DNA sequence plays a major role in determining nucleosome positions in yeast CUP1 chromatin

The role of DNA sequence in determining nucleosome positions in vivo was in vestigated by comparing the positions adopted by nucleosomes reconstituted on a yeast plasmid in vitro using purified core histones with those in nati ve chromatin containing the same DNA, described previously. Nucleosomes wer e reconstituted on a 2.5 kilobase pair DNA sequence containing the yeast TR P1ARS1 plasmid with CUP1 as an insert (TAC-DNA). Multiple, alternative, ove rlapping nucleosome positions were mapped on TAC-DNA. For the 58 positioned nucleosomes identified, the relative positioning strengths and the stabili ties to salt and temperature were determined. These positions were, with a few exceptions, identical to those observed in native, remodeled TAC chroma tin containing an activated CUP1 gene. Only some of these positions are uti lized in native, unremodeled chromatin. These observations suggest that DNA sequence is likely to play a very important role in positioning nucleosome s in vivo. We suggest that events occurring in yeast CUP1 chromatin determi ne which positions are occupied in vivo and when they are occupied.