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

Scientific Reports
Yoshito HirataKazuyuki Aihara

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.

References

May 4, 2010·Nature·Zhijun DuanWilliam S Noble
Jul 23, 2011·PLoS Computational Biology·Marc A Marti-Renom, Leonid A Mirny
Apr 24, 2012·Methods : a Companion to Methods in Enzymology·Davide Baù, Marc A Marti-Renom
Nov 13, 2012·Nucleic Acids Research·Dario Meluzzi, Gaurav Arya
Feb 6, 2013·PLoS Computational Biology·Ming HuJun S Liu
Nov 8, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Zhizhuo ZhangWing-Kin Sung
Jun 17, 2014·Bioinformatics·Nelle VaroquauxJean-Philippe Vert
Sep 23, 2014·Nature Methods·Annick LesneJulien Mozziconacci
May 20, 2015·FEBS Letters·François SerraMarc A Marti-Renom
Aug 12, 2015·PLoS Computational Biology·Jonas PaulsenPhilippe Collas

Citations

Jun 8, 2018·The International Journal of Biostatistics·Nelle Varoquaux
May 1, 2020·Briefings in Functional Genomics·Kimberly MacKay, Anthony Kusalik
Apr 4, 2017·Chaos·Michael McCulloughMichael Small
Nov 4, 2019·Chaos·Yoshito Hirata, Noriyoshi Sukegawa
Feb 11, 2021·Structure·Enrico GuarneraIgor N Berezovsky

Datasets Mentioned

BETA
GSE48262
GSM1173492
GSM1173493
GSM1173502

Methods Mentioned

BETA
single-cell Hi-C
Hi-C
single cell Hi-C.
single-cell
single-cell Hi-C.

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