FIG. 1.

Loop extrusion via a composite LEF, comprising an SMC complex, which forms a ring around two nucleosome-free sections of DNA, nucleosomes that block SMC translocation, and a remodeling complex which removes nucleosomes in front of the SMC. In our model, a single loop extrusion step starts when the remodeling complex forces a nucleosome from the DNA ahead of the remodeler, thus moving the junction (J1) between nucleosomal DNA and naked DNA one step forward. β₀ is the rate of nucleosome dissociation (a) or remodeling (f) when the remodeler is next to a nucleosome. Next, the remodeler moves into the resultant nucleosome-free region, (b) and (g). k₁₊ is the rate at which the remodeler steps forward, when the remodeler-nucleosome separation is one step. Then, the SMC complex moves into the new nucleosome-free region left behind the remodeler (c) and (h). m₊ is the rate at which the SMC steps forward on nucleosome-free DNA. Finally, a nucleosome rebinds behind the SMC complex, moving the second junction (J2) between nucleosomal DNA and naked DNA one step forward, and so preventing the SMC from subsequently backtracking. α is the rate of nucleosome rebinding (d) or reformation (i). After these four substeps, the LEF configuration is the same as before the first step, but the loop is one step larger, (e) and (j). The top row (a)–(e) illustrates a hypothetical scenario (models 1 and 2) in which the displaced nucleosome is in solution before rebinding DNA behind the SMC. The bottom row (f)–(j) illustrates an alternative “remodeled-nucleosome” scenario (model 3) in which the displaced nucleosome remains associated with the remodeling complex before rebinding DNA behind the SMC.