question: Which methods infer 3D genome structure without proximity ligation?
answer: SPRITE is a method that enables genome-wide detection of higher-order interactions within the nucleus.
  Transposase-mediated analysis of chromatin looping (Trac-looping) for simultaneous detection of multiscale genome-wide chromatin interactions among regulatory elements and chromatin accessibility.
  Genome architecture mapping (GAM) can be used for measuring chromatin contacts and other features of three-dimensional chromatin topology on the basis of sequencing DNA from a large collection of thin nuclear sections.