Identification of functional TFAP2A and SP1 binding sites in new TFAP2A-modulated genes

BMC Genomics

Table 3 TFAP2A binding site sequences present in the regulatory regions of some TFAP2A- modulated genes.

Gene Symbol	ENSEMBL ID	Microarray FC	TFAP2A binding sequence	TFAP2A binding score	Position
ESDN/DCBLD2	ENSG00000057019	5.7	GCCGCGGGG	12.74	-269
			GCCCGCAGC	11.54	-10
PPARG	ENSG00000132170	2.6	GCCTGAGGC	11.48	-851
			GCCGGGGGC	12.82	-280
			GCCGCGGGG	12.74	-176
			GCCCCGCGG	11.77	-175
			GCCGTGGGC	11.94	-134
			GCCCGGCGC	11.85	+10
			GCCCGCGGC	12.85	+42
EREG	ENSG00000124882	2.5	CCCTCGGGC	12.75	-101
CXCL1	ENSG00000163739	2.4	GCCCGGGGG	13.46	-64
			GCCCCCGGG	12.76	-63
			GCCCGGAGC	12.14	-56
			GCCGCAGGC	11.91	+13
CD59	ENSG00000085063	1.7	GCCCTGGGG	12.58	-336
			GCCCCAGGG	12.55	-335
			GCCGGGAGC	11.51	-37
			GCCGGGGGG	12.83	+3
ADAMTS1	ENSG00000154734	1.7	GCCCGCAGC	11.54	-142
			GCCGGGGGC	12.82	-107
SLIT2	ENSG00000145147	1.7	GCCGGGGGC	12.81	-679
			GCCCCGAGG	12.06	-248
CASP9	ENSG00000132906	-1.5	GCCCTGGGG	12.58	-734
			GCCCCCAGG	11.45	-463
			GCCCCCAGG	11.45	-370
			GCCCGCAGG	11.55	-182
			GCCCTGGGG	12.58	+4
			GCCCCCAGG	11.45	+69
			GCCCCGCGC	11.75	+2
TGFBI	ENSG00000120708	-1.6	GCCCTGGGG	12.58	-899
			GCCCCCAGC	11.44	-414
			GCCCTGGGC	12.57	-212
			GCCCTGGGC	12.57	+43
GLO1	ENSG00000124767	-2.0	GCCGCGGGC	12.72	-24
FASTK	ENSG00000164896	-2.2	GCCCGGAGG	12.15	-856
			GCCCCGAGC	12.04	-500
			GCCCGGGGC	13.45	-413
			GCCCCGGGG	13.36	-393
			GCCCCCGGG	12.76	-391
			GCCCTCGGC	11.97	-66
			GCCCGGCGC	11.85	-59
			GCCCGCGGG	12.86	-42
			GCCGGGAGC	11.51	-2
KRT16	ENSG00000186832	-2.5	GCCCTCGGG	11.98	-860
			GCCCCCGGG	12.76	-650
			GCCTGAGGC	11.48	-502
			GCCCCGAGG	12.06	-279
			GCCCTCGGG	11.98	-277
KRT17	ENSG00000186831	-2.7	GCCCCGGGG	13.36	-525
			GCCCCGGGG	13.36	-524
			GCCCCCAGC	11.44	-203
			GCCTGGGGG	12.30	+56
PLCXD2	ENSG00000144824	-1.5	CCCCCTTGGC	9.47*	-878
			GGCCAGGGC	9.04*	-64
IFI44	ENSG00000137965	-1.9	-	-	-

For each ChIP-validated TFAP2A target gene or negative control (see figure 3 and 6) Gene Symbol, ENSEMBL IDs, TFAP2A binding site sequence, score and position (referring to the TSS as +1) are shown. ADAMTS1: ADAM metallopeptidase with thrombospondin type 1 motif, 1; CASP9: caspase 9; CD59: CD59 molecule, complement regulatory protein; CXCL1: chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity alpha); DCLBD2/ESDN: Endothelial and smooth muscle cell derived neuropiline like molecule; EREG: Epiregulin; FASTK: fast kinase; GLO1: glyoxalase I; KRT16: keratin 16; KRT17: keratin 17; IFI44: interferon-induced protein 44; PLCXD2: pleckstrin homology-like domain family B member 2; PPARG: peroxisome proliferator activated receptor gamma; SLIT2: slit homolog 2 (Drosophila); TGFBI: Transforming Growth Factor Beta-Induced. * low score binding sites, used as negative controls.

ISSN: 1471-2164