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Chromatin boundary elements serve as cis-acting regulatory DNA signals required to protect genes from the effects of the neighboring heterochromatin. In the yeast genome, boundary elements act by establishing barriers for heterochromatin spreading and are sufficient to protect a reporter gene from transcriptional silencing when inserted between the silencer and the reporter gene. Here we dissected functional topography of silencers and boundary elements within circular minichromosomes in  Saccharomyces cerevisiae . We found that both  HML-E  and  HML-I  silencers can efficiently repress the  URA3  reporter on a multi-copy yeast minichromosome and we further showed that two distinct heterochromatin boundary elements STAR and  TEF2 -UASrpg are able to limit the heterochromatin spreading in circular minichromosomes. In surprising contrast to what had been observed in the yeast genome, we found that in minichromosomes the heterochromatin boundary elements inhibit silencing of the reporter gene even when just one boundary element is positioned at the distal end of the  URA 3 reporter or upstream of the silencer elements. Thus the STAR and  TEF2 -UASrpg boundary elements inhibit chromatin silencing through an antisilencing activity independently of their position or orientation in  S. cerevisiae  minichromosomes rather than by creating a position-specific barrier as seen in the genome. We propose that the circular DNA topology facilitates interactions between the boundary and silencing elements in the minichromosomes.

A Single Heterochromatin Boundary Element Imposes Position-Independent Antisilencing Activity in Saccharomyces cerevisiae Minichromosomes