Seemingly contradictory findings of single-molecule and in vivo experiments on a major mechanism of chromosome organization are reconciled by computationally investigating mechanisms of loop extrusion that are consistent with both.
Models of chromosome compaction by condensins demonstrate that two-sided loop extrusion and long residence times are required for high compaction, suggesting a tight coupling between these two properties in vivo.
A structure-based model of the chromosomal cohesin complex, accompanied by molecular-mechanistic simulations, explains cohesin's key role in topologically entrapping DNA, as well as its ability to alternatively extrude DNA loops.
Reconstitution of DNA loop extrusion in cellular contexts using Xenopus egg extracts shows that condensin extrudes DNA loops non-symmetrically in metaphase, whereas cohesin extrudes DNA loops symmetrically in interphase.
In vertebrates, large regulatory landscapes sometimes behave as coherent regulatory units, which may explain the lack of effect sometimes observed when single enhancer sequences are deleted in isolation.
Certain types of 3D chromatin loops are easy to predict from existing or easily obtainable 2D information, which benefits gene expression studies in tissues/cells/organisms without extensive pre-existing 3D information.