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 nameAccession numberGene nameMasscICATiTRAQ
ScoreaPeptidebWT/MUcScoreaPeptidebWT1/MU2dWT2/MU2d
bHLH transcription factor
    Activating enhancer-binding protein 4Q01664TFAP4387025921.96 ± 0.0719932.46 ± 0.601.96 ± 0.39
    Circadian locomoter output cycles protein kaputO15516CLOCK952446412.04 ± N/AN/AN/AN/AN/A
    Upstream stimulatory factor 2Q15853USF236932N/AeN/AN/A10843.36 ± 0.903.22 ± 0.71
Transcription factor
    Nuclear factor of activated T-cells, cytoplasmic 2Q13469NFATC21000836526.46 ± 2.108832.00 ± 0.582.05 ± 0.49
    Alpha-globin transcription factor CP2Q12800TFCP2572201019323.32 ± 1.5852292.26 ± 0.342.00 ± 0.33
    General transcription factor II-IP78347GTF2I11234614133.15 ± 0.82757281.74 ± 0.331.63 ± 0.36
    Upstream-binding protein 1Q9NZI7UBP160453903402.70 ± 0.45582121.88 ± 0.191.73 ± 0.19
    COUP transcription factor 1P10589NR2F14612631652.22 ± 2.1314332.13 ± 0.561.94 ± 0.49
    COUP transcription factor 2P24468NR2F24554222821.78 ± 0.0513611.99 ± N/A1.78 ± N/A
    Nuclear factor 1 C-typeP08651NFIC556408531.69 ± 0.1817521.73 ± 0.061.75 ± 0.05
    Nuclear receptor subfamily 2 group F member 6P10588NR2F6429527834.28 ± 0.27N/AN/AN/AN/A
    Homeobox protein PKNOX1P55347PKNOX1475773713.69 ± N/AN/AN/AN/AN/A
    Stimulatory protein 1P08047SP1806449212.59 ± N/AN/AN/AN/AN/A
    Nuclear factor 1 A-typeQ12857NFIA559097522.10 ± 0.21N/AN/AN/AN/A
    Breast cancer type 1 susceptibility proteinP38398BRCA12075923812.03 ± N/AN/AN/AN/AN/A
    Zinc fingers and homeoboxes protein 3Q9H4I2ZHX31045926021.82 ± 1.12N/AN/AN/AN/A
    Zinc finger and BTB domain-containing protein 7BO15156ZBTB7B57990N/AN/AN/A6724.25 ± 0.744.19 ± 0.95
    Transcription factor Sp3Q02447SP381876N/AN/AN/A11022.60 ± 0.071.98 ± 0.03
    Steroid hormone receptor ERR1P11474ESRRA55404N/AN/AN/A5011.76 ± N/A1.99 ± N/A
DNA damage response protein
    DNA-(apurinic or apyrimidinic site) lyaseP27695APEX135532766258.10 ± 3.21782264.58 ± 1.434.18 ± 1.62
    Telomeric repeat-binding factor 2-interacting protein 1Q9NYB0TERF2IP442336635.73 ± 2.579323.18 ± 0.764.39 ± 2.67
    High mobility group protein B3O15347HMGB3229658525.51 ± 0.3213242.45 ± 0.302.33 ± 0.24
    DNA topoisomerase 2-binding protein 1Q92547TOPBP11705714012.77 ± N/A4112.43 ± N/A2.45 ± N/A
    Mediator of DNA damage checkpoint protein 1Q14676MDC1226529278161.92 ± 1.35427101.28 ± 0.211.34 ± 0.44
    High mobility group protein B2P26583HMGB224019497110.01 ± N/AN/AN/AN/AN/A
    DNA polymerase epsilon subunit 2P56282POLE2594993418.66 ± N/AN/AN/AN/AN/A
    High mobility group protein B1P09429HMGB12487860395.37 ± 0.48N/AN/AN/AN/A
    Proliferating cell nuclear antigenP12004PCNA2875020283.12 ± 1.43N/AN/AN/AN/A
    Poly(ADP-ribose) polymerase 2Q9UGN5PARP2661644521.73 ± 0.11N/AN/AN/AN/A
    Telomeric repeat-binding factor 2Q15554TERF255517N/AN/AN/A18873.96 ± 0.633.64 ± 0.40
    High mobility group protein 1-like 10Q9UGV6HMG1L1024203N/AN/AN/A4812.08 ± N/A2.31 ± N/A
    DNA repair protein RAD50Q92878RAD50153797N/AN/AN/A8341.96 ± 0.271.81 ± 0.25
Repressor and corepressor
    Zinc finger and BTB domain-containing protein 7AO95365ZBTB7A61401886155.66 ± 1.905623.32 ± 0.263.09 ± 0.17
    C-terminal-binding protein 1Q13363CTBP1475054012.27 ± N/A17751.68 ± 0.381.71 ± 0.12
    Protein wizO95785WIZ178563117101.96 ± 0.40801261.68 ± 0.301.61 ± 0.25
    CCCTC binding factorP49711CTCF827323419.68 ± N/AN/AN/AN/AN/A
    Transcription factor CP2-like protein 1Q9NZI6TFCP2L15459333122.61 ± 0.38N/AN/AN/AN/A
    Paired amphipathic helix protein Sin3bO75182SIN3B132983N/AN/AN/A8731.77 ± 0.491.74 ± 0.71
