Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots

Sci Rep. 2016 Oct 11;6:34982. doi: 10.1038/srep34982.


Single-cell analysis of the three-dimensional (3D) chromosome structure can reveal cell-to-cell variability in genome activities. Here, we propose to apply recurrence plots, a mathematical method of nonlinear time series analysis, to reconstruct the 3D chromosome structure of a single cell based on information of chromosomal contacts from genome-wide chromosome conformation capture (Hi-C) data. This recurrence plot-based reconstruction (RPR) method enables rapid reconstruction of a unique structure in single cells, even from incomplete Hi-C information.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cells, Cultured
  • Chromosome Structures*
  • Chromosomes / ultrastructure*
  • Imaging, Three-Dimensional / methods*
  • Mice
  • Models, Theoretical
  • Single-Cell Analysis
  • Spatio-Temporal Analysis
  • Th1 Cells / chemistry