Table I. List of the potential AP-4-interacting proteins differentially bound to the HDM2-P2 promoter E-box sequence.
Proteins from HCT116 p53+/+ cell nuclear extracts enriched on the HDM2-P2 promoter E-box sequence (enrichment ratio ≥ 1.6) were identified by quantitative proteomics using cICAT and iTRAQ labeling methods and were categorized according to their known molecular function(s). Complete information of enriched proteins labeled by cICAT and iTRAQ was summarized in supplemental Tables 1 and 2 respectively.
| Protein name | Accession number | Gene name | Mass | cICAT |
iTRAQ |
|||||
|---|---|---|---|---|---|---|---|---|---|---|
| Scorea | Peptideb | WT/MUc | Scorea | Peptideb | WT1/MU2d | WT2/MU2d | ||||
| bHLH transcription factor | ||||||||||
| Activating enhancer-binding protein 4 | Q01664 | TFAP4 | 38702 | 59 | 2 | 1.96 ± 0.07 | 199 | 3 | 2.46 ± 0.60 | 1.96 ± 0.39 |
| Circadian locomoter output cycles protein kaput | O15516 | CLOCK | 95244 | 64 | 1 | 2.04 ± N/A | N/A | N/A | N/A | N/A |
| Upstream stimulatory factor 2 | Q15853 | USF2 | 36932 | N/Ae | N/A | N/A | 108 | 4 | 3.36 ± 0.90 | 3.22 ± 0.71 |
| Transcription factor | ||||||||||
| Nuclear factor of activated T-cells, cytoplasmic 2 | Q13469 | NFATC2 | 100083 | 65 | 2 | 6.46 ± 2.10 | 88 | 3 | 2.00 ± 0.58 | 2.05 ± 0.49 |
| Alpha-globin transcription factor CP2 | Q12800 | TFCP2 | 57220 | 1019 | 32 | 3.32 ± 1.58 | 522 | 9 | 2.26 ± 0.34 | 2.00 ± 0.33 |
| General transcription factor II-I | P78347 | GTF2I | 112346 | 141 | 3 | 3.15 ± 0.82 | 757 | 28 | 1.74 ± 0.33 | 1.63 ± 0.36 |
| Upstream-binding protein 1 | Q9NZI7 | UBP1 | 60453 | 903 | 40 | 2.70 ± 0.45 | 582 | 12 | 1.88 ± 0.19 | 1.73 ± 0.19 |
| COUP transcription factor 1 | P10589 | NR2F1 | 46126 | 316 | 5 | 2.22 ± 2.13 | 143 | 3 | 2.13 ± 0.56 | 1.94 ± 0.49 |
| COUP transcription factor 2 | P24468 | NR2F2 | 45542 | 228 | 2 | 1.78 ± 0.05 | 136 | 1 | 1.99 ± N/A | 1.78 ± N/A |
| Nuclear factor 1 C-type | P08651 | NFIC | 55640 | 85 | 3 | 1.69 ± 0.18 | 175 | 2 | 1.73 ± 0.06 | 1.75 ± 0.05 |
| Nuclear receptor subfamily 2 group F member 6 | P10588 | NR2F6 | 42952 | 78 | 3 | 4.28 ± 0.27 | N/A | N/A | N/A | N/A |
| Homeobox protein PKNOX1 | P55347 | PKNOX1 | 47577 | 37 | 1 | 3.69 ± N/A | N/A | N/A | N/A | N/A |
| Stimulatory protein 1 | P08047 | SP1 | 80644 | 92 | 1 | 2.59 ± N/A | N/A | N/A | N/A | N/A |
| Nuclear factor 1 A-type | Q12857 | NFIA | 55909 | 75 | 2 | 2.10 ± 0.21 | N/A | N/A | N/A | N/A |
| Breast cancer type 1 susceptibility protein | P38398 | BRCA1 | 207592 | 38 | 1 | 2.03 ± N/A | N/A | N/A | N/A | N/A |
