The most novel structural insight revealed by single-nucleotide-resolution epigenomic assays has been the recent discovery of asymmetric nucleosomes associated with the budding yeast genome. Nucleosome asymmetry was revealed by ChIP-exo analysis of several core histones and histone modifications (Rhee et al. 2014) and independently by analysis of H4S47C chemical cleavage maps (Ramachandran et al. 2015). Both of these studies reveal a surprising profusion of genomic regions characterized by asymmetric histone-DNA interactions, suggesting either hemi-nucleosomes comprised of single copies of the four histone proteins (which are typically present in two copies per nucleosome), or more likely, nucleosomes with a bulge of dissociated DNA on one side which precludes crosslinking to the histone proteins. These asymmetric nucleosomes occur at the 5′ ends of genes, and in general at locations exhibiting rapid replication-independent histone turnover. It will be interesting to determine whether asymmetric nucleosomes play functional roles in gene regulation or represent relatively transient assembly/disassembly intermediates.
