The epigenome contains genomic information, including acquired effects (chemical modifications to DNA and histone proteins, chromatin accessibility and chromatin conformation) that do not involve changes in the DNA sequence. Until recently, the studies of these epigenetic modifications based on populations of cells have classified them as being associated with active or repressed transcriptional states. But such generalizations often obscure the more complex relationship between the epigenome and gene expression. Epigenome sequencing at the single-cell level has the potential to refine our understanding of DNA modifications as regulatory epigenetic marks. Microfluidics-based single-cell methods allow analyses of epigenetic–transcriptional correlations thereby enabling detailed investigations of how epigenetic states are associated with phenotype.
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