Table 1.

Common features of an active enhancer.

Feature	Commonly Used Methods for Detection	References
Chromatin accessibility	DNase-seq, ATAC-seq, and FAIRE-seq	[11,38–40]
Histone modification H3K4me1	ChIP-qPCR, ChIP-chip, and ChIP-seq	[10,52,53]
Histone modification H3K27Ac	ChIP-qPCR, ChIP-chip, and ChIP-seq	[10,60,61]
Enhancer-promoter looping	3C, 4C, HiC, and Hi-ChIP	[45–50,163,165–167,176]
Binding of transcription factors, co-factors, and RNA Pol II	ChIP-qPCR, ChIP-chip, and ChIP-seq	[10,18–20,52,55,56,58]
Production of eRNAs	GRO-seq, CAGE, PRO-seq, Total RNA-seq RT-qPCR (using random hexamer primers)	[21,97,152,156–158]