REGULATORY PROTEIN CTCF INTERACTS WITH AN UNUSUAL CONFORMATION OF THECHICK C-MYC ONCOGENE PROMOTER

In order to identify the regions of the chick c-myc oncogene promoter that are necessary for binding of the regulatory nuclear protein CTCF, we have used a synthetic analog of the natural binding site that cont ains three correctly spaced copies of the CCCTC pentanucleotide repeat known to be involved in CTCF-binding [1]. Gel retardation experiments failed to show any complex formation between the protein and this syn thetic analog. We believe that G-C transversions in the sequences flan king the synthetic CCCTC repeats interfere with CTCF binding. S1 nucle ase analysis of the secondary structure of natural and modified promot er regions inserted into supercoiled plasmid DNA revealed a non-B heli cal conformation in the natural promoter but not in the synthetic anal og. Several S1 hypersensitive sites were detected in the region of the CCCTC motifs. Thus, an unusual secondary structure may be important f or CTCF recognition in vivo.