SAF-Box, a conserved protein domain that specifically recognizes scaffold attachment region DNA

SARs (scaffold attachment regions) are candidate DNA elements for partition ing eukaryotic genomes into independent chromatin loops by attaching DNA to proteins of a nuclear scaffold or matrix. The interaction of SARs with the nuclear scaffold is evolutionarily conserved and appears to be due to spec ific DNA binding proteins that recognize SARs by a mechanism not yet unders tood. We describe a novel, evolutionarily conserved protein domain that spe cifically binds to SARs but is not related to SAR binding motifs of other p roteins. This domain was first identified in human scaffold attachment fact or A (SAF-A) and was thus designated SAF-Box. The SAF-Box is present in man y different proteins ranging from yeast to human in origin and appears to b e structurally related to a homeodomain. We show here that SAF-Boxes from f our different origins, as well as a synthetic SAF-Box peptide, bind to natu ral and artificial SARs with high specificity. Specific SAR binding of the novel domain is achieved by an unusual mass binding mode, is sensitive to d istamycin but not to chromomycin, and displays a clear preference for long DNA fragments. This is the first characterization of a specific SAR binding domain that is conserved throughout evolution and has DNA binding properti es that closely resemble that of the unfractionated nuclear scaffold.