  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.
