Identification of new Rel/NFkappaB regulatory networks by focused genome location analysis

Cell Cycle. 2009 Jul 1;8(13):2093-100. doi: 10.4161/cc.8.13.8926. Epub 2009 Jul 5.


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

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • 14-3-3 Proteins / genetics
  • 14-3-3 Proteins / metabolism
  • Ataxia Telangiectasia Mutated Proteins
  • Cell Cycle Proteins / genetics
  • Cell Cycle Proteins / metabolism
  • Cell Line
  • Chromatin Immunoprecipitation
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • E1A-Associated p300 Protein / genetics
  • E1A-Associated p300 Protein / metabolism
  • Gene Expression Profiling
  • Gene Regulatory Networks*
  • Humans
  • L-Selectin / genetics
  • L-Selectin / metabolism
  • Matrix Metalloproteinase 1 / genetics
  • Matrix Metalloproteinase 1 / metabolism
  • NF-kappa B / genetics
  • NF-kappa B / metabolism*
  • Oligonucleotide Array Sequence Analysis
  • Promoter Regions, Genetic
  • Protein Serine-Threonine Kinases / genetics
  • Protein Serine-Threonine Kinases / metabolism
  • Proto-Oncogene Proteins c-rel / genetics
  • Proto-Oncogene Proteins c-rel / metabolism*
  • RNA Interference
  • T-Lymphocytes / immunology
  • T-Lymphocytes / metabolism
  • Transforming Growth Factor beta1 / genetics
  • Transforming Growth Factor beta1 / metabolism
  • Tumor Suppressor Proteins / genetics
  • Tumor Suppressor Proteins / metabolism


  • 14-3-3 Proteins
  • Cell Cycle Proteins
  • DNA-Binding Proteins
  • NF-kappa B
  • Proto-Oncogene Proteins c-rel
  • Transforming Growth Factor beta1
  • Tumor Suppressor Proteins
  • L-Selectin
  • E1A-Associated p300 Protein
  • ATM protein, human
  • Ataxia Telangiectasia Mutated Proteins
  • Protein Serine-Threonine Kinases
  • Matrix Metalloproteinase 1