Histone post-translational modifications articles within Nature

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  • 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 |

    Cellular lysine residues can be both methylated and acetylated on the same sidechain to form Nε-acetyl-Nε-methyllysine (Kacme), which is found on histone H4 across a range of species and across mammalian tissues and is associated with active chromatin.

    • William J. Lu-Culligan
    • , Leah J. Connor
    •  & Matthew D. Simon

  • Article
    | Open Access

    Missegregated chromosomes that are sequestrated in micronuclei are subject to changes in histone modifications leading to abnormalities in chromatin accessibility that remain long after the chromosomes have been reincorporated into the primary nucleus.

    • Albert S. Agustinus
    • , Duaa Al-Rawi
    •  & Samuel F. Bakhoum

  • 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 |

    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 |

    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 |

    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 |

    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 |

    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 |

    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 |

    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 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

  • Letter |

    Crystal structures of the Polycomb-like proteins PHF1 and MTF2 with bound DNA and histone peptides show that extended homologous regions of the two proteins form a winged-helix structure that has an unexpected mechanism of binding to unmethylated CpG-containing DNA motifs.

    • Haojie Li
    • , Robert Liefke
    •  & Zhanxin Wang

  • 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

  • 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.

    • Xiaoyu Liu
    • , Chenfei Wang
    •  & Shaorong Gao

  • Letter |

    A cryo-electron microscopy structure of the DNA damage repair protein 53BP1 bound to a nucleosome illuminates the way 53BP1 recognizes two types of histone modifications (a methyl group and a ubiquitin moiety), and provides insight into the highly specified recognition and recruitment of 53BP1 to modified chromatin.

    • Marcus D. Wilson
    • , Samir Benlekbir
    •  & Daniel Durocher

  • Letter |

    We have a limited understanding of how cells mark and identify newly replicated genomic loci that have a sister chromatid; here, unmethylated K20 in the tail of new histone H4 is shown to serve as a signature of post-replicative chromatin, which is specifically recognized by the homologous recombination complex TONSL–MMS22L.

    • Giulia Saredi
    • , Hongda Huang
    •  & Anja Groth

  • Article |

    Crystal structures of the SET domains of MLL3 and a mutant MLL1 either unbound or complexed with domains from RBBP5 and ASH2L are determined; a combination of structural, biochemical and computational analyses reveals a two-step activation mechanism of MLL family proteins, which may be relevant for other histone methyltransferases.

    • Yanjing Li
    • , Jianming Han
    •  & Ming Lei

  • Article |

    A ChIP-seq analysis of the DNA-binding properties of mutant gain-of-function p53 protein compared to wild-type p53 reveals the gain-of-function proteins bind to and activate a distinct set of genes including chromatin modifying enzymes such as the histone methyltransferase MLL; small molecular inhibitors of MLL function may represent a new target for cancers with mutant p53.

    • Jiajun Zhu
    • , Morgan A. Sammons
    •  & Shelley L. Berger

  • Letter |

    T-cell acute lymphoblastic leukaemia (T-ALL) is a haematological malignancy with a poor prognosis and no available targeted therapies; now two histone H3 lysine 27 demethylases, JMJD3 and UTX, are shown to have contrasting roles in human T-ALL cells and a mouse model of the disease, and a small molecule demethylase inhibitor is found to inhibit the growth of T-ALL cell lines, introducing a potential therapeutic avenue for acute leukaemia.

    • Panagiotis Ntziachristos
    • , Aristotelis Tsirigos
    •  & Iannis Aifantis

  • Letter |

    Global transcriptional and epigenomic analyses in diverse cell types reveal that the primary action of Myc is to up- and downregulate transcription of distinct groups of genes, rather than to amplify transcription of all active genes; general RNA amplification, when observed, is better explained as an indirect consequence of Myc’s action on cellular physiology.

    • Arianna Sabò
    • , Theresia R. Kress
    •  & Bruno Amati

  • Letter |

    This study shows that PADI4-mediated citrullination occurs during pluripotency and that citrullination of H1 results in loosening of chromatin compaction; furthermore, citrullination is shown to be important for the activation of stem-cell genes, for iPS cell reprogramming and to maintain pluripotent cells in the early mouse embryo.

    • Maria A. Christophorou
    • , Gonçalo Castelo-Branco
    •  & Tony Kouzarides

  • Letter |

    The malaria parasite Plasmodium falciparum escapes immune detection by expressing one of 60 antigenically distinct var genes at any one time during the course of infection: here it is shown that the P. falciparum protein PfSETvs has a key role in var gene silencing through the trimethylation of histone H3K36.

    • Lubin Jiang
    • , Jianbing Mu
    •  & Louis H. Miller

  • Article |

    This study shows that 53BP1 recruitment to sites of DNA damage involves dual recognition of H4K20me2 and H2AK15 histone ubiquitination; the ubiquitin mark and the surrounding epitope on H2A are read by a region of 53BP1 designated the ubiquitination-dependent recruitment motif.

    • Amélie Fradet-Turcotte
    • , Marella D. Canny
    •  & Daniel Durocher

  • Letter |

    In Arabidopsis, RNA-directed DNA methylation is a poorly understood gene silencing pathway in which small interfering RNAs generated by RNA polymerase IV (Pol-IV) target a DNA methyltransferase to its sites of action; here structural and genomic analyses demonstrate that SHH binds chromatin via repressive histone modifications and recruits Pol-IV to enable siRNA production.

    • Julie A. Law
    • , Jiamu Du
    •  & Steven E. Jacobsen

  • Article |

    A rare cell subpopulation within mouse embryonic stem cell cultures is identified that exhibits properties of two-cell (2C) embryos; the interconversion of ES cells to 2C cells correlates with endogenous retroviral activity.

    • Todd S. Macfarlan
    • , Wesley D. Gifford
    •  & Samuel L. Pfaff

  • Letter |

    Genome-wide analysis shows that H2B S112 O-linked to N-acetylglucosamine is frequently located near transcribed genes, suggesting that histone GlcNAcylation facilitates transcription of the genes.

    • Ryoji Fujiki
    • , Waka Hashiba
    •  & Shigeaki Kato

  • Letter |

    The lysine residues of histone proteins can be acetylated or methylated, with important effects on gene expression. Until recently the protein modules that bind acetyl-lysine have been limited to bromodomains. However, the tandem plant homeodomain (PHD) finger of human DPF3b — which is involved in gene activation — has also been reported to bind to acetylated histones. Here, three-dimensional solution structures of DPF3b offer mechanistic insight into how this protein recognizes acetylation marks.

    • Lei Zeng
    • , Qiang Zhang
    •  & Ming-Ming Zhou

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