At the level of individual nucleosomes, the strong correlation observed between many histone modifications raises the question of whether histone modifications co-occur on the same nucleosome in a given cell, or whether “co-occurring” modifications occur at the same genomic location but in different cells throughout a population (e.g., cells at different cell-cycle phases, or due to cell-to-cell variation in expression). At the level of multiple nucleosomes, ensemble measurements leave open the question of which multinucleosome configurations are feasible or probable. In other words, if three adjacent nucleosomes all have an overall occupancy of ∼80%, do these nucleosomes always co-occur, with 20% of cells carrying a naked DNA template, or are these nucleosomes independent? Elegant EM studies from the Boeger lab find that upon activation of the PHO5 promoter, at most two of three promoter nucleosomes are evicted, but the configuration where all three are evicted is not observed, indicating that these eviction events are not independent (Brown et al. 2013; Brown and Boeger 2014). In another study, DNA methyltransferase was used to footprint nucleosomes in individual cells, with bisulfite sequencing
