Table 2.
Summary of long-read footprinting assays
| Method | Enzymes used | Theoretical resolution in humansa | Sequencing platform | Demonstrated uses |
|---|---|---|---|---|
| Methyltransferase treatment followed by single-molecule long-read sequencing (MeSMLR-seq)91 | M.CviPI (5mC GC) | Medium (>20 bp) | ONT | Nucleosome positioning, chromatin accessibility, chromatin coordination on single molecules |
| Occupancy measurement via DNA methylation and high-throughput sequencing (ODM-seq)92 | M.CviPI (5mC GC), M.SssI (5mC CG) | Medium (>20 bp) | ONT | Nucleosome positioning, chromatin accessibility, transcription factor footprinting |
| Nanopore sequencing of nucleosome occupancy and methylome (nanoNOMe)93 | M.CviPI (5mC GC) | Medium (>20 bp) | ONT | Nucleosome positioning, chromatin accessibility, transcription factor footprinting |
| Single-molecule long-read accessible chromatin mapping sequencing assay (SMAC-seq)96 | M.CviPI (5mC GC), M.SssI (5mC CG), EcoGII (m6dA on all A) | High (<5 bp) | ONT | Nucleosome positioning, chromatin accessibility, transcription factor footprinting, chromatin coordination on single molecules |
| Fiber-seq97 | Hia5 (m6dA on all A) | High (<5 bp) | PacBio | Nucleosome positioning, chromatin accessibility, transcription factor footprinting, chromatin coordination on single molecules |
| Single-molecule adenine methylated oligonucleosome sequencing assay (SAMOSA)99 | EcoGII (m6dA on all A), MNase | High (<5 bp) | PacBio | Oligonucleosome patterns, chromatin accessibility, transcription factor footprinting |
| Tagmentation-assisted single-molecule adenine methylated oligonucleosome sequencing assay (SAMOSA-Tag)100 |
EcoGII (m6dA on all A), Tn5 transposase |
High (<5 bp) | PacBio | Nucleosome positioning, chromatin accessibility, transcription factor footprinting, PacBio library preparation |
| Directed methylation with long-read sequencing (DiMeLo-seq)104 | pA–Hia5 or pAG–Hia5 | Low (within 200 bp) |
PacBio, ONT |
Protein–DNA interactions, coordination between binding sites on single molecules |
| BIND&MODIFY105 | pA–EcoGII (m6dA on all A) | Low (within 100 bp) | ONT | Measuring protein–DNA interactions |
5mC, 5-methylcytosine; m6dA, N6-methyladenine; MNase, micrococcal nuclease; ONT, Oxford Nanopore Technologies; PacBio, Pacific Biosciences; pA–EcoGII, fusion of protein A and EcoGII; pAG–Hia5, fusion of proteins A and G with Hia5. aEstimates of theoretical resolution are based on analysis described previously96.