Purification and characterization of W-protein. A DNA-binding protein showing high affinity for the W chromosome-specific repetitive DNA sequences of chicken

A protein component, which binds with high afinity to the W chromosome-specific XhoI family repetitive DNA of chicken (Tone, M., Sakaki, Y., Hashiguchi, T., and Mizuno, S. (1984) Chromosoma (Berl.) 89, 228-237), was detected in the 0.35 M NaCl extract of the female chicken liver nuclei. This protein, designated as W-protein, was substantially purified by phosphocellulose, hydroxyapatite, and DEAE-Toyopearl column chromatography. Molecular weight of W-protein was estimated to be about 72,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, but it seems to form multimeric structure having apparent molecular weight of about 2.3 x 10⁶ under nondenaturing conditions. W-Protein binds strongly to both 0.7- and 1.1-kb repeating units of the XhoI family, both of which show curved DNA characteristics, and weakly to the AATAT-satellite sequence of Drosophila melanogaster. Stable binding of W-protein requires ≥300 base pairs of the 0.7-kilobases sequence, or more than 14 tandem repeats of the 21-base pair internal repeating unit of the 0.7-kilobase sequence. DNA footprint analysis and effects of some DNA-binding compounds suggest that the DNA double helix wraps around W-protein or its multimeric form contacting through A-T-rich minor grooves. A possible role of W-protein in the formation of W heterochromatic body is discussed.