Table 2.

Methods utilized for identifying epigenetic layers and players

Method abbreviation	Method description	Refs
ChIP-seq	Chromatin immunoprecipitation with high throughput sequencing to identify DNA bound to target proteins	[36]
RNA-seq	RNA-sequencing to identify genome-wide transcriptome	[36]
3C, 4C	Chromosome conformation capture (3C) on microarray (4C)	[98] [39]
HiC	3C variant interrogating genome wide with high throughput sequencing	[95] [96]
HMM	Hidden Markov model, a computer learning tool used for defining and segmenting chromatin and methylation states based on sequencing data	[36] [3]
MethylC-seq	Methyl cytosine bisulfite conversion plus high throughput sequencing	[3, 12]
FISH	Fluorescent in situ hybridization to characterize the subcellular localization and expression of RNAs and homologous pairing of chromomsomes	[60] [86] [87]
ChIA-PET	Chromatin interaction analysis with paired end tag sequencing	[97]
ChIP-loop	Chromatin immunoprecipitation combined with loci specific PCR	[100]