Table 2 TFs with methyl-plus and mixed-effect methyl-binding preferences, as inferred by JAMS using in vivo data. For mixed-effect TFs, both the position at which a positive methylation effect was observed as well as the position with a negative methylation effect are indicated. See Additional file 1: Fig S8 for motif logos
Protein | Family | JAMS call | Effect of methylation by position | SELEX call [5] | |
|---|---|---|---|---|---|
Positive | Negative | ||||
CEBPB | bZIP | Methyl-plus | 6 | Â | Methyl-plus |
SCRT1 | C2H2 ZF | Methyl-plus | 3 | Â | Methyl-plus |
CEBPG | bZIP | Methyl-plus | 6 | Â | Methyl-plus |
ZBTB33 (KAISO) | C2H2 ZF (BTB) | Methyl-plus | 5, 7 | Â | Methyl-plus |
TCF7 | HMG/Sox | Methyl-plus | 2 | Â | Methyl-minus |
ZKSCAN1 | C2H2 ZF (KRAB+SCAN) | Methyl-plus | 2 | Â | Â |
ZNF793 | C2H2 ZF (KRAB) | Methyl-plus | 7 | Â | Â |
ZNF141 | C2H2 ZF (KRAB) | Methyl-plus | 17 | Â | Â |
ZNF320 | C2H2 ZF (KRAB) | Methyl-plus | 17 | Â | Â |
ZNF605 | C2H2 ZF (KRAB) | Methyl-plus | 15 | Â | Â |
ZNF479 | C2H2 ZF (KRAB) | Methyl-plus | 11 | Â | Â |
ZNF490 | C2H2 ZF (KRAB) | Methyl-plus | 7 | Â | Â |
ZNF506 | C2H2 ZF (KRAB) | Methyl-plus | 5 | Â | Â |
ZNF417 | C2H2 ZF (KRAB) | Methyl-plus | 16 | Â | Â |
NR2F2 | Nuclear receptor | Methyl-plus | 5, 8 | Â | Â |
TFAP4 | bHLH | Methyl-plus | 7 | Â | Â |
SP1 | C2H2 ZF | Mixed-effect | 5 | 8 | Methyl-plus |
USF1 | bHLH | Mixed-effect | 7 | 5 | Methyl-minus |
USF2 | bHLH | Mixed-effect | 7 | 5 | Methyl-minus |
NFYB | NFYB/HAP3 | Mixed-effect | 9 | 13 | Â |