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

  • Research | | open

    Chromatin is folded into Topologically Associating domains (TADs), with the organization and folding hierarchy of the TADs being highly dynamic. Here the authors develop a parsimonious randomly cross-linked (RCL) polymer model that maps high frequency encounters present in Hi-C data within and between TADs and reconstruct TADs across cell differentiation, revealing local chromatin re-organization.

    • O. Shukron
    • , V. Piras
    • , D. Noordermeer
    •  & D. Holcman
  • Research | | open

    Gene expression dysregulation domains (GEDDs) have been reported in Down syndrome (DS) cells, where changes in gene expression are clustered. Here the authors find that, while GEDDs are present in DS cells and in the Dp1Tyb mouse model of DS, GEDDs do not depend on the DS genotype and occur whenever gene expression changes, suggesting they result from the clustering of co-regulated genes as a function of mammalian genome organisation.

    • Helena Ahlfors
    • , Nneka Anyanwu
    • , Edvinas Pakanavicius
    • , Natalia Dinischiotu
    • , Eva Lana-Elola
    • , Sheona Watson-Scales
    • , Justin Tosh
    • , Frances Wiseman
    • , James Briscoe
    • , Karen Page
    • , Elizabeth M. C. Fisher
    •  & Victor L. J. Tybulewicz
  • Research |

    HiChIRP combines a modified chromosome conformation capture protocol with enrichment of RNA-associated chromosome conformation to visualize genome-wide looping linked to an RNA of interest.

    • Maxwell R. Mumbach
    • , Jeffrey M. Granja
    • , Ryan A. Flynn
    • , Caitlin M. Roake
    • , Ansuman T. Satpathy
    • , Adam J. Rubin
    • , Yanyan Qi
    • , Zhaozhao Jiang
    • , Shadi Shams
    • , Bryan H. Louie
    • , Jimmy K. Guo
    • , David G. Gennert
    • , M. Ryan Corces
    • , Paul A. Khavari
    • , Maninjay K. Atianand
    • , Steven E. Artandi
    • , Katherine A. Fitzgerald
    • , William J. Greenleaf
    •  & Howard Y. Chang
    Nature Methods 16, 489-492
  • Research | | open

    Chromatin looping allows for enhancer–promoter interactions that regulate transcription. Here the authors show that activation of embryonic myogenesis is associated with establishment of long-range chromatin interactions centred on Pax3-bound loci and find that Ldb1 functions as the mediator of looping interactions at a subset of Pax3 binding sites.

    • Alessandro Magli
    • , June Baik
    • , Pruthvi Pota
    • , Carolina Ortiz Cordero
    • , Il-Youp Kwak
    • , Daniel J. Garry
    • , Paul E. Love
    • , Brian D. Dynlacht
    •  & Rita C. R. Perlingeiro
  • 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

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