Background: The chromosome conformation capture (3C) derived techniques, such as 4C, 5C, ChIA-PET and Hi-C, have revealed that the chromatin is organized in a hierarchical way in three-dimensional (3D) space to provide another layer of chromatin regulation.Then it is important to develop computational frameworks to analyze and reconstruct the chromatin 3D organization.Here we present an approach to identify topological domains and boundaries from Hi-C chromatin interactions.A newly developed chromatin 3D modeling method, called AutoChrom3D, can be used to reconstruct the 3D structures of selected chromatin regions.