Table 1.
Methods of super enhancer identification
| Methods | Description | Advantages | Disadvantages | Ref. |
|---|---|---|---|---|
| ChIP-seq (Chromatin Immunoprecipitation sequencing) | A method for detecting genome-wide DNA segments interacting with histones and transcription factors. | 1) Provides a high-resolution map of genomic expression regulation with less samples; 2) No signal noise deviations as direct sequencing method is used. |
1) Unstable data accuracy as it is greatly influenced by the quality of antibodies; 2) High cost of building ChIP-seq workflow. |
14, 15 |
| 3C-seq (Chromosome conformation capture) | A method for detecting the DNA-DNA interactions between enhancer regions and one other transcriptional regulatory elements. | 1) Combine with quantitative PCR (qPCR) to reveal the results quantitatively; 2) No sequencing is required so the cost is low. |
1) Low-throughput because interactions must be tested one at a time; 2) Not unbiased because genomic positions must be chosen to test for interactions. |
16, 17 |
| 4C-seq (Circularized chromosome conformation capture) | A method for detecting genome-wide DNA-DNA interactions with a single chosen genomic location of interest. | 1) Provides a high-resolution map of chromatin interactions with a chosen 'viewpoint'; 2) Fewer samples are needed for sufficient sequencing depth. |
1) Inefficient because primers must be redesigned specifically before each 'viewpoint' tested; 2) Improvement is needed for data normalization and unbiased estimate. |
17, 18 |
| Hi-C (High-throughput chromosome conformation capture) | A method for detecting pairwise contacts between virtually any pair of genomic loci. | 1) A matrix-balancing normalization method associated with high-resolution sequencing is developed; 2) Combines with visualization platforms to construct the 3D structure of chromatin interaction. |
1) High signal noise because of polymerization state and dynamic chromatin interactions; 2) Insufficient genome-wide resolution to bridge 3D information to gene function perfectly. |
19, 20 |
| STARR-seq (self-transcribing active regulatory region sequencing) | A method to identify transcriptional enhancers and to assess their activity quantitatively by cloning DNA fragments downstream of a core promoter. | 1) Provides genome-wide cell type-specific quantitative enhancer activity maps of any cell type; 2) Not affected by the location of the sequences. |
Repeated identification may exist because of lack of accurate context markers. | 21, 22 |