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

Yoshito Hirata; Arisa Oda; Kunihiro Ohta; Kazuyuki Aihara

doi:10.1038/srep34982

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

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

Authors

Yoshito Hirata¹, Arisa Oda², Kunihiro Ohta², Kazuyuki Aihara¹

Affiliations

¹ Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.
² Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.

Abstract

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