THE SCS' BOUNDARY-ELEMENT - CHARACTERIZATION OF BOUNDARY ELEMENT-ASSOCIATED FACTORS

Boundary elements are thought to define the peripheries of chromatin d omains and to restrict enhancer-promoter interactions to their target genes within their domains. We previously characterized a cDNA encodin g the BEAF-32A protein (32A), which binds with high affinity to the sc s' boundary element from the Drosophila melanogaster 87A7 hsp70 locus. Here, we report a second protein, BEAF-32B, that differs from 32A onl y in its amino terminus. Unlike 32A, it has the same DNA binding speci ficity as the complete BEAF activity affinity purified from Drosophila . We characterize three domains in these proteins. Heterocomplex forma tion is mediated by their identical carboxy-terminal domains, and DNA binding is mediated by their unique amino-terminal domains, The identi cal middle domains of 32A and 32B are dispensable for the functions de scribed here, although they may be important for boundary element func tion. 32A and 32B apparently form trimers, and the ratio of 32A to 32B varies at different loci on polytene chromosomes as judged by immunof luorescence. The scs' element contains a high- and low-affinity bindin g site for BEAF. We observed that interaction with the low-affinity si te is facilitated by binding to the high-affinity site some 200 bp dis tant.