Fig. 6

Static and dynamic chromatin domain accessibility. Model for domain accessibility of heterochromatin, euchromatin, TSA-treated and ATP-depleted chromatin. A certain volume fraction of the domain (blue) is not accessible (checkered) for soluble factors (red) due to steric hindrance. The domain is virtually static on time scales long enough for a single molecule to roam the domain volume by diffusion (~1 ms; light red), resulting in an unaccessible volume significantly larger than the net fiber volume. The single molecule is highly unlikely to return to a previously visited domain so that it only senses the static, snapshot-like unaccessible volume. Thus, accessibility for low-abundance molecules is defined by the apparently static conformation during the ms passage time. This effect is more pronounced for compact heterochromatin than for open euchromatin. On the time scale of domain reorganization (~100–200 ms), molecules can search different domain areas such that the effectively unaccessible volume decreases toward the net fiber volume (including ‘classical’ excluded volume effects). Accordingly, high-abundance molecules effectively sense a significantly higher accessible volume, i.e., accessibility depends on molecular concentration in addition to a binding reaction itself. Moreover, it is determined by the size of the molecule or complex (arrows in 1D plots), confirming previous findings on static chromatin accessibility. Thus, formation of domains consisting of dynamic loops provides an additional degree of freedom to differentially regulate chromatin accessibility. Chemical modifications and chromatin remodeling processes take place on significantly longer time scales so that access for required molecules can be regulated by domain and loop dynamics