Multiscale Identification of Topological Domains in Chromatin
Recent chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types, are 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 modifications at the boundaries.
Keywordschromosome conformation capture topological domains weighted interval scheduling
Unable to display preview. Download preview PDF.
- 8.Goldberg, A.V.: Finding a maximum density subgraph. Computer Science Division. University of California, Berkeley (1984)Google Scholar
- 11.Kleinberg, J., Tardos, É.: Algorithm Design. Addison-Wesley, Boston (2005)Google Scholar
- 13.Lieberman-Aiden, E., van Berkum, N.L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., Dorschner, M.O., et al.: Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950), 289–293 (2009)CrossRefGoogle Scholar
- 14.Lin, Y.C., Benner, C., Mansson, R., Heinz, S., Miyazaki, K., Miyazaki, M., Chandra, V., Bossen, C., Glass, C.K., Murre, C.: Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. Nature Immunology 13(12), 1196–1204 (2012)CrossRefGoogle Scholar