  Combining genome-wide structural models with phenomenological data is at the
forefront of efforts to understand the organizational principles regulating the
human genome. Here, we use chromosome-chromosome contact data as
knowledge-based constraints for large-scale three-dimensional models of the
human diploid genome. The resulting models remain minimally entangled and
acquire several functional features that are observed in vivo and that were
never used as input for the model. We find, for instance, that gene-rich,
active regions are drawn towards the nuclear center, while gene poor and
lamina-associated domains are pushed to the periphery. These and other
properties persist upon adding local contact constraints, suggesting their
compatibility with non-local constraints for the genome organization. The
results show that suitable combinations of data analysis and physical modelling
can expose the unexpectedly rich functionally-related properties implicit in
chromosome-chromosome contact data. Specific directions are suggested for
further developments based on combining experimental data analysis and genomic
structural modelling.
