Remodeling of Yeast CUP1 Chromatin Involves Activator-Dependent Repositioning of Nucleosomes over the Entire Gene and Flanking Sequences

Abstract

The yeast CUP1 gene is activated by the copper-dependent binding of the transcriptional activator, Ace1p. An episome containing transcriptionally active or inactiveCUP1 was purified in its native chromatin structure from yeast cells. The amount of RNA polymerase II on CUP1 in the purified episomes correlated with its transcriptional activity in vivo. Chromatin structures were examined by using the monomer extension technique to map translational positions of nucleosomes. The chromatin structure of an episome containing inactive CUP1 isolated from ace1Δ cells is organized into clusters of overlapping nucleosome positions separated by linkers. Novel nucleosome positions that include the linkers are occupied in the presence of Ace1p. Repositioning was observed over the entire CUP1 gene and its flanking regions, possibly over the entire episome. Mutation of the TATA boxes to prevent transcription did not prevent repositioning, implicating a chromatin remodeling activity recruited by Ace1p. These observations provide direct evidence in vivo for the nucleosome sliding mechanism proposed for remodeling complexes in vitro and indicate that remodeling is not restricted to the promoter but occurs over a chromatin domain including CUP1 and its flanking sequences.

ACKNOWLEDGMENTS

We thank Ramin Akhavan for the ace1Δ strain; Carolyn Neal for the mutant strain; Yossi Shiloach and Loc Trinh for fermenter-grown cells; and A. Dean, D. Hu, J. Thorner, and the American Type Culture Collection for plasmids. We thank Chris Szent-Györgyi for useful discussions; Ann Dean, Jurrien Dean, Rohinton Kamakaka, Alan Kimmel, and Alan Wolffe for comments on the manuscript; and Anne Dranginis for communicating unpublished results.