Identification of alternative topological domains in chromatin

• Published in: Algorithms for molecular biology Vol. 9; no. 1; p. 14
• Main Authors: Filippova, Darya, Patro, Rob, Duggal, Geet, Kingsford, Carl
• Format: Journal Article
• Language: English
• Published: London BioMed Central 03.05.2014; BioMed Central Ltd; Springer Nature B.V
• Subjects: Algorithms; Analysis; Bioinformatics; Biomedical and Life Sciences; Cellular and Medical Topics; Chromatin; Chromosomes; Computational Biology/Bioinformatics; Experiments; Gene expression; Genomes; Heuristic; Life Sciences; Physiological; Wildlife conservation; Williams, Annie Morris; Chromatin conformation capture; Alternative topological domains; Dynamic programming
• ISSN: 1748-7188; 1748-7188
• DOI: 10.1186/1748-7188-9-14

Chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a number of analyses. However, functionally-relevant domains may exist at multiple length scales. We introduce a new and efficient algorithm that is able to capture persistent domains across various resolutions by adjusting a single scale parameter. The ensemble of domains we identify allows us to quantify the degree to which the domain structure is hierarchical as opposed to overlapping, and our analysis reveals a pronounced hierarchical structure in which larger stable domains tend to completely contain smaller domains. The identified novel domains are substantially different from domains reported previously and are highly enriched for insulating factor CTCF binding and histone marks at the boundaries.