| Zinc fingers and homeoboxes protein 3 | Q9H4I2 | ZHX3 | 104592 | 60 | 2 | 1.82 ± 1.12 | N/A | N/A | N/A | N/A |
| Zinc finger and BTB domain-containing protein 7B | O15156 | ZBTB7B | 57990 | N/A | N/A | N/A | 67 | 2 | 4.25 ± 0.74 | 4.19 ± 0.95 |
| Transcription factor Sp3 | Q02447 | SP3 | 81876 | N/A | N/A | N/A | 110 | 2 | 2.60 ± 0.07 | 1.98 ± 0.03 |
| Steroid hormone receptor ERR1 | P11474 | ESRRA | 55404 | N/A | N/A | N/A | 50 | 1 | 1.76 ± N/A | 1.99 ± N/A |
| DNA damage response protein | ||||||||||
| DNA-(apurinic or apyrimidinic site) lyase | P27695 | APEX1 | 35532 | 766 | 25 | 8.10 ± 3.21 | 782 | 26 | 4.58 ± 1.43 | 4.18 ± 1.62 |
| Telomeric repeat-binding factor 2-interacting protein 1 | Q9NYB0 | TERF2IP | 44233 | 66 | 3 | 5.73 ± 2.57 | 93 | 2 | 3.18 ± 0.76 | 4.39 ± 2.67 |
| High mobility group protein B3 | O15347 | HMGB3 | 22965 | 85 | 2 | 5.51 ± 0.32 | 132 | 4 | 2.45 ± 0.30 | 2.33 ± 0.24 |
| DNA topoisomerase 2-binding protein 1 | Q92547 | TOPBP1 | 170571 | 40 | 1 | 2.77 ± N/A | 41 | 1 | 2.43 ± N/A | 2.45 ± N/A |
| Mediator of DNA damage checkpoint protein 1 | Q14676 | MDC1 | 226529 | 278 | 16 | 1.92 ± 1.35 | 427 | 10 | 1.28 ± 0.21 | 1.34 ± 0.44 |
| High mobility group protein B2 | P26583 | HMGB2 | 24019 | 497 | 1 | 10.01 ± N/A | N/A | N/A | N/A | N/A |
| DNA polymerase epsilon subunit 2 | P56282 | POLE2 | 59499 | 34 | 1 | 8.66 ± N/A | N/A | N/A | N/A | N/A |
| High mobility group protein B1 | P09429 | HMGB1 | 24878 | 603 | 9 | 5.37 ± 0.48 | N/A | N/A | N/A | N/A |
| Proliferating cell nuclear antigen | P12004 | PCNA | 28750 | 202 | 8 | 3.12 ± 1.43 | N/A | N/A | N/A | N/A |
| Poly(ADP-ribose) polymerase 2 | Q9UGN5 | PARP2 | 66164 | 45 | 2 | 1.73 ± 0.11 | N/A | N/A | N/A | N/A |
| Telomeric repeat-binding factor 2 | Q15554 | TERF2 | 55517 | N/A | N/A | N/A | 188 | 7 | 3.96 ± 0.63 | 3.64 ± 0.40 |
| High mobility group protein 1-like 10 | Q9UGV6 | HMG1L10 | 24203 | N/A | N/A | N/A | 48 | 1 | 2.08 ± N/A | 2.31 ± N/A |
| DNA repair protein RAD50 | Q92878 | RAD50 | 153797 | N/A | N/A | N/A | 83 | 4 | 1.96 ± 0.27 | 1.81 ± 0.25 |
| Repressor and corepressor | ||||||||||
| Zinc finger and BTB domain-containing protein 7A | O95365 | ZBTB7A | 61401 | 886 | 15 | 5.66 ± 1.90 | 56 | 2 | 3.32 ± 0.26 | 3.09 ± 0.17 |
| C-terminal-binding protein 1 | Q13363 | CTBP1 | 47505 | 40 | 1 | 2.27 ± N/A | 177 | 5 | 1.68 ± 0.38 | 1.71 ± 0.12 |
| Protein wiz | O95785 | WIZ | 178563 | 117 | 10 | 1.96 ± 0.40 | 801 | 26 | 1.68 ± 0.30 | 1.61 ± 0.25 |
| CCCTC binding factor | P49711 | CTCF | 82732 | 34 | 1 | 9.68 ± N/A | N/A | N/A | N/A | N/A |
| Transcription factor CP2-like protein 1 | Q9NZI6 | TFCP2L1 | 54593 | 331 | 2 | 2.61 ± 0.38 | N/A | N/A | N/A | N/A |
