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Several diagnostic differences that distinguish human Alu subfamilies are clustered just downstream from the B box of the RNA polymerase III promoter; we tentatively refer to this diagnostic region as the DB box. Assuming that this region might determine the relative transcriptional activity of Alu subfamilies, we examined the interaction of nuclear proteins with DB box sequences representing different Alu subfamilies. Gel mobility shift assays suggest the existence of two factors which discriminate among the DB boxes of different Alu subfamilies: 1) An abundant, ca. 50 kd, protein binds more stably to a young 'PV' Alu subfamily (PVS) than to the older major subfamily (MS). 2) Methylation of CpG dinucleotides stimulates the binding of a less abundant, ca. 70 kd, protein to the DB boxes of younger Alu subfamilies.

Human retrotransposons, Alu‐family DNA repeats (AFRs), have variable nucleotide sequence but conservative short elements, which may have important functions, are also present. In our previous reports we have described human nuclear DNA‐binding protein interacting with AFRs and evidence was presented that the protein recognizes sequence motif 5′‐GGAGGC‐3′ which is conserved in the spacer of RNA polymerase III promoter of AFRs and in the SV40 T‐antigen‐dependent replication origin of AFRS. In this study it was found that double‐stranded synthetic oligonucleotides containing indicated conservative sequences of AFRs actually have high‐affinity binding site for HeLa nuclear protein. The data suggest that non‐infected human cells contain nuclear DNA‐binding protein which recognizes the conservative sequence motif of AFRs — GGAGGC.

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