Figure 2.

Models of accessibility control mechanisms by chromatin. (a) Steric occlusion at binding sites by nucleosomes or oligo-nucleosome contacts can prevent productive binding interactions and reduce the effective concentration of a TF or polymerase (blue circles) in a genomic region. If all binding sites are obscured, the protein is not concentrated in the genomic region, even though diffusion may be unaffected. (b) Liquid-liquid phase separation of chromatin and associated proteins can prevent proteins from entering three-dimensional regions of the nucleus (compartments) based on the proteins’ chemical properties such as charge. (c) If chromatin is crosslinked into a gel, it would exclude proteins larger than the pore size of the gel regardless of their chemical properties. (d) Volume exclusion due to crowding can reduce the concentration of soluble protein in a manner that depends more weakly on size than a gel (c).