Table 1.
Current genome-wide high-throughput chromatin accessibility assays
| Cell type/Number | Sequencing type | Traditional approach | Genomic target | Experimental considerations | Key references | |
|---|---|---|---|---|---|---|
| MNase-seq | Any cell type 1 to 10 million cells | Paired-end or Single-end | MNase digests unprotected DNA | Maps the total nucleosome population in a qualitative and quantitative manner | 1. Requires many cells. | [37, 46, 49] |
| 2. Laborious enzyme titrations. | ||||||
| 3. Probes total nucleosomal population, not active regulatory regions only. | ||||||
| 4. Degrades active regulatory regions, making their detection possible only indirectly. | ||||||
| 5. Requires 150 to 200 million reads for standard accessibility studies of the human genome. | ||||||
| DNase-seq | Any cell type 1 to 10 million cells | Paired-end or Single-end | DNase I cuts within unprotected DNA | Maps open chromatin | 1. Requires many cells. | [61, 75, 76] |
| 2. Time-consuming and complicated sample preparations. | ||||||
| 3. Laborious enzyme titrations. | ||||||
| 4. Requires 20 to 50 million reads for standard accessibility studies of the human genome. | ||||||
| FAIRE-seq | Any cell type 100,000 to 10 million cells | Paired-end or Single-end | Based on the phenol-chloroform separation of nucleosome-bound and free sonicated areas of a genome, in the interphase and aqueous phase respectively | Maps open chromatin | 1. Low signal-to-noise ratio, making computational data interpretation very difficult. | [86–90] |
| 2. Results depend highly on fixation efficiency. | ||||||
| 3. Requires 20 to 50 million reads for standard accessibility studies of the human genome. | ||||||
| ATAC-seq | 500 to 50,000 freshly isolated cells | Paired-end | Unfixed nuclei are tagged in vitro with adapters for NGS by purified Tn5 transposase. Adapters are integrated into regions of accessible chromatin | Maps open chromatin, TF and nucleosome occupancy | 1. Contamination of generated data with mitochondrial DNA. | [103] |
| 2. Immature data analysis tools. | ||||||
| 3. Requires 60 to 100 million reads for standard accessibility studies of the human genome. |
ATAC: assay for transposase-accessible chromatin; DNase I: deoxyribonuclease I; FAIRE: formaldehyde-assisted isolation of regulatory elements; MNase: micrococcal nuclease.