Table 4.
Description of current experimental techniques for determining regulatory elements (adapted from [137])
| Technique name | Description | Advantages | Limitations |
|---|---|---|---|
| Chromosome conformation capture (3C) | Analyse chromatin structure by quantifyng interactions between two selected loci. | Reveal the role of particular regulatory elements in genes at high resolution | The region of interest must be previously specified and no dimensional information of the interactions is provided |
| Chromosome conformation capture-on-chip (4C) | Analyse the chromatin structure by quantifyng interactions between a specific locus and other loci. | High resolution for chromosome variants identification | Elements that interact must be close in the sample |
| Chromosome conformation capture carbon copy (5C) | Analyse the chromatin structure by quantifyng all possible interactions within different genomic regions. | Detects and quantifies a large number of DNA interactions at the same time | Expensive costs and a reference sample requirement |
| Hi-C | Analyse the genome-wide chromatin structure using high-throughput sequencing techniques | High resolution, useful to characterize the whole genome structure when no reference is available | Expensive costs, high workload and less resolution when fewer loci are analysed |
| Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) | Combination of ChIP-based methods with 3C and sequencing for identifying chromatin interactions | Detection of protein–DNA interactions and long binding sites | Low resolution when identifying if a protein interacts with a given genomic element |
| Luciferase reporter assay | Quantitative technique for detecting the activity of genomic functional elements | Useful to detect changes in gene expression when the activity of regulatory elements involved in transcriptional regulation is dysregulated | Requires a construct and cell culture system |
| DNA fluorescence in situ hybridization (FISH) | Cytogenetic technique for locating specific DNA sequences within chromosomes | Allows the identification of gene position and detection of genetic aberrations for medical studies | Limited efficiency when loci has repeated DNA sequences |