Chromatin articles within Nature

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  • Article |

    Gene activation may involve the formation of a DNA loop that connects enhancer-bound transcription factors with the transcription apparatus at the core promoter. But this process is not well understood. Here, two proteins, mediator and cohesin, are shown to connect the enhancers and core promoters of active genes in embryonic stem cells. These proteins seem to generate cell-type-specific DNA loops linked to the gene expression program of each cell.

    • Michael H. Kagey
    • , Jamie J. Newman
    •  & Richard A. Young

  • 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

  • Article |

    Cardiac hypertrophy is associated with a decrease in expression of the adult isoform of the molecular motor myosin heavy chain (α-MHC) and the induction of expression of its fetal isoform (β-MHC). Here the authors reveal the mechanism regulating this switch in expression, which impairs heart function. Cardiac stress in adult hearts reactivates the developmental chromatin-modifying complex Brg1/BAF, which interacts with histone deacetylase and poly (ADP ribose) polymerase to induce a pathological α-MHC-to-β-MHC shift.

    • Calvin T. Hang
    • , Jin Yang
    •  & Ching-Pin Chang

  • Letter |

    Nucleosomes are composed of around 147 bases of DNA wrapped around an octamer of histone proteins. Here, a genome-wide analysis of nucleosome positioning in Arabidopsis thaliana has been combined with profiles of DNA methylation at single base resolution, revealing 10-base periodicities in the DNA methylation status of nucleosome-bound DNA. The results indicate that nucleosome positioning influences the pattern of DNA methylation throughout the genome.

    • Ramakrishna K. Chodavarapu
    • , Suhua Feng
    •  & Matteo Pellegrini

  • Letter |

    Most human gene promoters are embedded within CpG islands that lack DNA methylation and coincide with sites at which histone H3 lysine 4 is trimethylated (H3K4me3 sites). Here, a zinc-finger protein, Cfp1, is found to be associated with non-methylated CpG islands and H3K4me3 sites throughout the genome in the mouse brain. A primary function of non-methylated CpG islands might be to genetically determine the local chromatin modification state by interaction with Cfp1 and perhaps other CpG-binding proteins.

    • John P. Thomson
    • , Peter J. Skene
    •  & Adrian Bird

  • Letter |

    To study the changes in chromatin structure that accompany zygotic genome activation and pluripotency during the maternal–zygotic transition (MZT), the genomic locations of histone H3 modifications and RNA polymerase II have been mapped during this transition in zebrafish embryos. H3 lysine 27 trimethylation and H3 lysine 4 trimethylation are only detected after MZT; evidence is provided that the bivalent chromatin domains found in cultured embryonic stem cells also exist in embryos.

    • Nadine L. Vastenhouw
    • , Yong Zhang
    •  & Alexander F. Schier

  • Letter |

    The amino-terminal tails of histone proteins are subject to a variety of post-translational modifications; addition or removal of these 'marks' facilitates gene activation or silencing. Here, a mechanism is defined that modulates the activity of the dual-specificity histone demethylase LSD1 during androgen-dependent transcription. Androgen-dependent signalling through protein kinase C beta I leads to phosphorylation of a histone amino acid, which prevents demethylation of an adjacent amino acid by LSD1.

    • Eric Metzger
    • , Axel Imhof
    •  & Roland Schüle

  • News & Views |

    When environmental temperatures rise, plants seek help from their core molecular mechanisms to adapt. The chromatin protein H2A.Z, which regulates gene expression, is one such rescue molecule.

    • Roger B. Deal
    •  & Steven Henikoff

  • Letter |

    Endogenous retroviruses (ERVs) are widely dispersed in mammalian genomes, and are silenced in somatic cells by DNA methylation. Here, an ERV silencing pathway independent of DNA methylation is shown to operate in embryonic stem cells. The pathway involves the histone H3K9 methyltransferase ESET and might be important for ERV silencing during the stages in embryogenesis when DNA methylation is reprogrammed.

    • Toshiyuki Matsui
    • , Danny Leung
    •  & Yoichi Shinkai

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