Chromatin structure

Chromatin structure describes the physical structure of chromatin within the eukaryotic nucleus and how structure affects chromatin processes such as transcription. The repeating unit of chromatin, the nucleosome, consists of approximately 147 base pairs of DNA wrapped around eight histone protein cores. Linker DNA, upwards of 80 base pairs long, connects two histones between each nucleosome core unit.

Latest Research and Reviews

  • Reviews |

    For appropriate control of gene expression, enhancers must communicate with the right target genes at the right time, typically over large genomic distances. In this Review, Schoenfelder and Fraser discuss our latest understanding of long-range enhancer–promoter crosstalk, including target-gene specificity, interaction dynamics, protein and RNA architects of interactions, roles of 3D genome organization and the pathological consequences of regulatory rewiring.

    • Stefan Schoenfelder
    •  & Peter Fraser
  • Research | | open

    Risk loci for type 2 diabetes (T2D) reside in pancreatic islet enhancers. Here, the authors generate high-resolution maps of islet chromatin conformation using Hi-C which they combine with ATAC-seq and ChIP-seq data to annotate candidate target genes of enhancers and validate IGF2BP2 activity in mouse islets.

    • William W. Greenwald
    • , Joshua Chiou
    • , Jian Yan
    • , Yunjiang Qiu
    • , Ning Dai
    • , Allen Wang
    • , Naoki Nariai
    • , Anthony Aylward
    • , Jee Yun Han
    • , Nikita Kadakia
    • , Laura Regue
    • , Mei-Lin Okino
    • , Frauke Drees
    • , Dana Kramer
    • , Nicholas Vinckier
    • , Liliana Minichiello
    • , David Gorkin
    • , Joseph Avruch
    • , Kelly A. Frazer
    • , Maike Sander
    • , Bing Ren
    •  & Kyle J. Gaulton
  • Research | | open

    Methodological advances have increased our understanding of chromatin structure through chromosome conformation capture techniques and high resolution imaging, but integration of these datasets is challenging. Here the authors propose GEM-FISH, a method for reconstructing the 3D models of chromosomes through systematically integrating both Hi-C and FISH data with the prior biophysical knowledge of a polymer model.

    • Ahmed Abbas
    • , Xuan He
    • , Jing Niu
    • , Bin Zhou
    • , Guangxiang Zhu
    • , Tszshan Ma
    • , Jiangpeikun Song
    • , Juntao Gao
    • , Michael Q. Zhang
    •  & Jianyang Zeng
  • Research | | open

    Dopamine dysregulation is centrally linked to major psychosis. Here, the authors characterise the hypomethylation of an enhancer within the insulin-like growth factor 2 gene in neurons of patients with major psychosis and provide evidence that this enhancer targets the tyrosine hydroxylase gene, responsible for dopamine synthesis.

    • Shraddha Pai
    • , Peipei Li
    • , Bryan Killinger
    • , Lee Marshall
    • , Peixin Jia
    • , Ji Liao
    • , Arturas Petronis
    • , Piroska E. Szabó
    •  & Viviane Labrie
  • Research | | open

    Analysis of Hi-C datasets is limited by the current existing methods for data normalization, with detection of features such as TADs and chromatin loops being inconsistent amongst different approaches. Here the authors develop Binless, a method that allows for reproducible normalization of Hi-C data independent of its resolution and compare how Binless performs in comparison with other methods.

    • Yannick G. Spill
    • , David Castillo
    • , Enrique Vidal
    •  & Marc A. Marti-Renom

News and Comment

  • News and Views |

    Chromatin organization in the nucleus plays an important role in cell-type-specific gene expression. A new study reports reconstruction of the 3D genome in single sensory neurons and provides insights into the regulation of genes encoding odorant receptors.

    • Lúcia M. Armelin-Correa
    •  & Bettina Malnic
  • Research Highlights |

    Nair et al. contrast events at specific super-enhancers after acute and chronic ligand-induced activation and show that biomolecular condensates at these enhancers undergo physical changes over time that affect chromatin conformation and gene expression.

    • Linda Koch
  • Research Highlights |

    Chromosomal inversions that relocate a limb enhancer establish patterns of asymmetric chromatin contacts, so-called architectural stripes, that result in ectopic gene expression and congenital limb phenotypes, according to a study in Nature Cell Biology.

    • Michelle Trenkmann
  • Research Highlights |

    A new technique named ChIA-Drop combines chromatin interaction analysis (ChIA) with droplet-based and barcode-linked high-throughput sequencing to capture multiplex chromatin interactions at the single-molecule level.

    • Linda Koch