    Methyl-CpG-binding domain protein 2Q9UBB5MBD243228N/AN/AN/A14731.64 ± 0.191.68 ± 0.25
SWI·SNF-related protein
    SWI·SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1Q12824SMARCB1441136942.97 ± 0.73317131.84 ± 0.291.77 ± 0.26
    AT-rich interactive domain-containing protein 1AO14497ARID1A2418923432.25 ± 0.25367101.79 ± 0.281.76 ± 0.24
SWI·SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 2Q8TAQ2SMARCC21327971529512.07 ± 0.391430301.64 ± 0.401.61 ± 0.36
    SWI·SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1Q969G3SMARCE1466217142.03 ± 0.121142281.88 ± 0.301.76 ± 0.28
    AT-rich interactive domain-containing protein 2Q68CP9ARID21972681226421.95 ± 0.511357501.80 ± 0.341.67 ± 0.30
Histone-modifiying protein
    Euchromatic histone-lysine N-methyltransferase 1Q9H9B1EHMT11381661231582.60 ± 1.0222672.05 ± 0.431.91 ± 0.42
    Euchromatic histone-lysine N-methyltransferase 2Q96KQ7EHMT2132287870372.45 ± 0.56922232.02 ± 0.321.83 ± 0.31
    Histone deacetylase complex subunit SAP130Q9H0E3SAP1301102555231.93 ± 0.257921.37 ± 0.051.22 ± 0.12
    Histone deacetylase 1Q13547HDAC15506817551.66 ± 0.22808151.71 ± 0.551.47 ± 0.28
    Histone deacetylase 2Q92769HDAC25532916481.66 ± 0.1963181.29 ± 0.211.28 ± 0.20
Basic transcription machinery
    Transcription termination factor 2Q9UNY4TTF21295084321.73 ± 0.02261141.30 ± 0.221.21 ± 0.18
    TATA-binding protein-associated factor 172O14981BTAF12067569741.70 ± 0.10N/AN/AN/AN/A
Others
    Deoxynucleotidyltransferase terminal-interacting protein 1Q9H147DNTTIP136990481124.80 ± 1.3013252.01 ± 0.631.83 ± 0.99
    Serine/threonine-protein kinase VRK1Q99986VRK14544712434.14 ± 0.61278112.42 ± 0.422.28 ± 0.40
    Zinc finger protein 462Q96JM2ZNF4621614269533.62 ± 0.617622.02 ± 0.201.90 ± 0.17
    Bromodomain-containing protein 7Q9NPI1BRD77409222383.33 ± 0.9520781.77 ± 0.381.69 ± 0.24
    UPF0609 protein C4orf27Q9NWY4C4orf273938311153.10 ± 1.3724081.80 ± 0.451.72 ± 0.46
    Chromatin accessibility complex protein 1Q9NRG0CHRAC11470133092.67 ± 1.224712.92 ± N/A2.50 ± N/A
    YEATS domain-containing protein 2Q9ULM3YEATS21506889742.26 ± 0.4319871.82 ± 0.381.62 ± 0.31
    ZZ-type zinc finger-containing protein 3Q8IYH5ZZZ31019609431.96 ± 0.208231.77 ± 0.101.60 ± 0.18
    Protein S100-A8P05109S100A8108285618.91 ± N/AN/AN/AN/AN/A
    Uncharacterized protein C14orf43Q6PJG2C14orf4311491815862.67 ± 0.14N/AN/AN/AN/A
    Zinc finger protein 335Q9H4Z2ZNF3351448025722.55 ± 0.92N/AN/AN/AN/A
    E3 ubiquitin-protein ligase UHRF2Q96PU4UHRF28992818251.92 ± 0.22N/AN/AN/AN/A
    PR domain zinc finger protein 16Q9HAZ2PRDM161401724421.85 ± 0.02N/AN/AN/AN/A
    Coiled-coil domain-containing protein 95Q8NBZ0INO80E26462295141.76 ± 0.52N/AN/AN/AN/A
    SAPS domain family member 3Q5H9R7SAPS3976084011.63 ± N/AN/AN/AN/AN/A
    GTP-binding nuclear protein RanP62826RAN24408N/AN/AN/A4512.86 ± N/A1.68 ± N/A
    Thymocyte nuclear protein 1Q9P016THYN125681N/AN/AN/A13812.52 ± N/A2.19 ± N/A
    Calcineurin-binding protein cabin-1Q9Y6J0CABIN1246197N/AN/AN/A5112.07 ± N/A1.75 ± N/A
    Cytoskeleton-associated protein 5Q14008CKAP5225366460N/A17332.07 ± 0.142.12 ± 0.38
    Neuron navigator 3Q8IVL0NAV3255461N/AN/AN/A4011.93 ± N/A2.01 ± N/A
    Ephexin-1Q8N5V2NGEF82445N/AN/AN/A4011.93 ± N/A1.63 ± N/A
    Spliceosome RNA helicase BAT1Q13838BAT1489601570N/A21411.88 ± N/A1.83 ± N/A
    Metastasis-associated protein MTA3Q9BTC8MTA367461N/AN/AN/A9521.82 ± 0.261.74 ± 0.07
    Uncharacterized protein C6orf174 precursorQ5TF21C6orf174103136N/AN/AN/A15271.78 ± 0.171.67 ± 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.