Comparison of computational methods for the identification of topologically associating domains.

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State: Public
Version: Final published version
Serval ID
serval:BIB_9D5DBEB6BBFB
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Comparison of computational methods for the identification of topologically associating domains.
Journal
Genome biology
Author(s)
Zufferey M., Tavernari D., Oricchio E., Ciriello G.
ISSN
1474-760X (Electronic)
ISSN-L
1474-7596
Publication state
Published
Issued date
10/12/2018
Peer-reviewed
Oui
Volume
19
Number
1
Pages
217
Language
english
Notes
Publication types: Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't ; Validation Studies
Publication Status: epublish
Abstract
Chromatin folding gives rise to structural elements among which are clusters of densely interacting DNA regions termed topologically associating domains (TADs). TADs have been characterized across multiple species, tissue types, and differentiation stages, sometimes in association with regulation of biological functions. The reliability and reproducibility of these findings are intrinsically related with the correct identification of these domains from high-throughput chromatin conformation capture (Hi-C) experiments.
Here, we test and compare 22 computational methods to identify TADs across 20 different conditions. We find that TAD sizes and numbers vary significantly among callers and data resolutions, challenging the definition of an average TAD size, but strengthening the hypothesis that TADs are hierarchically organized domains, rather than disjoint structural elements. Performances of these methods differ based on data resolution and normalization strategy, but a core set of TAD callers consistently retrieve reproducible domains, even at low sequencing depths, that are enriched for TAD-associated biological features.
This study provides a reference for the analysis of chromatin domains from Hi-C experiments and useful guidelines for choosing a suitable approach based on the experimental design, available data, and biological question of interest.
Keywords
Animals, Chromatin Assembly and Disassembly, Chromosomes, Genomics/methods, Humans, Mice, Hi-C, Method comparison, Topologically associating domain
Pubmed
Web of science
Open Access
Yes
Create date
05/01/2019 16:42
Last modification date
20/08/2019 15:03
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