Table 1.
Commonly used approaches for chromatin accessibility profiling.
| DNase-Seq | MNase-Seq | FAIRE-Seq | ATAC-Seq | NicE-Seq | |
|---|---|---|---|---|---|
| Type of input cells/tissue | Fresh/formaldehyde cross-linked/FFPE (Formalin-Fixed Paraffin-Embedded) | Fresh/formaldehyde cross-linked | Formaldehyde cross-linked | Fresh/formaldehyde cross-linked (less efficient in fixed) | Formaldehyde cross-linked/FFPE |
| Application to FFPE (PubMed) | 1 | 0 | 1 | 2 | 2 |
| Number of input cells | 106–107 | 103–107 | 103–107 | 1 cell—5 × 104 | 25 cells—105 |
| Fragment size (i.e., resolution) | ~200 bp | ~200 bp | ~300 bp | ~100–200 bp | ~300 bp |
| Key features | DNase I (endonuclease) cuts unprotected DNA | MNase (endo-exonuclease) digests unprotected DNA | Sonicate unprotected DNA in cross-linked material | Tn5 transposase tagments open region with DNA adapters | Nt-CviPII nickase cuts/labels CCD sites in unprotected DNA |
| Sequencing type | Single/paired end | Single/paired end | Single/paired end | Single/paired end | Single/paired end |
| Target region | NDR | Linker DNA between Nucleosomes | NDR | NDR | NDR |
| Sequencing depth (human genome; ~3 billion bp) | 20–50 million mapped reads | 150–200 million mapped reads | 20–50 million mapped reads | 25–30 million mapped reads (non-mitochondrial) | 20–30 million mapped reads |
| Cleavage bias | Yes | Yes | No | Yes | Yes |
|
Advantages
/ disadvantages |
No prior knowledge of the sequence or binding protein is required / time consuming, requires laborious enzyme titrations and calibrations, requires high sequencing depth |
Nucleosome positioning can be inferred / requires laborious enzyme titrations and calibrations, requires high sequencing depth, indirect profiling of open regions |
No enzymes optimization or titration required / low signal-to-noise ratio, relatively complex computational data analysis and interpretation, results are highly fixation-dependent |
Simple, fast, and sensitive approach; high signal-to-noise ratio / High mitochondrial DNA counts (unless nuclei isolated), requires two independent tagmentation events in opposite orientation, Tn5 sequence bias and promoter-enrichment bias |
Simple enzymatic approach, <5% mitochondrial DNA counts, optimal in fixed or FFPE samples, can be used in clinical settings, efficiently profiles promoters and enhancers / AT-rich sequences may be underrepresented |
| References | [26,28] | [12,13,14,44,45] | [46] | [47,48] | [49,50,51] |