NEGATIVE PROTEIN-1, WHICH IS REQUIRED FOR FUNCTION OF THE CHICKEN LYSOZYME GENE SILENCER IN CONJUNCTION WITH HORMONE RECEPTORS, IS IDENTICAL TO THE MULTIVALENT ZINC-FINGER REPRESSOR CTCF

The transcriptional repressor negative protein 1 (NeP1) binds specific ally to the F1 element of the chicken lysozyme gene silencer and media tes synergistic repression by v-ERBA, thyroid hormone receptor, or ret inoic acid receptor, Another protein, CCCTC-binding factor (CTCF), spe cifically binds to 50-bp-long sequences that contain repetitive CCCTC elements in the vicinity of vertebrate c-myc genes, Previously cloned chicken, mouse, and human CTCF cDNAs encode a highly conserved Il-Zn-f inger protein, Here, NeP1 was purified and DNA bases critical for NeP1 -F1 interaction were determined, NeP1 is found to bind a 50-bp stretch of nucleotides without any obvious sequence similarity to known CTCF binding sequences, Despite this remarkable difference, these two prote ins are identical, They have the same molecular weight, and NeP1 conta ins peptide sequences which are identical to sequences in CTCF, Moreov er, NeP1 and CTCF specifically recognize each other's binding DNA sequ ence and induce identical conformational alterations in the Fl DNA. Th erefore, we propose to replace the name NeP1,vith CTCF, To analyze the puzzling sequence divergence in CTCF binding sites, we studied the DN A binding of 12 CTCF deletions,vith serially truncated Zn fingers, Whi le fingers 4 to 11 are indispensable for CTCF binding to the human c-m yc P2 promoter site A, a completely different combination of fingers, namely, 1 to 8 or 5 to 11, was sufficient to bind the lysozyme silence r site F1, Thus, CTCF is a true multivalent factor with multiple repre ssive functions and multiple sequence specificities.