Single-cell Hi-C bridges microscopy and genome-wide sequencing approaches to study 3D chromatin organization

Bioessays. 2017 Oct;39(10). doi: 10.1002/bies.201700104. Epub 2017 Aug 9.


Recent years have witnessed an explosion of the single-cell biochemical toolbox including chromosome conformation capture (3C)-based methods that provide novel insights into chromatin spatial organization in individual cells. The observations made with these techniques revealed that topologically associating domains emerge from cell population averages and do not exist as static structures in individual cells. Stochastic nature of the genome folding is likely to be biologically relevant and may reflect the ability of chromatin fibers to adopt a number of alternative configurations, some of which could be transiently stabilized and serve regulatory purposes. Single-cell Hi-C approaches provide an opportunity to analyze chromatin folding in rare cell types such as stem cells, tumor progenitors, oocytes, and totipotent cells, contributing to a deeper understanding of basic mechanisms in development and disease. Here, we review key findings of single-cell Hi-C and discuss possible biological reasons and consequences of the inferred dynamic chromatin spatial organization.

Keywords: CTCF/cohesin-anchored loop; TAD; chromatin; chromatin compartment; genome spatial organization; single-cell Hi-C.

Publication types

  • Review
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin / metabolism*
  • Chromatin Assembly and Disassembly / genetics
  • Chromatin Assembly and Disassembly / physiology
  • Chromosome Mapping
  • Microscopy / methods*


  • Chromatin