title: Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots.
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.
authors.affiliation: Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.
authors.forename: Yoshito
authors.initials: Y
authors.lastname: Hirata
authors.affiliation: Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
authors.forename: Arisa
authors.initials: A
authors.lastname: Oda
authors.affiliation: Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
authors.forename: Kunihiro
authors.initials: K
authors.lastname: Ohta
authors.affiliation: Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.
authors.forename: Kazuyuki
authors.initials: K
authors.lastname: Aihara
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D022004:Chromosome Structures; D002875:Chromosomes / Q000648:ultrastructure*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D051379:Mice; D008962:Models, Theoretical; D059010:Single-Cell Analysis; D062211:Spatio-Temporal Analysis; D018417:Th1 Cells / Q000737:chemistry