Fig. 1: Scheme of the investigated polymer models.

We used Molecular Dynamics simulations to investigate polymer models where folding is based on two different physical processes: (i) DNA loop-extrusion and (ii) polymer phase-separation, recapitulated respectively by the LE^19,20 and by the SBS models^43,45. a Microscopy median distance⁶ and ENCODE⁶⁷ CTCF data are shown for the studied 2 Mb wide locus in human IMR90 cells. b We considered a simple Loop-Extrusion (LE) model²⁰ where active motors extrude polymer loops until encountering another motor or CTCF anchor points with opposite orientation, which are fixed and equal in all single-molecule simulations (anchor probability = 1). c We also considered an extended version of the LE (eLE) whose anchor site locations are optimized, independently of CTCF, to best reproduce Hi-C and average microscopy data. To represent the epigenetic heterogeneity of single cells, those anchor sites have a finite probability to be present in a model single molecule²⁹. d In the Strings and Binders (SBS) model³⁵, a chromatin filament is represented as a self-avoiding chain of beads including different types of binding sites (colors) for diffusing cognate binders that can bridge those sites. The model undergoes a phase-separation of the chain in distinct globules³⁵. The binding site locations are determined by the PRISMR method and correlate with different combinations of chromatin architecture factors including, but not limited to, CTCF and cohesin^28,35. e We also considered a polymer model (LE + SBS) where in a single molecule both the eLE and SBS mechanisms act simultaneously.