| Paired amphipathic helix protein Sin3b | O75182 | SIN3B | 132983 | N/A | N/A | N/A | 87 | 3 | 1.77 ± 0.49 | 1.74 ± 0.71 |
| Methyl-CpG-binding domain protein 2 | Q9UBB5 | MBD2 | 43228 | N/A | N/A | N/A | 147 | 3 | 1.64 ± 0.19 | 1.68 ± 0.25 |
| SWI·SNF-related protein | ||||||||||
| SWI·SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 | Q12824 | SMARCB1 | 44113 | 69 | 4 | 2.97 ± 0.73 | 317 | 13 | 1.84 ± 0.29 | 1.77 ± 0.26 |
| AT-rich interactive domain-containing protein 1A | O14497 | ARID1A | 241892 | 34 | 3 | 2.25 ± 0.25 | 367 | 10 | 1.79 ± 0.28 | 1.76 ± 0.24 |
| SWI·SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 2 | Q8TAQ2 | SMARCC2 | 132797 | 1529 | 51 | 2.07 ± 0.39 | 1430 | 30 | 1.64 ± 0.40 | 1.61 ± 0.36 |
| SWI·SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 | Q969G3 | SMARCE1 | 46621 | 71 | 4 | 2.03 ± 0.12 | 1142 | 28 | 1.88 ± 0.30 | 1.76 ± 0.28 |
| AT-rich interactive domain-containing protein 2 | Q68CP9 | ARID2 | 197268 | 1226 | 42 | 1.95 ± 0.51 | 1357 | 50 | 1.80 ± 0.34 | 1.67 ± 0.30 |
| Histone-modifiying protein | ||||||||||
| Euchromatic histone-lysine N-methyltransferase 1 | Q9H9B1 | EHMT1 | 138166 | 1231 | 58 | 2.60 ± 1.02 | 226 | 7 | 2.05 ± 0.43 | 1.91 ± 0.42 |
| Euchromatic histone-lysine N-methyltransferase 2 | Q96KQ7 | EHMT2 | 132287 | 870 | 37 | 2.45 ± 0.56 | 922 | 23 | 2.02 ± 0.32 | 1.83 ± 0.31 |
| Histone deacetylase complex subunit SAP130 | Q9H0E3 | SAP130 | 110255 | 52 | 3 | 1.93 ± 0.25 | 79 | 2 | 1.37 ± 0.05 | 1.22 ± 0.12 |
| Histone deacetylase 1 | Q13547 | HDAC1 | 55068 | 175 | 5 | 1.66 ± 0.22 | 808 | 15 | 1.71 ± 0.55 | 1.47 ± 0.28 |
| Histone deacetylase 2 | Q92769 | HDAC2 | 55329 | 164 | 8 | 1.66 ± 0.19 | 631 | 8 | 1.29 ± 0.21 | 1.28 ± 0.20 |
| Basic transcription machinery | ||||||||||
| Transcription termination factor 2 | Q9UNY4 | TTF2 | 129508 | 43 | 2 | 1.73 ± 0.02 | 261 | 14 | 1.30 ± 0.22 | 1.21 ± 0.18 |
| TATA-binding protein-associated factor 172 | O14981 | BTAF1 | 206756 | 97 | 4 | 1.70 ± 0.10 | N/A | N/A | N/A | N/A |
| Others | ||||||||||
| Deoxynucleotidyltransferase terminal-interacting protein 1 | Q9H147 | DNTTIP1 | 36990 | 481 | 12 | 4.80 ± 1.30 | 132 | 5 | 2.01 ± 0.63 | 1.83 ± 0.99 |
| Serine/threonine-protein kinase VRK1 | Q99986 | VRK1 | 45447 | 124 | 3 | 4.14 ± 0.61 | 278 | 11 | 2.42 ± 0.42 | 2.28 ± 0.40 |
| Zinc finger protein 462 | Q96JM2 | ZNF462 | 161426 | 95 | 3 | 3.62 ± 0.61 | 76 | 2 | 2.02 ± 0.20 | 1.90 ± 0.17 |
| Bromodomain-containing protein 7 | Q9NPI1 | BRD7 | 74092 | 223 | 8 | 3.33 ± 0.95 | 207 | 8 | 1.77 ± 0.38 | 1.69 ± 0.24 |
