the yeast SWI/SNF complex bound to a nucleosome substrate provides insights into the chromatin-remodelling function of this family of protein complexes and suggests mechanisms by which the mutated proteins may cause cancer.

    • Yan Han
    • , Alexis A Reyes
    •  & Yuan He
  • Article |

    The yeast E3 ligase Bre1 forms a core–shell condensate with the scaffold protein Lge1, implicating liquid–liquid phase separation as a mechanism in the ubiquitination of histone H2B along gene bodies.

    • Laura D. Gallego
    • , Maren Schneider
    •  & Alwin Köhler
  • Article |

    The cryo-electron microscopy structure of the 16-subunit yeast SWI/SNF complex RSC in complex with a nucleosome substrate provides insights into the chromatin-remodelling function of this family of protein complexes.

    • Felix R. Wagner
    • , Christian Dienemann
    •  & Patrick Cramer
  • Article |

    Structural studies on the yeast transcription coactivator complex SAGA (Spt–Ada–Gcn5–acetyltransferase) provide insights into the mechanism of initiation of regulated transcription by this multiprotein complex, which is conserved among eukaryotes.

    • Haibo Wang
    • , Christian Dienemann
    •  & Patrick Cramer
  • Article |

    The topoisomerase Top2 and the chromatin-binding protein Hmo1 maintain under-wound and over-wound DNA at different regions within a gene and thereby modulate the topology of genes.

    • Yathish Jagadheesh Achar
    • , Mohamood Adhil
    •  & Marco Foiani
  • Article |

    The crystal structure of the SA2–SCC1 subunits of human cohesin in complex with CTCF reveals the molecular basis of the cohesin–CTCF interaction that enables the dynamic regulation of chromatin folding.

    • Yan Li
    • , Judith H. I. Haarhuis
    •  & Daniel Panne
  • Article |

    DNA replication in eukaryotes requires the histone variant H2A.Z, which binds the enzyme SUV420H1 to promote the dimethylation of histone H4, in turn recruiting the origin-recognition complex to activate early replication origins.

    • Haizhen Long
    • , Liwei Zhang
    •  & Guohong Li
  • Article |

    Two cryo-electron-microscopy images of the histone chaperone FACT interacting with components of nucleosomes shed light on how FACT manipulates nucleosomes to promote transcription, DNA repair and DNA replication.

    • Yang Liu
    • , Keda Zhou
    •  & Karolin Luger
  • Article |

    The lactylation of lysine residues on histones in mammalian cells is stimulated by hypoxia and bacterial challenges, and increased histone lactylation induces genes involved in wound healing.

    • Di Zhang
    • , Zhanyun Tang
    •  & Yingming Zhao
  • Article |

    Acetate that is produced from the breakdown of alcohol contributes to histone acetylation in the brain, indicating that there is a direct link between alcohol metabolism and gene expression.

    • P. Mews
    • , G. Egervari
    •  & S. L. Berger