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Table 1 Survey of current and emerging single-cell epigenetics techniques

From: Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity

Technique Epigenomic feature Method Approach Single cell
Cytosine modification 5mC BS-seq Bisulfite converts C but not 5mC (or 5hmC) to U so only methylated sites are sequenced as “C” Yes [68]
5mC MeDIP-seq Immunoprecipitation of 5mC DNA followed by sequencing Not currently possible
5mC Methyl-seq Restriction enzyme specific for 5mC followed by sequencing Possible
5hmC oxBS-seq 5hmC is oxidized to 5caC so that only 5mC survives bisulfite conversion. Readout is pure 5mC and subtraction from BS-seq determines 5hmC Not possible for measuring 5hmC due to the need for subtraction
5hmC TAB-seq Maps 5hmC by enzymatic oxidation prior to bisulfite treatment: only 5hmC survives conversion Possible
5hmC hMeDIP-seq Immunoprecipitation of 5hmC DNA followed by sequencing Not currently possible
5hmC Aba-seq Restriction enzyme specific for 5hmC Possible
Protein–DNA interaction Histone modification ChIP-seq Immunoprecipitation of DNA bound to a specific histone variant or transcription factor Yes [17]
Transcription factor binding DamID Cells are transfected with a fusion of a transcription factor gene and Dam protein which methylates adenine residues in proximity to the binding site. 6 mA specific restriction digest is used to map Yes for nuclear lamina interactions [18]
Chromatin structure Nucleosome positioning MNase-seq Microcococal nuclease digestion of chromatin and sequencing of the product which are regions protected by nucleosomes Possible
Nucleosome positioning NOME-seq GpC methylation of DNA not protected by nucleosomes followed by BS-seq Possible
DNA accessibility DNase-seq DNaseI digestion of open chromatin into small fragments suitable for library preparation and sequencing Yes [23]
DNA accessibility FAIRE-seq Chromatin is crosslinked, sonicated, and then purified by phenol–chloroform extraction. The aqueous layer contains only DNA not associated with protein Not currently possible
DNA accessibility ATAC-seq Tn5 transposase enzyme fragments and attaches adapters to open chromatin Yes [21, 22]
Three-dimensional organization Chromosome conformation HiC DNA is crosslinked, then restriction digested to fragment before ligation and reversal of the crosslinks. Resulting fragments are hybrids from separate genomic locations that were in close proximity in three-dimensional space. Paired-end sequencing is used to link the two regions Yes [29]
  1. C cytosine, 5caC 5-carboxylcytosine, 5hmC hydroxymethylcytosine, 5mC methylcytosine, U uracil