Abstract
AbstractTopologically associating domains (TADs) are the organizational units of chromosome structures. TADs can contain TADs, thus forming a hierarchy. TAD hierarchies can be inferred from Hi-C data through coding trees. However, the current method for computing coding trees is not optimal. In this paper, we propose optimal algorithms for this computation. In comparison with seven state-of-art methods using two public datasets, from GM12878 and IMR90 cells, SuperTAD shows a significant enrichment of structural proteins around detected boundaries and histone modifications within TADs and displays a high consistency between various resolutions of identical Hi-C matrices.
Funder
City University of Hong Kong
Publisher
Springer Science and Business Media LLC
Reference39 articles.
1. Berkum NLV, Lieberman-Aiden E, Williams L, Imakaev M, Lander ES. Hi-C: a method to study the three-dimensional architecture of genomes. JoVE. 2010; 39(39):e1869.
2. Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA, Noble WS. A three-dimensional model of the yeast genome. Nature. 2010; 465(7296):363–7.
3. Rodley CDM, Bertels F, Jones B, O’Sullivan JM. Global identification of yeast chromosome interactions using Genome conformation capture. Fungal Genet Biol. 2009; 46(11):879–86.
4. Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen C-A, Schmitt AD, Espinoza CA, Ren B. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature. 2013; 503(7475):290–4.
5. Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P. Nature. 2013; 502:59–64.
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