RRAD, IL4I1, CDKN1A, and SERPINE1 genes are potentially co-regulated by NF-κB and p53 transcription factors in cells exposed to high doses of ionizing radiation

Table 1 Genes which expression was potentially dependent on RelA-containing NF-κB and/or p53 in cells exposed to ionizing radiation

Gene ID	IR-induced TF binding				Gene expression		Effects of siRNA on IR-induced expression
	RelA		p53		IR/Ctr fold change (wt)		siRELA/siCTR ratio		siTP53/siCTR ratio
	2 h	4 h	2 h	4 h	4 Gy	10 Gy	4 Gy	10 Gy	4 Gy	10 Gy
BBC3	+	+	+	+	2.14*	2.99*	0.86	0.87	0.45	0.42
BTG2	–	–	+	–	3.28*	3.92*	0.69	0.68	0.40	0.42
*CDKN1A*	+	+	+	+	2.69*	3.68*	1.16	1.16	0.44	0.46
CNN1	–	–	+	–	1.21	1.61*	1.60	1.72	1.49	1.54
DDB2	–	–	–	+	1.34*	1.53*	0.94	0.94	0.43	0.48
EDA2R	–	–	–	+	2.06*	2.24*	1.10	1.06	0.49	0.49
FHL2	+	+	+	–	2.40*	2.92*	1.02	1.06	0.61	0.63
GRHL3	–	–	+	–	1.90*	2.23*	1.04	0.87	0.52	0.37
PHLDA3	–	–	–	+	1.72*	2.06*	0.91	0.93	0.45	0.40
PLK2	–	–	+	+	1.96*	2.22*	1.08	1.09	0.60	0.64
*SERPINE1*	–	+	+	–	2.15*	2.79*	0.98	0.99	0.56	0.56
SLC30A1	–	–	+	+	1.81*	1.77*	1.12	1.09	0.73	0.66
TRIM22	–	–	+	+	1.56	1.80*	0.87	0.87	0.42	0.44
ZMAT3	–	–	–	+	1.81*	1.84*	1.05	1.08	0.48	0.50
BIRC3	+	+	–	–	7.04*	17.23*	0.52	0.47	1.41	1.27
CD83	–	+	–	–	2.23*	4.03*	0.71	0.62	0.94	0.95
CXCL8	+	+	–	–	3.89*	11.53*	0.42	0.37	1.87	1.95
CYP4F11	+	–	–	–	1.52*	1.64*	0.63	0.68	0.56	0.74
IL32	+	+	–	–	1.35	2.72*	0.48	0.43	1.08	1.06
NFKB1	+	+	–	–	2.10*	3.31*	0.72	0.66	1.08	1.13
NFKB2	+	+	–	–	1.44	2.21*	0.64	0.63	1.13	1.11
*NFKBIA*	+	+	+	–	1.86*	3.26*	0.65	0.63	1.25	1.28
NFKBIE	+	+	–	–	1.65	2.72*	0.59	0.59	1.12	1.08
RELB	+	+	–	–	2.60*	4.44*	0.66	0.65	1.06	0.99
TNFAIP3	–	+	–	–	3.07*	6.01*	0.70	0.66	1.03	1.02
TRAF1	–	+	–	–	2.42*	7.14*	0.47	0.39	2.97	2.06
*IL4I1*	+	+	+	+	1.83*	3.32*	0.48	0.39	1.58	1.23
*RRAD*	+	–	–	+	1.66*	3.56*	0.68	0.65	0.68	0.49

Indicated is RelA and p53 binding in putative gene regulatory regions revealed by the ChIP-Seq in wt cells 2 and 4 h after 10 Gy exposure. Gene expression (analyzed by RNA-Seq) is shown as a fold-change 4 h after 4 or 10 Gy dose against untreated wt control (asterisks mark p < 0.05). The effect of downregulation of either RELA or TP53 gene on a target gene expression is shown as a signal ratio in cells transfected with siRNA specific for RELA or TP53 and control siRNA (siCTR) analyzed 4 h after 4 or 10 Gy dose. Three groups of protein-coding genes are listed: putatively regulated by p53 (upper 14), RelA-containing NF-κB (middle 12), and both transcription factors (bottom 2); genes selected for validation are in bold characters

ISSN: 1471-2164