Chromosome folding by loop extrusion on busy genome

We will review our recent progress in understanding loop extrusion and its interference with other biological processes on DNA. First, we will discuss how the process of transcription can serve as a directional boundary to extrusion. A model where loop-extruding factors can bypass a polymerase after some pausing can explain a broad range of data from bacterial and eukaryotes. Second, we will show the effect of random barriers on loop extrusion and provide evidence that such barriers are abundant in the cell. Third, we will show new experimental data which indicate that loop-extruding factors can bypass each other when they meet. Together, these results suggest that loop extruding factors can bypass a variety of obstacles. We posit that the bypassing activity enables SMC complexes to spatially organize a functional and busy genome.