| UPF0609 protein C4orf27 | Q9NWY4 | C4orf27 | 39383 | 111 | 5 | 3.10 ± 1.37 | 240 | 8 | 1.80 ± 0.45 | 1.72 ± 0.46 |
| Chromatin accessibility complex protein 1 | Q9NRG0 | CHRAC1 | 14701 | 330 | 9 | 2.67 ± 1.22 | 47 | 1 | 2.92 ± N/A | 2.50 ± N/A |
| YEATS domain-containing protein 2 | Q9ULM3 | YEATS2 | 150688 | 97 | 4 | 2.26 ± 0.43 | 198 | 7 | 1.82 ± 0.38 | 1.62 ± 0.31 |
| ZZ-type zinc finger-containing protein 3 | Q8IYH5 | ZZZ3 | 101960 | 94 | 3 | 1.96 ± 0.20 | 82 | 3 | 1.77 ± 0.10 | 1.60 ± 0.18 |
| Protein S100-A8 | P05109 | S100A8 | 10828 | 56 | 1 | 8.91 ± N/A | N/A | N/A | N/A | N/A |
| Uncharacterized protein C14orf43 | Q6PJG2 | C14orf43 | 114918 | 158 | 6 | 2.67 ± 0.14 | N/A | N/A | N/A | N/A |
| Zinc finger protein 335 | Q9H4Z2 | ZNF335 | 144802 | 57 | 2 | 2.55 ± 0.92 | N/A | N/A | N/A | N/A |
| E3 ubiquitin-protein ligase UHRF2 | Q96PU4 | UHRF2 | 89928 | 182 | 5 | 1.92 ± 0.22 | N/A | N/A | N/A | N/A |
| PR domain zinc finger protein 16 | Q9HAZ2 | PRDM16 | 140172 | 44 | 2 | 1.85 ± 0.02 | N/A | N/A | N/A | N/A |
| Coiled-coil domain-containing protein 95 | Q8NBZ0 | INO80E | 26462 | 295 | 14 | 1.76 ± 0.52 | N/A | N/A | N/A | N/A |
| SAPS domain family member 3 | Q5H9R7 | SAPS3 | 97608 | 40 | 1 | 1.63 ± N/A | N/A | N/A | N/A | N/A |
| GTP-binding nuclear protein Ran | P62826 | RAN | 24408 | N/A | N/A | N/A | 45 | 1 | 2.86 ± N/A | 1.68 ± N/A |
| Thymocyte nuclear protein 1 | Q9P016 | THYN1 | 25681 | N/A | N/A | N/A | 138 | 1 | 2.52 ± N/A | 2.19 ± N/A |
| Calcineurin-binding protein cabin-1 | Q9Y6J0 | CABIN1 | 246197 | N/A | N/A | N/A | 51 | 1 | 2.07 ± N/A | 1.75 ± N/A |
| Cytoskeleton-associated protein 5 | Q14008 | CKAP5 | 225366 | 46 | 0 | N/A | 173 | 3 | 2.07 ± 0.14 | 2.12 ± 0.38 |
| Neuron navigator 3 | Q8IVL0 | NAV3 | 255461 | N/A | N/A | N/A | 40 | 1 | 1.93 ± N/A | 2.01 ± N/A |
| Ephexin-1 | Q8N5V2 | NGEF | 82445 | N/A | N/A | N/A | 40 | 1 | 1.93 ± N/A | 1.63 ± N/A |
| Spliceosome RNA helicase BAT1 | Q13838 | BAT1 | 48960 | 157 | 0 | N/A | 214 | 1 | 1.88 ± N/A | 1.83 ± N/A |
| Metastasis-associated protein MTA3 | Q9BTC8 | MTA3 | 67461 | N/A | N/A | N/A | 95 | 2 | 1.82 ± 0.26 | 1.74 ± 0.07 |
| Uncharacterized protein C6orf174 precursor | Q5TF21 | C6orf174 | 103136 | N/A | N/A | N/A | 152 | 7 | 1.78 ± 0.17 | 1.67 ± 0.17 |
a Mascot protein score.
b The number of nondegenerate (unique) peptide used for quantification.
c cICAT ratios, WT and MU indicate proteins enriched on WT and MU DNA beads, respectively.
d iTRAQ ratios, WT1 and WT2, indicate proteins enriched on WT DNA beads, whereas MU1 and MU2 indicate proteins enriched on MU DNA-beads, respectively.
e Not available.