Table 1 Approaches for identifying super-enhancers (SEs)
From: Effects of super-enhancers in cancer metastasis: mechanisms and therapeutic targets
Methods | Description | Advantages | Disadvantages | Required number of cells |
|---|---|---|---|---|
ChIP-seq | A tool for identifying the DNA regions bound by a specific protein of interest | High resolution, low noise, and large genome coverage | High cost for library construction and critically on the quality of the antibody | 107~108 |
ChIP-exo | A tool for mapping an interest protein-binding DNA locations with lambda exonuclease digestion (exo) | High resolution, low background, and precise at near-base pair resolution | More expensive, complex, and technically challenging | 107~108 |
ChIA-PET | A tool for studying chromatin interactions mediating by a specific protein of interest | Identify both proximal and distal 3D chromatin interactions at the whole-genome scale | The sequencing platform is expensive and takes a long to run | 107~108 |
Hi-ChIP | A tool for examining the regulatory interactions between distal DNA elements modulating by a protein of interest | Few cells required, low noise, and high efficiency | Only capture DNA interactions mediated by a specific target protein | 105~106 |
ChIA-Drop | A tool for investigating multiplex chromatin interactions regulating by a protein of interest in single-molecule resolution | Few cells required, simple, stable and high efficiency | Raw sequencing reads are huge and difficult to map and analyze | 103~104 |
PLAC-seq | A tool for identifying certain protein-mediated chromatin interactions | High resolution and accuracy, fast, sensitive, and high efficiency | Only detect chromatin sequences that are associated with specific proteins | 106~108 |
HiCA | A tool for analyzing open chromatin anchored interactions | Low-input cells, high-resolution, sensitive, and cost-effective | Less sensitive to capture weak open chromatin peaks | 104~106 |
CUT&Tag | A tool for the detecting DNA regions bound by a specific protein of interest with the enzyme-tethering strategy | High resolution, low background and small amount of starting material | Not very suitable for analyzing genome regions that are silent or contain heterochromatin | 100~104 |
ATAC-seq | A tool for assessing regions of open chromatin, providing insights into gene regulation and accessibility | Fast, sensitive and a small amount of sample | High background noise and sensitive to experimental conditions | 100~105 |
DNase-seq | A tool for identifying regions of open chromatin across the genome by sequencing DNA that is accessible to DNase I enzyme digestion | High resolution and precise | Large amounts of starting material and the results can vary depending on the DNase I digestion efficiency | 106~108 |
MNase-seq | A tool for mapping of nucleosome positioning and chromatin structure across the genome | High-resolution and accurate | Biases due to differential accessibility of regions to micrococcal nuclease | 106~107 |
FAIRE-seq | A tool for identifying regions of open chromatin | Simpler and less expensive | High background noise and lower resolution | 106~107 |
STARR-seq | A tool for quantitatively assessing the enhancer activity across the genome | Directly measure the enhancer activity | Large amounts of input DNA, high complexity and technical demands | 107~108 |
Luciferase reporter assay | A tool for measuring the activity of the regulatory sequence by linking it to a reporter gene | Sensitive, quantitative and high-resolution | Require careful control of experimental variables to avoid artifacts | 103~105 |
CRISPR/Cas9 | A tool for precise alterations to the DNA sequence at specific sites, enabling targeted gene modification | High specificity and efficiency | Sometimes introduce off-target effects or mutations at non-target sites | 103~105 |
CRISPRa | A tool for utilizing a modified CRISPR/Cas9 system paired with transcriptional activators to selectively enhance gene expression | High specificity and efficiency | Off-target effects | 103~105 |
CRISPRi | A tool for utilizing a modified CRISPR/Cas9 system paired with transcriptional repressors to selectively inhibit gene expression | High specificity and efficiency | Off-target effects | 103~105 |