Spatial arrangement mediated _trans_ interactions

[cerebis]

Real data from the S.stipitis genome demonstrates the characteristic X modulation of trans interactions. This pattern is theorised to be due to spatial organisation of chromosomes. In particular, the collective gathering of their centromeres. A recent paper (algorithm name: Centurion) predicts the location of centromeres from HiC contact information.

This could be perhaps be modelled within the simulation.

As of right now, the simulation does not look like real yeast data. Where in real data, it appears that longer range cis and trans interactions have roughly equivalent probability.

As cis interaction distance increases beyond the very short range (dominating constraint: primary structure), folding must quickly dominate as the mechanism bringing elements into close proximity. For trans and cis to be similar in probability, it suggests that the physical separation of chromosomes within a cell is on-par with that achieved from the folding of an individual chromosome.

For the S.stipitis genome, there does not appear to be an appreciable difference between cis and trans. Implying tightly intermingled chromosomes.

Note, log scale could be misleading. There be "some" difference.