Cross-linked chromatin is digested using one or more restriction enzymes, which results in restriction fragments whose ends re-ligate thereby forming ligation junctions.

[pnrobinson]

This is not entirely accurate -- at least with some protocols, the ends are filled in with biotinylated nucleotides before blunt-end religation

[hansenp]

This is from mapping.rst in section Formation of Hi-C fragments.

I skipped this detail (and many others) in order to put the focus on concept with the three categories.