NUCLEOSOME POSITIONING ON THE MMTV LTR RESULTS FROM THE FREQUENCY-BIASED OCCUPANCY OF MULTIPLE FRAMES

The translational positions of nucleosomes in the promoter region of t he mouse mammary tumor virus (MMTV) were defined at high resolution. N ucleosome boundaries were determined in primer extension assays using full-length single-stranded mononucleosomal DNA prepared from cells tr eated with formaldehyde, a reversible protein-DNA cross-linking agent. Multiple boundaries were observed in both the nucleosome A (Nuc-A) an d Nuc-B region of the promoter, indicating multiple nucleosome transla tional frames. The different nucleosome frames in both the Nuc-A and N uc-B regions were occupied unequally. The most frequently occupied fra mes were found clustered within 50-60 bases of each other, resulting i n a distribution centered in the positions defined previously at low r esolution for Nuc-A and Nuc-B. The most abundant 5' ends of the frames in the B region were found between -235 and -187, and the 3' ends bet ween -86 and -36, whereas in the A region the most abundant 5' ends we re between -22 and +42, and the 3' ends between +121 and +186. Althoug h frames in the Nuc-B region of the LTR extend at a low frequency in t he 5' direction toward the Nuc-C region, there is a sharp discontinuit y in the 3' direction toward Nuc-A, suggesting the presence of a bound ary constraint in the A-B linker. The positions and relative occupanci es of nucleosome frames, in either the B or the A region, did not chan ge when the promoter was activated with dexamethasone.