Identification of new Rel/NF-kappaB regulatory networks by focused genome location analysis

NF-κB is an inducible transcription factor that controls kinetically complex patterns of gene expression. Several studies reveal multiple pathways linking NF-κB to the promotion and progression of various cancers. Despite extensive interest and characterization, many NF-κB controlled genes still remain to be identified. We used chromatin immunoprecipitation combined with microarray technology (ChIP/Chip) to investigate the dynamic interaction of NF-κB with the promoter regions of 100 genes known to be expressed in mitogen-induced T-cells. Six previously unrecognized NF-κB controlled genes (ATM, EP300, TGFβ, Selectin, MMP-1, and SFN) were identified. Each gene is induced in mitogen-stimulated T-cells, repressed by pharmacological NF-κB blockade, reduced in cells deficient in the p50 NF-κB subunit and dramatically repressed by RNAi specifically designed against cRel. A coregulatory role for Ets transcription factors in the expression of the NF-κB controlled genes was predicted by comparative promoter analysis and confirmed by ChIP and by functional disruption of Ets. NF-κB deficiency produces a deficit in ATM function and DNA repair indicating an active role for NF-κB in maintaining DNA integrity. These results define new potential targets and transcriptional networks governed by NF-κB and provide novel functional insights for the role of NF-κB in genomic stability, cell cycle control, cell-matrix and cell-cell interactions during tumor progression.