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

BMC Genomics. 2018 Nov 12;19(1):813. doi: 10.1186/s12864-018-5211-y.

Abstract

Background: The cellular response to ionizing radiation involves activation of p53-dependent pathways and activation of the atypical NF-κB pathway. The crosstalk between these two transcriptional networks include (co)regulation of common gene targets. Here we looked for novel genes potentially (co)regulated by p53 and NF-κB using integrative genomics screening in human osteosarcoma U2-OS cells irradiated with a high dose (4 and 10 Gy). Radiation-induced expression in cells with silenced TP53 or RELA (coding the p65 NF-κB subunit) genes was analyzed by RNA-Seq while radiation-enhanced binding of p53 and RelA in putative regulatory regions was analyzed by ChIP-Seq, then selected candidates were validated by qPCR.

Results: We identified a subset of radiation-modulated genes whose expression was affected by silencing of both TP53 and RELA, and a subset of radiation-upregulated genes where radiation stimulated binding of both p53 and RelA. For three genes, namely IL4I1, SERPINE1, and CDKN1A, an antagonistic effect of the TP53 and RELA silencing was consistent with radiation-enhanced binding of both p53 and RelA. This suggested the possibility of a direct antagonistic (co)regulation by both factors: activation by NF-κB and inhibition by p53 of IL4I1, and activation by p53 and inhibition by NF-κB of CDKN1A and SERPINE1. On the other hand, radiation-enhanced binding of both p53 and RelA was observed in a putative regulatory region of the RRAD gene whose expression was downregulated both by TP53 and RELA silencing, which suggested a possibility of direct (co)activation by both factors.

Conclusions: Four new candidates for genes directly co-regulated by NF-κB and p53 were revealed.

Keywords: Co-regulation; Integrative genomics; Radiation response; Transcription network.

MeSH terms

  • Binding Sites
  • Biomarkers, Tumor / genetics*
  • Biomarkers, Tumor / metabolism
  • Bone Neoplasms / genetics*
  • Bone Neoplasms / pathology
  • Bone Neoplasms / radiotherapy
  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation
  • Cyclin-Dependent Kinase Inhibitor p21 / genetics
  • Cyclin-Dependent Kinase Inhibitor p21 / metabolism
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic*
  • Gene Regulatory Networks
  • Genome, Human
  • High-Throughput Nucleotide Sequencing
  • Humans
  • L-Amino Acid Oxidase / genetics
  • L-Amino Acid Oxidase / metabolism
  • NF-kappa B / genetics
  • NF-kappa B / metabolism
  • Osteosarcoma / genetics*
  • Osteosarcoma / pathology
  • Osteosarcoma / radiotherapy
  • Plasminogen Activator Inhibitor 1 / genetics
  • Plasminogen Activator Inhibitor 1 / metabolism
  • Radiation, Ionizing*
  • Transcriptional Activation
  • Tumor Cells, Cultured
  • Tumor Suppressor Protein p53 / genetics
  • Tumor Suppressor Protein p53 / metabolism
  • ras Proteins / genetics
  • ras Proteins / metabolism

Substances

  • Biomarkers, Tumor
  • CDKN1A protein, human
  • Chromatin
  • Cyclin-Dependent Kinase Inhibitor p21
  • NF-kappa B
  • Plasminogen Activator Inhibitor 1
  • RRAD protein, human
  • SERPINE1 protein, human
  • TP53 protein, human
  • Tumor Suppressor Protein p53
  • IL4I1 protein, human
  • L-Amino Acid Oxidase
  • ras Proteins