Functional Aspects of Chromosome Organization: Scaffold Attachment Regions and their Ligands

Abstract

Publisher Summary This chapter discusses the nature of the DNA scaffold interaction, identifies the proteins involved in this binding, and analyzes the role of scaffold attached regions (SAR)-mediated loop or domain organization in DNA replication and transcriptional control. The scaffold-attachment assay identifies all DNA sequences with the potential to bind the scaffold. The affinity of SARs for the scaffold appears to be maintained in metaphase. In Drosophila, the SAR fragments identified by association with the interphase scaffold were mapped for association with metaphase scaffolds, both from Drosophila and Hela cells. No major differences in the binding specificity are detected among the seven SARs tested in Drosophila. The more surprising aspects of SARs is the cross-species' conservation of binding. Drosophila -derived SARs have been shown to bind human, rat, mouse, and yeast scaffolds. SARs from various other sources show similar abilities to bind heterologous scaffolds. In view of the lack of a strictly defined SAR consensus sequence, it seems likely that a conserved DNA conformation defines the binding properties of a scaffold attachment region. Studies of SARs in lithium 3’5’-diiodosalicylate (LIS)-extracted scaffolds have shown that in both budding and fission yeast origins of replication (ARS elements) are specifically associated with the nuclear scaffold. Despite the difficulty of identifying replication origins in higher eukaryotic cells, there is also suggestive evidence that the origins of replication located 5‘ of the chick α-globin gene and 3’ of the Chinese hamster dehydrofolate reductase gene are both close to scaffold attachment sites.