Dynamic simulations of transcriptional control during cell reprogramming reveal spatial chromatin caging

ABSTRACT Chromosome structure is a crucial regulatory factor for a wide range of nuclear processes. Chromosome Conformation Capture (3C)-based experiments combined with computational modelling are pivotal for unveiling 3D chromosome structure. Here, we introduce TADdyn, a new tool that integrates time-course 3C data, restraint-based modelling, and molecular dynamics to simulate the structural rearrangements of genomic loci in a completely data-driven way. We applied TADdyn on in-situ Hi-C time-course experiments studying the reprogramming of murine B cells to pluripotent cells, and characterized the structural rearrangements that take place upon changes in the transcriptional state of 11 genomic loci. TADdyn simulations show that structural cages form around the transcription starting site of active loci to stabilize their dynamics, by initiating ( hit ) and maintaining ( stick ) interactions with regulatory regions. Consistent findings with TADdyn for all loci under study suggest that this hit-and-stick mechanism may represent a general mechanism to trigger and stabilize transcription.