  Chromatin loop extrusion by Structural Maintenance of Chromosome (SMC)
complexes is thought to underlie intermediate-scale chromatin organization
inside cells. Motivated by a number of experiments suggesting that nucleosomes
may block loop extrusion by SMCs, such as cohesin and condensin complexes, we
introduce and characterize theoretically a composite loop extrusion factor
(composite LEF) model. In addition to an SMC complex that creates a chromatin
loop by encircling two threads of DNA, this model includes a remodeling complex
that relocates or removes nucleosomes as it progresses along the chromatin, and
nucleosomes that block SMC translocation along the DNA. Loop extrusion is
enabled by SMC motion along nucleosome-free DNA, created in the wake of the
remodeling complex, while nucleosome re-binding behind the SMC acts as a
ratchet, holding the SMC close to the remodeling complex. We show that, for a
wide range of parameter values, this collection of factors constitutes a
composite LEF that extrudes loops with a velocity, comparable to the velocity
of remodeling complex translocation on chromatin in the absence of SMC, and
much faster than loop extrusion by an isolated SMC that is blocked by
nucleosomes.
