Scaffold/matrix-attached regions: topological switches with multiple regulatory functions.

The nuclear matrix or scaffold that can be prepared and investigated in vitro has an affinity for distinct topological forms of DNA and for sequences that permit the induction of such a topology by their association with a corresponding set of proteins (so-called matrix- or scaffold-attached regions, S/MARS). As a consequence, S/MARS are regarded as topological sinks that can be regulated according to activity-related requirements. Here we develop a switching model to understand the biological functions of S/MARS, which are able to augment transcriptional processes and form barriers between independently regulated domains. The current literature is screened for examples supporting such a mechanism and novel approaches are suggested for their further elucidation.