The epigenetic chromatin modifications are known to play an important role in the regulation of gene expression in plants as well as in animals. The flexible nature of the epigenome assures the responses to internal and external cues. Besides, within the same organism, it varies depending on tissues and cell types. While the ChIP-seq approach on the dissected tissue samples can generally provide an overview of the global distribution of the chromatin marks, it is more challenging to detect the cell-type-specific epigenetic marks in a context of a multicellular organism.

Nevertheless, to better understand the role of the tissue-specific epigenetic code in the specification of the cell faith and organism morphogenesis it is crucial to look at the single-cell epigenome. Within the past years, a great step forward in such techniques as cell-sorting, microdissection, and high-resolution imaging has been made. Elaborate combinations of these approaches result in elegant new ways to look at the single-cell epigenome.

Some of the protocols have been tested in multiple model organisms, while the others are developed for an application with a specific system. This Methods Collection aims at representing recent advances in the techniques to study the cell type-specific epigenome in a variety of model organisms with a hope to encourage their wider application.