Specialized regions of chromatin flank the edges of transcriptionally silent DNA, separating it from euchromatin. For example, such boundary elements insulate the silent mating type loci (HMR and HML) in yeast. The molecular nature of these boundaries has remained obscure. Now, Tackett et al. (page 35) have identified protein complexes that are important for maintaining such boundaries.

The team tagged numerous chromatin-associated proteins with protein A and then used a modified form of ChIP to purify protein complexes together with their cognate DNA and nucleosomes. They uncovered several overlapping protein complexes that contained Dpb4, including chromatin-remodeling and DNA polymerase ε holoenzyme complexes. The histones that copurified with these complexes had a unique pattern of acetylation and methylation, intermediate between the patterns seen in active and inactive chromatin. When the team amplified the DNA that purified with the Dpb4 complexes, they found known boundary regions, such as HMR and HML, as well as numerous sequences localized to the ends of chromosomes, and a large number of previously unstudied loci.

Significantly, disruption of the protein complexes perturbed boundary function, as detected by the expression of reporter genes inserted in and near the HMR locus.

Because the polymerase complex associates with the regions in a cell cycle–dependent manner, Tackett et al. are currently working to test whether it helps conserve the epigenetic signals during replication. They are also investigating the roles of the boundary complexes at the other loci that they identified.