We have focused attention on the 1.2 kb insulator DNA sequence at the 5 end of the chicken beta-globin locus, and elements upstream of it. This insulator is capable both of blocking the influence of outside enhancers and of preventing the encroachment of condensed chromatin that might shut down expression of the entire region. We have shown previously that enhancer blocking activity is associated with binding of a single protein, CTCF, to a site within the enhancer. We have shown that this protein is responsible for regulation of imprinted gene expression at several imprinted loci. In order to understand the mechanism of action of CTCF we have continued to extend our earlier studies showing that CTCF molecules interact with co-factors. Work in other laboratories has shown that the cohesin complex is associated with CTCF at many of its binding sites, and is essential for stabilizing long range contacts and for insulator activity involving those sites. We have recently shown that the only cohesin subunit that makes direct contact with CTCF is SA2, which is external to the cohesin ring. We have also explored the role of various biochemical modifications in CTCF function. In other work, we are extending our studies of the interaction between CTCF and the DEAD box helicase, p68. We reported this interaction in an earlier publication. We also showed that a non-coding RNA, SRA, which forms a complex with p68, is essential for this interaction. We are now investigating the nature of the p68-SRA interaction, and the role of the RNA in insulator activity of CTCF.
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