Recent 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 identified novel domains are substantially different from domains reported previously and are highly enriched for insulating factor CTCF binding and histone modfications at the boundaries.
More information can be found here or in the paper:
Darya Filippova†, Rob Patro†, Geet Duggal† and Carl Kingsford. Identification of alternative topological domains in chromatin. Algorithms for Molecular Biology 9:14 (2014).