Gene expression profile of NFκB repressing factor (NKRF) knockdown cells by microarray analysis


Human NFB repressing factor (NKRF) is a negative regulation transcription factor, which is able to repress transcription by binding to the negative regulatory element (NRE) near the NFκB binding site in certain genes’ promoters. Current researches reveals that NKRF represses the activation of IFN-, IL-8, hiNOS and HIV-1 by NFκB. We used optical fiber beadchip to analysis the different gene expression patterns of RNAi mediated NKRF knockdown HEK293 cells and found that several genes showed significant change of expression levels. Real-time PCR was performed to verify the changes of expression of candidate genes. We analyzed the function of candidate genes by searching the gene ontology databases and publications and revealed that these genes functioned in cell cycle, cell proliferation, apoptosis, cell migration, DNA repair, transcription, metabolism, response to stimulus and signal transduction. This study provides new perspectives on NKRF’s potential multiple functions.

This is a preview of subscription content, access via your institution.


  1. 1.

    Nourbakhsh, M. & Hauser, H. Constitutive silencing of IFN-beta promoter is mediated by NRF(NF-kappaBrepressing factor), a nuclear inhibitor of NF-kappaB. EMBO J. 18, 6415–6425 (1999).

    Article  CAS  Google Scholar 

  2. 2.

    Nourbakhsh, M. et al. The NF-kappa b repressing factor is involved in basal repression and interleukin (IL)-1-induced activation of IL-8 transcription by binding to a conserved NF-kappa b-flanking sequence element. J. Biol. Chem. 276, 4501–4508 (2001).

    Article  CAS  Google Scholar 

  3. 3.

    Feng, X. et al. Identification of a negative response element in the human inducible nitric-oxide synthase (hiNOS) promoter: The role of NF-kappa B-repressing factor (NRF) in basal repression of the hiNOS gene. Proc. Natl. Acad. Sci. U S A 99, 14212–14217 (2002).

    Article  CAS  Google Scholar 

  4. 4.

    Dreikhausen, U., Hiebenthal-Millow, K., Bartels, M., Resch, K. & Nourbakhsh, M. NF-kappaB-repressing factor inhibits elongation of human immunodeficiency virus type 1 transcription by DRB sensitivity-inducing factor. Mol. Cell. Biol. 25, 7473–7483 (2005).

    Article  CAS  Google Scholar 

  5. 5.

    Reboll, M.R. et al. Mapping of NRF binding motifs of NF-kappaB p65 subunit. J. Biochem. 150, 553–562 (2011).

    Article  CAS  Google Scholar 

  6. 6.

    Niedick, I. et al. Nucleolar localization and mobility analysis of the NF-kappaB repressing factor NRF. J. Cell Sci. 117, 3447–3458 (2004).

    Article  CAS  Google Scholar 

  7. 7.

    Oumard, A., Hennecke, M., Hauser, H. & Nourbakhsh, M. Translation of NRF mRNA is mediated by highly efficient internal ribosome entry. Mol. Cell. Biol. 20, 2755–2759 (2000).

    Article  CAS  Google Scholar 

  8. 8.

    Reboll, M.R. et al. NRF IRES activity is mediated by RNA binding protein JKTBP1 and a 14-nt RNA element. RNA 13, 1328–1340 (2007).

    Article  CAS  Google Scholar 

  9. 9.

    Lerner-Marmarosh, N., Miralem, T., Gibbs, P.E. & Maines, M.D. Human biliverdin reductase is an ERK activator; hBVR is an ERK nuclear transporter and is required for MAPK signaling. Proc. Natl. Acad. Sci. U S A 105, 6870–6875 (2008).

    Article  CAS  Google Scholar 

  10. 10.

    Peng, B. et al. CPAP is a novel stat5-interacting cofactor that augments stat5-mediated transcriptional activity. Mol. Endocrinol. 16, 2019–2033 (2002).

    Article  CAS  Google Scholar 

  11. 11.

    Koyanagi, M., Hijikata, M., Watashi, K., Masui, O. & Shimotohno, K. Centrosomal P4.1-associated protein is a new member of transcriptional coactivators for nuclear factor-kappaB. J. Biol. Chem. 280, 12430–12437 (2005).

    Article  CAS  Google Scholar 

  12. 12.

    Lacombe, C. & Mayeux, P. Biology of erythropoietin. Haematologica 83, 724–732 (1998).

    CAS  Google Scholar 

  13. 13.

    Lee, S.M. et al. EPO receptor-mediated ERK kinase and NF-kappaB activation in erythropoietin-promoted differentiation of astrocytes. Biochem. Biophys. Res. Commun. 320, 1087–1095 (2004).

    Article  CAS  Google Scholar 

  14. 14.

    Liu, Y. et al. Structural basis and binding properties of the second bromodomain of Brd4 with acetylated histone tails. Biochemistry 47, 6403–6417 (2008).

    Article  CAS  Google Scholar 

  15. 15.

    You, J. et al. Regulation of aurora B expression by the bromodomain protein Brd4. Mol. Cell. Biol. 29, 5094–5103 (2009).

    Article  CAS  Google Scholar 

  16. 16.

    Zhang, J. & Herrup, K. Cdk5 and the non-catalytic arrest of the neuronal cell cycle. Cell Cycle 7, 3487–3490 (2008).

    Article  CAS  Google Scholar 

  17. 17.

