Chromosome conformation capture-based methods

Chromosome conformation capture (3C)-based methods reveal chromosome organization within the nucleus by determining the physical proximity of pairs of points along chromatin. They preserve chromatin interactions by cross-linking followed by fragmentation, ligation and sequencing of interacting regions. Genome organization affects processes such as transcription, repair and DNA replication.

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
  • Reviews |

    High-resolution studies of chromosome conformation are revealing that the 3D genome is organized into smaller structural features than was previously supposed and is primarily composed of compartmental domains and CTCF loops. In this Perspectives article Rowley and Corces describe the latest views on the organizational drivers and principles of the 3D genome, and the interplay between genome activity and organization.

    • M. Jordan Rowley
    •  & Victor G. Corces
  • Protocols |

    Chrom3D is a computational platform designed to simulate the spatial positioning of chromosome domains relative to each other and to the nuclear periphery, starting from, for example, chromosome conformation capture and lamin ChIP-sequencing data.

    • Jonas Paulsen
    • , Tharvesh Moideen Liyakat Ali
    •  & Philippe Collas
    Nature Protocols 13, 1137-1152
  • Protocols |

    This protocol describes targeted chromatin capture (T2C), a high-resolution method to interrogate 3D chromatin organization and genomic interactions at sub-kilobase-pair resolution that requires minimal cell numbers and sequencing depth.

    • Petros Kolovos
    • , Rutger W W Brouwer
    • , Christel E M Kockx
    • , Michael Lesnussa
    • , Nick Kepper
    • , Jessica Zuin
    • , A M Ali Imam
    • , Harmen J G van de Werken
    • , Kerstin S Wendt
    • , Tobias A Knoch
    • , Wilfred F J van IJcken
    •  & Frank Grosveld
    Nature Protocols 13, 459-477
  • Research |

    Schalbetter et al. show by Hi-C and modelling that mitotic chromosome compaction in budding yeast occurs by cis-looping of chromatin, and reveal distinct roles for cohesin and condensin depending on chromatin context.

    • Stephanie Andrea Schalbetter
    • , Anton Goloborodko
    • , Geoffrey Fudenberg
    • , Jon-Matthew Belton
    • , Catrina Miles
    • , Miao Yu
    • , Job Dekker
    • , Leonid Mirny
    •  & Jonathan Baxter
    Nature Cell Biology 19, 1071-1080

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