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...
