Table 3.
| A. Motifs over-represented at RBP-Jκ reactivation peaks at early promoters | Motif IDa |
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|---|---|---|---|---|---|---|---|
| BCL11A | MNT | MAF B | TCF12 | EN2 | KLF12 | Rta-c | |
| Jk 2/Jk 5b | 6.9 | 5.8 | 4.6 | 3.8 | 3.8 | 3.5 | 2.9 |
| (9.4e-5) | (0.004) | (0.014) | (0.0007) | (0.03) | (0.003) | (0.03) | |
| Jk 2 + Rta/Jk 2c | 1.4 | -4.0 | 1.9 | 0 | 2.8 | 1.7 | 2.7 |
| (0.11) | (0.027) | (0.03) | (0.0004) | (0.0006) | (0.03) | (0.03) | |
| No. of promotersd | 10 | 7 | 7 | 12 | 8 | 14 | 8 |
| B. Motifs over-represented at RBP-Jκ reactivation/Rta co-peaks at early promoters | Motif IDa |
||||||
|---|---|---|---|---|---|---|---|
| POU4F1 | EN2 | Rta-c | POU3F4 | MZF1 | HMGA1/SOX5 | ZNF740/ZIC1 | |
| Jk 2 + Rta/Jk 2c | 3.6 | 2.8 | 2.7 | 2.7 | 2.4 | 2.4 | 2.2 |
| (NA) | (.00006) | (0.03) | (0.02) | (0.05) | (0.02) | (0.005) | |
| Jk 2/Jk 5b | −4.8 | 3.8 | 2.9 | −2.1 | −1.1 | 1.3 | 2.3 |
| (0.06) | (0.03) | (0.03) | (0.12) | (0.42) | (0.35) | (0.067) | |
| No. of promotersd | 5 | 8 | 8 | 9 | 14 | 7 | 10 |
| C. Motifs over-represented at RBP-Jκ latency peaks in early promoters | Motif IDa |
|||||
|---|---|---|---|---|---|---|
| POU3F3 | POU6F1/2 | GRHL1 | POU4F1 | ZEB1/NR1I3 | POU5F1 | |
| Jk 2/Jk 5b | −14.4 | −6.0 | −5.2 | −4.8 | −3.6 | −3.6 |
| (0.0004) | (0.03) | (0.002) | (0.06) | (0.05) | (0.05) | |
| Jk 2 + Rta/Jk 2c | 0 | 0 | 1.2 | 3.6 | 1.8 | 0 |
| (NA) | (NA) | (0.43) | (NA) | (0.25) | (0.18) | |
| No. of promotersd | 8 | 6 | 12 | 5 | 6 | 6 |
| D. Localization of POU Motifs at RBP-Jκ and Rta peaks | Motif IDa |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| POU3F3 | POU6F1/2 | POU4F1 | POU5F1 | POU5F1B | POU3F2 | POU3F4 | Oct-v | POU4F2 | POU2F3 | |
| Jk 2/Jk 5b | −14.4 | −6.0 | −4.8 | −3.6 | −2.4 | −2.4 | −2.1 | −1.5 | 1.0 | 1.9 |
| (0.0004) | (0.03) | (0.06) | (0.05) | (0.24) | (0.24) | (0.12) | (0.29) | (0.46) | (0.14) | |
| Jk 2 + Rta/Jk 2c | 0 | 0 | 3.6 | 0 | 0 | 0 | 2.7 | 2.0 | 2.1 | 1.6 |
| (NA) | (NA) | (NA) | (0.18) | (0.08) | (NA) | (0.02) | (0.04) | (0.06) | (NA) | |
| No. of promotersd | 8 | 6 | 5 | 6 | 4 | 3 | 9 | 10 | 7 | 7 |
a Best Match by TOMTOM Search of Homo sapiens Comprehensive Model Collection (HOCOMOCO) (48, 49). BCL11A = B-Cell CLL/Lymphoma 11A; EN2 = Engrailed Homeobox 2/HME4; GRHL1 = Grainyhead-like Transcription Factor 1; HMGA1/SOX5 = High Mobility Group AT-Hook 1/SRY-Box 5; KLF12 = Kruppel-like Factor 12; MAF B = MAF BZIP Transcription Factor B; MNT = MAX Network Transcriptional Repressor; MZF1 = Myeloid Zinc Finger 1; NR1I3 = Nuclear Receptor Subfamily 1 Group I Member 3; POU2F3 = POU Class 2 Homeobox 3; POU3F2 = POU Class 3 Homeobox 2; POU3F3 = POU Class 3 Homeobox 3; POU3F4 = POU Class 3 Homeobox 4; POU4F1 = POU Class 4 Homeobox 1; POU4F2 = POU Class 4 Homeobox 2; POU5F1 = POU Class 5 Homeobox 1; POU5F1B = POU Class 5 Homeobox 1B; POU6F1/2 = POU Class 6 Homeobox ½; TCF12 = Transcription Factor 12/HTF4; ZEB1 = Zinc Finger E-Box Binding Homeobox 1; ZNF740/ZIC1 = Zinc Finger Protein 740/Zic Family Member 1.
b Number of motifs <61 bp to RBP-Jκ Class 2 (“Jk2”) peak was divided by number of motifs <61 bp to RBP-Jκ Class 5 peak (“Jk5”) in early promoters, expressed as fold relative to actual ratio of Jk2/Jk5 peaks, which was 1.2. Number in parentheses is Z-test p value compared with the observed ratio of peaks.
c Number of motifs <61 bp to RBP-Jκ Class 2 peak/Rta peak (“Jk2 + Rta”) was divided by number of motifs <61 bp to RBP-Jκ Class 2 peak (“Jk2”) in early promoters, expressed as fold relative to actual ratio of Jk2/Jk5 peaks, which was 0.28. Number in parentheses is Z-test p value compared with the observed ratio of peaks; “NA” = not applicable.
d The number of promoters with co-localized Class 2 or Class 5 RBP-Jκ peak is shown.