Repository logo

Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols.

Published version

Change log


Stevens, Tim J 
Laue, Ernest D 


Single-cell chromosome conformation capture approaches are revealing the extent of cell-to-cell variability in the organization and packaging of genomes. These single-cell methods, unlike their multi-cell counterparts, allow straightforward computation of realistic chromosome conformations that may be compared and combined with other, independent, techniques to study 3D structure. Here we discuss how single-cell Hi-C and subsequent 3D genome structure determination allows comparison with data from microscopy. We then carry out a systematic evaluation of recently published single-cell Hi-C datasets to establish a computational approach for the evaluation of single-cell Hi-C protocols. We show that the calculation of genome structures provides a useful tool for assessing the quality of single-cell Hi-C data because it requires a self-consistent network of interactions, relating to the underlying 3D conformation, with few errors, as well as sufficient longer-range cis- and trans-chromosomal contacts.



Chromosome conformation capture, Hi-C, fluorescence microscopy, genome structure, nuclear architecture, Chromosomes, Humans, Imaging, Three-Dimensional, Models, Molecular, Single-Cell Analysis

Journal Title


Conference Name

Journal ISSN


Volume Title



Informa UK Limited
Wellcome Trust (082010/Z/07/Z)
Medical Research Council (MR/M010082/1)
Medical Research Council (MR/P019471/1)
Wellcome Trust (206291/Z/17/Z)
European Commission (277899)