Formation of Boundaries of Transcriptionally Silent Chromatin by Nucleosome-Excluding Structures

Abstract

The eukaryotic genome is divided into chromosomal domains of distinct gene activities. Transcriptionally silent chromatin tends to encroach upon active chromatin. Barrier elements that can block the spread of silent chromatin have been documented, but the mechanisms of their function are not resolved. We show that the prokaryotic LexA protein can function as a barrier to the propagation of transcriptionally silent chromatin in yeast. The barrier function of LexA correlates with its ability to disrupt local chromatin structure. In accord with this, (CCGNN)_n and poly(dA-dT), both of which do not favor nucleosome formation, can also act as efficient boundaries of silent chromatin. Moreover, we show that a Rap1p-binding barrier element also disrupts chromatin structure. These results demonstrate that nucleosome exclusion is one of the mechanisms for the establishment of boundaries of silent chromatin domains.

We thank Danesh Moazed for the gift of α-Sir3p antibody, David Allis for α-H3-Ac and α-H4-Ac, and Zu-Wen Sun, David Allis, Kevin Struhl, Virginia Zakian, Roger Brent, and Philip James for gifts of plasmids and strains. We thank Hengping Xu, Ya-Hui Chiu, Travis Foland, Dan Schellhorn, and John Bishay for assistance. We also thank the reviewers for suggestions on improving this work.

This work was supported by National Institutes of Health grant GM 62484 to X.B.