Title
Identification of alternative topological domains in chromatin.
Abstract
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.
Year
DOI
Venue
2014
10.1186/1748-7188-9-14
Algorithms for Molecular Biology
Keywords
Field
DocType
alternative topological domains,chromatin conformation capture,dynamic programming,biomedical research,algorithms,bioinformatics
Topology,Histone,Computer science,Bioinformatics,CTCF,Chromatin,Chromosome conformation capture
Journal
Volume
Issue
ISSN
9
1
1748-7188
Citations 
PageRank 
References 
15
1.16
5
Authors
4
Name
Order
Citations
PageRank
Darya Filippova1385.83
Robert Patro2314.69
Geet Duggal3314.50
Carl Kingsford469554.27