Multiplex chromatin interactions with single-molecule precision

Nature. 2019 Feb;566(7745):558-562. doi: 10.1038/s41586-019-0949-1. Epub 2019 Feb 18.


The genomes of multicellular organisms are extensively folded into 3D chromosome territories within the nucleus1. Advanced 3D genome-mapping methods that combine proximity ligation and high-throughput sequencing (such as chromosome conformation capture, Hi-C)2, and chromatin immunoprecipitation techniques (such as chromatin interaction analysis by paired-end tag sequencing, ChIA-PET)3, have revealed topologically associating domains4 with frequent chromatin contacts, and have identified chromatin loops mediated by specific protein factors for insulation and regulation of transcription5-7. However, these methods rely on pairwise proximity ligation and reflect population-level views, and thus cannot reveal the detailed nature of chromatin interactions. Although single-cell Hi-C8 potentially overcomes this issue, this method may be limited by the sparsity of data that is inherent to current single-cell assays. Recent advances in microfluidics have opened opportunities for droplet-based genomic analysis9 but this approach has not yet been adapted for chromatin interaction analysis. Here we describe a strategy for multiplex chromatin-interaction analysis via droplet-based and barcode-linked sequencing, which we name ChIA-Drop. We demonstrate the robustness of ChIA-Drop in capturing complex chromatin interactions with single-molecule precision, which has not been possible using methods based on population-level pairwise contacts. By applying ChIA-Drop to Drosophila cells, we show that chromatin topological structures predominantly consist of multiplex chromatin interactions with high heterogeneity; ChIA-Drop also reveals promoter-centred multivalent interactions, which provide topological insights into transcription.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites / genetics
  • Cell Line
  • Chromatin / chemistry
  • Chromatin / genetics*
  • Chromatin / metabolism*
  • Drosophila melanogaster / cytology
  • Drosophila melanogaster / genetics
  • Microfluidics / methods*
  • Microfluidics / standards
  • Nucleic Acid Conformation
  • Promoter Regions, Genetic / genetics
  • Protein Binding
  • RNA Polymerase II / chemistry
  • RNA Polymerase II / metabolism
  • Sequence Analysis, DNA / methods*
  • Single Molecule Imaging / methods*
  • Single Molecule Imaging / standards*
  • Transcription, Genetic


  • Chromatin
  • RNA Polymerase II