High-throughput assays of three-dimensional interactions of chromosomes have 
shed considerable light on the structure of animal chromatin. Despite this 
progress, the precise physical nature of observed structures and the forces that 
govern their establishment remain poorly understood. Here we present high 
resolution Hi-C data from early Drosophila embryos. We demonstrate that 
boundaries between topological domains of various sizes map to DNA elements that 
resemble classical insulator elements: short genomic regions sensitive to DNase 
digestion that are strongly bound by known insulator proteins and are frequently 
located between divergent promoters. Further, we show a striking correspondence 
between these elements and the locations of mapped polytene interband regions. 
We believe it is likely this relationship between insulators, topological 
boundaries, and polytene interbands extends across the genome, and we therefore 
propose a model in which decompaction of boundary-insulator-interband regions 
drives the organization of interphase chromosomes by creating stable physical 
separation between adjacent domains.