Stated more broadly, single-cell epigenomics will facilitate insights into the combinatorial nature of chromatin—which combinations of marks and structures are possible, what mechanisms enforce such constraints, and whether these depend on global aspects of cell state (e.g., cell-cycle stage) or on more local factors. An alternative strategy to understand these questions is by combinatorial assays. For example, sequential ChIP (also known as re-ChIP) in which the output of one ChIP is subjected to another ChIP for a second epitope can determine whether two chromatin marks co-appear on the same chromatin fragment. Until recently such assays have been constrained by the small amount of material from the first ChIP. Recent advances in ChIP in low-volume conditions and multiplexing (Lara-Astiaso et al. 2014) make us optimistic that reliable combinatorial ChIP will be realizable in the near future and allow researchers to elucidate the constraints on combinations of marks.
