  Loop extrusion convincingly describes how certain Structural Maintenance of
Chromosome (SMC) proteins mediate the formation of large DNA loops. Yet, most
of the existing computational models cannot reconcile recent in vitro
observations showing that condensins can traverse each other, bypass large
roadblocks and perform steps longer than its own size. To fill this gap, we
propose a three-dimensional (3D) "trans-grabbing" model for loop extrusion
which not only reproduces the experimental features of loop extrusion by one
SMC complex, but also predicts the formation of so-called "Z-loops" via the
interaction of two or more SMCs extruding along the same DNA substrate. By
performing Molecular Dynamics simulations of this model we discover that the
experimentally observed asymmetry in the different types of Z-loops is a
natural consequence of the DNA tethering in vitro. Intriguingly, our model
predicts this bias to disappear in absence of tethering and a third type of
Z-loop, which has not yet been identified in experiments, to appear. Our model
naturally explains road-block bypassing and the appearance of steps larger than
the SMC size as a consequence of non-contiguous DNA grabbing. Finally, it is
the first to our knowledge to address how Z-loops and bypassing might occur in
a way that is broadly consistent with existing cis-only 1D loop extrusion
models.
