Table 3.
Approaches to interrogating the epigenome and their utility in zebrafish samples
| Approach | Application | Level | Resolution | Genome coverage | Enriched | Cost | Zebrafish reference |
|---|---|---|---|---|---|---|---|
| IHC/IF/immunoblot | DNA and Histone | Global | Lowest | High | No | $ | Mudhary et al. (2014) [5], Jacoh et al. (2015) [11] |
| Methylation sensitive restriction digest | DNA methylation | Global | Low | High | No | $ | Mudbhary et al. (2011) [130] |
| MNase assay | Nucleosome position | Global | Low | High | No | $ | |
| Methylation array | DNA methylation | Locus specific | Moderate | Moderate | No | $$ | Mirbahai et al. (2011) [4] |
| MSP | DNA methylation | Locus specific | High | Lowest | No | $$ | |
| BSP | DNA methylation | Locus specific | Highest | Lowest | No | $$ | |
| Chip-seq | Histone modification | Global/specific | Moderate | Moderate | Yes | $$$ | Lindeman et al. (2009) [116] |
| RRBS | DNA methylation | Global/Specific | Moderate | Moderate | Yes | $$$ | Chatterjee et al. (2013) [131] |
| WG-BS | DNA methylation | Global/Specific | Highest | Highest | No | $$$$ | – |
Different techniques used for analyzing the prevalence and distribution of different epigenetic marks are ranked based on genomic coverage, resolution and cost