The dynamic genome now can be simulated using data-driven approaches. Great work by many in our labs (Graf and @MarciusLab from @cnag_eu @CRGenomica). But most credit go to @MarcDiEsse.
https://www.nature.com/articles/s41467-020-16396-1

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1/4 TADdyn ( https://tinyurl.com/yd65rb2x ) provides ways of simulating smooth transitions between two or more observed genome conformations. As such, TADdyn allows to study dynamic processes occurring in the genome based on Hi-C time-series datasets.

2/4 Our work shows that TADdyn simulations are an accurate dynamic representation of the input Hi-C data. We have applied it to the study of genome activation/inactivation during B to iPSC reprogramming for 21 different loci in the human genome.

3/4 The application of TADdyn to 21 differentially regulated loci shows that the dynamic structural reorganization of genomic domains correlates with local transcriptional changes.

4/4 Interestingly, we found that gene activation correlates with the appearance of “cage”-like structures, which prompted us to propose the formation of 3D active chromatin hubs as a general structural signature of transcription activation. "The 4DN" http://sgt.cnag.cat/3dg/datasets/files/Sox2.mov