Table 1. Comparison of QmRLFS-finder prediction with experimental R-loop detection.
| Gene | Cell line/Cell type | Reference | R-loop identification method | R-loop forming signal | RLFS predicted by QmRLFS-finder |
|---|---|---|---|---|---|
| Immunoglobulin* | Primary mammalian B lymphocytes | (12) | R-loop foot-printing | + | + |
| MYC | In vitro | (7,8) | electron microscopy and mutagenic action of AID | + | + |
| BCL6 | In vitro | (13) | electron microscopy | + | + |
| RHOH | In vitro | (13) | electron microscopy | + | + |
| ACTB** | Hela | (14) | DRIP-qPCR | + | + |
| FMR1 | Fibroblast/Fragile X Syndrome patient GM03200 | (9,10) | DRIP-qPCR and R-loop foot-printing | + | + |
| SNRPN | Ntera2 | (11) | DRIP-seq and R-loop foot printing combined to RNase H digestion | + | + |
| HK2 | Ntera2 | (11) | DRIP-seq | + | + |
| CHTF8 | Ntera2 | (11) | DRIP-seq | + | + |
| CIRH1A | Ntera2 | (11) | DRIP-seq | + | + |
| APOE | Ntera2 | (11) | DRIP-seq and R-loop foot-printing combined to RNase H digestion | + | + |
| FHIT*** | B-cell | (15) | Overexpressed or knocked down RNase H | + | + |
| FLC | Arabidopsis | (18) | DRIP-qPCR and R-loop foot-printing | + | − |
| Pkd2l1** | Mouse testes | (17) | DRIP-PCR | + | + |
| Foxo4** | Mouse testes | (17) | DRIP-PCR | + | + |
| Airn | Mouse embryonic stem cell | (11) | R-loop foot-printing | + | + |
| C9orf72 | In vitro | (16) | RNase H digestion | + | + |
| JTB | SKOV3 | in-house study | DRIP-qPCR | − | − |
| PPMD1 | SKOV3 | in-house study | DRIP-qPCR | − | − |
| TP53 | SKOV3 | in-house study | DRIP-qPCR | − | − |
| PBX1 | SKOV3 | in-house study | DRIP-qPCR | − | + |
| PTEN | SKOV3 | in-house study | DRIP-qPCR | + | + |
+: positive signal; −: negative signal; *switch region; **3′ end; ***fragile site FRA3B on chromosome 3.