Studies on Scaffold Attachment Sites and Their Relation to Genome Function

Abstract

This chapter focuses on the evidence for loops in the genome and on the potential function of this higher-order folding. The loop hypothesis for the organization of DNA arose largely from observation—by electron microscope—of loops emanating from histone-depleted chromosomes and nuclei. The proteinaceous structures that remained after membrane and histone extraction are variously called “scaffolds,” “nuclear matrices,” “cages,” “nucleo- or karyoskeletons,” or the “nuclear matrix-pore complex-lamina fraction (NMPCL).” Electron microscopy of histone-depleted scaffolds and scaffold-attached regions (SAR)-mapping studies favors a model in which the 30-nm solenoid fiber is constrained in looped domains. The nuclear matrices and scaffolds are considered useful tools for subfractionation and purification of various nuclear components. The specificity of the DNA–scaffold interaction and the conservation of these binding sites between higher eukaryotes and yeast are encouraging. The characterization of the SAR-binding scaffolding proteins is necessary to evaluate the role this level of nuclear architecture plays in promoting and coordinating various nuclear activities during the cell cycle.