Table 2. Correlation between presence of the E-box consensus sequences (CACGTG) and c-Mycdependent transcriptional responses.
| A. Number of E-box (yes) or E-box like (no) motives tested by EMSA | ||
|---|---|---|
| E-box consensus (#tested) | EMSA score1 | Gene specific sequences |
| no (36) | - | 17 |
| + | 16 | |
| ++ | 2 | |
| +++ | 1 | |
| yes (40) | - | 0 |
| + | 0 | |
| ++ | 4 | |
| +++ | 36 | |
| B. Number of E-box or E-box like motives, strength of DNA binding in EMSA assays, c-Myc-dependent transactivation, ChIP-seq data from the literature and ChIP qPCR in human cells over-expressing c-Myc | ||||||
|---|---|---|---|---|---|---|
| Gene | # E-box or E-box-like1 | E-box Consensus | EMSA score2 | Luciferase Assay3 | ChIP-Seq4 | ChIP qPCR5 |
| Adam19 | 3 (0) | no | + | 1.12 ± 0.07 | no | yes |
| no | n.a. | |||||
| no | n.a. | |||||
| Map2k1 | 5 (2) | yes | n.a. | 1.50 ± 0.07 | yes | yes |
| no | n.a. | |||||
| yes | n.a. | |||||
| no | +/++ | |||||
| no | n.a. | |||||
| Prc1 | 3 (1) | no | n.a. | 0.99 ± 0.01 | yes | yes |
| yes | n.a. | |||||
| no | + | |||||
| Traf4 | 3 (1) | no | + | 3.17 ± 0.60 | yes | yes |
| no | n.a. | |||||
| yes | n.a. | |||||
| Hk1 | 4 (4) | yes | n.a. | 3.0 ± 0.58 | yes | yes |
| yes | +++ | |||||
| yes | n.a. | |||||
| yes | n.a. | |||||
| Rpsa | 3 (2) | no | n.a. | 1.73 ± 0.05 | yes | yes |
| yes | n.a. | |||||
| yes | +++ | |||||
| Npm3 | 3 (2) | yes | n.a. | 1.60 ± 0.10 | yes | yes |
| no | n.a. | |||||
| yes | +++ | |||||
| Rcl1 | 3 (1) | yes | n.a. | 1.71 ± 0.05 | yes | yes |
| no | n.a. | |||||
| no | + | |||||
| Srm | 6 (5) | no | n.a. | 2.37 + 0.07 | yes | yes |
| yes | n.a. | |||||
| yes | n.a. | |||||
| yes | n.a. | |||||
| yes | +++ | |||||
| yes | n.a. | |||||
| Birc5 | 0 | no | n.a. | 1.30 + 0.06 | yes | yes |
1Number of E-box, or E-box-like, sequences (indicated in brackets is the number of canonical E-boxes, CACGTG) within 2kb (centered around the TSS) of the regulatory regions found in genes differentially expressed in PLACs. They are fully listed in the adjacent column from the most distal to the more proximal site in respect to the TSS.
2Value of the signal obtained with EMSA assays. “-“ = lack of shifted bands; “+” = weak, “++”medium, “+++” strong bandshift signal. “n.a.” stands for “not analyzed” sequence.
3Average fold changes and standard deviations of the reporter (containing the putative c-Myc responsive region) obtained in human cells with ectopic over-expression of c-Myc as compared to control cells with endogenous c-Myc expression.
4ChIP-seq data were retrieved by analyzing eight independent experiments with human cell lines deposited in the ENCODE database from UCSC genome browser. “Yes” in the table indicates overlapping c-MYC binding sites that were identified in at least three independent experiments.
5ChIP qPCR validated c-Myc occupancy within the promoter region of candidate genes in cells ectopically over-expressing c-Myc.