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” | |
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 | ||
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] |