    Mayor, T., Stierhof, Y.D., Tanaka, K., Fry, A.M. & Nigg, E.A. The centrosomal protein C-Nap1 is required for cell cycle-regulated centrosome cohesion. J. Cell Biol. 151, 837–846 (2000).

    Article  CAS  Google Scholar 

  18. 18.

    Nakayama, K. et al. A BTB/POZ protein, NAC-1, is related to tumor recurrence and is essential for tumor growth and survival. Proc. Natl. Acad. Sci. U S A 103, 18739–18744 (2006).

    Article  CAS  Google Scholar 

  19. 19.

    Jinawath, N. et al. NAC-1, a potential stem cell pluripotency factor, contributes to paclitaxel resistance in ovarian cancer through inactivating Gadd45 pathway. Oncogene 28, 1941–1948 (2009).

    Article  CAS  Google Scholar 

  20. 20.

    Lin, H., Chen, M.C., Chiu, C.Y., Song, Y.M. & Lin, S.Y. Cdk5 regulates STAT3 activation and cell proliferation in medullary thyroid carcinoma cells. J. Biol. Chem. 282, 2776–2784 (2007).

    Article  CAS  Google Scholar 

  21. 21.

    Uddin, S. et al. Role of leptin and its receptors in the pathogenesis of thyroid cancer. Int. J. Clin. Exp. Pathol. 4, 637–643 (2011).

    CAS  Google Scholar 

  22. 22.

    Ray, A., Shakya, A., Kumar, D. & Ray, B.K. Overexpression of serum amyloid A-activating factor 1 inhibits cell proliferation by the induction of cyclin-dependent protein kinase inhibitor p21WAF-1/Cip-1/Sdi-1 expression. J. Immunol. 172, 5006–5015 (2004).

    CAS  Google Scholar 

  23. 23.

    Baumann, S. et al. An unexpected role for FosB in activation-induced cell death of T cells. Oncogene 22, 1333–1339 (2003).

    Article  CAS  Google Scholar 

  24. 24.

    Ishii, H. et al. Frag1, a homolog of alternative replication factor C subunits, links replication stress surveil-lance with apoptosis. Proc. Natl. Acad. Sci. U S A 102, 9655–9660 (2005).

    Article  CAS  Google Scholar 

  25. 25.

    Gao, J. et al. IRF-1 transcriptionally upregulates PUMA, which mediates the mitochondrial apoptotic pathway in IRF-1-induced apoptosis in cancer cells. Cell Death Differ. 17, 699–709 (2010).

    Article  CAS  Google Scholar 

  26. 26.

    Park, S.Y. et al. IFN-gamma enhances TRAIL-induced apoptosis through IRF-1. Eur. J. Biochem. 271, 4222–4228 (2004).

    Article  CAS  Google Scholar 

  27. 27.

    Chu, Z.L. et al. A novel enhancer of the Apaf1 apoptosome involved in cytochrome c-dependent caspase activation and apoptosis. J. Biol. Chem. 276, 9239–9245 (2001).

    Article  CAS  Google Scholar 

  28. 28.

    Liu, F. et al. Expression of NALP1 in cerebellar granule neurons stimulates apoptosis. Cell. Signal. 16, 1013–1021 (2004).

    CAS  Google Scholar 

  29. 29.

    Zhang, L. et al. Role for the pleckstrin homology domain-containing protein CKIP-1 in AP-1 regulation and apoptosis. EMBO J. 24, 766–778 (2005).

    Article  CAS  Google Scholar 

  30. 30.

    Zhang, L. et al. Selective involvement of BH3-only proteins and differential targets of Noxa in diverse apoptotic pathways. Cell Death Differ. 18, 864–873 (2011).

    Article  CAS  Google Scholar 

  31. 31.

    Chen, H. et al. JWA as a functional molecule to regulate cancer cells migration via MAPK cascades and Factin cytoskeleton. Cell. Signal. 19, 1315–1327 (2007).

    Article  CAS  Google Scholar 

  32. 32.

    Liu, R. et al. Cdk5-mediated regulation of the PIKEA-Akt pathway and glioblastoma cell invasion. Proc. Natl. Acad. Sci. U S A 105, 7570–7575 (2008).

    Article  CAS  Google Scholar 

  33. 33.

    Huang, C.Y. et al. Leptin increases motility and integrin up-regulation in human prostate cancer cells. J. Cell. Physiol. 226, 1274–1282 (2011).

    Article  CAS  Google Scholar 

  34. 34.

    Wang, S. et al. JWA regulates XRCC1 and functions as a novel base excision repair protein in oxidative-stressinduced DNA single-strand breaks. Nucleic Acids Res. 37, 1936–1950 (2009).

    Article  CAS  Google Scholar 

  35. 35.

    Courapied, S. et al. The cdk5 kinase regulates the STAT3 transcription factor to prevent DNA damage upon topoisomerase I inhibition. J. Biol. Chem. 285, 26765–26778 (2010).

    Article  CAS  Google Scholar 

  36. 36.

    Tano, K., Shiota, S., Collier, J., Foote, R.S. & Mitra, S. Isolation and structural characterization of a cDNA clone encoding the human DNA repair protein for O6-alkylguanine. Proc. Natl. Acad. Sci. U S A 87, 686–690 (1990).

    Article  CAS  Google Scholar 

  37. 37.

    Huang, B., Yang, X.D., Zhou, M.M., Ozato, K. & Chen, L.F. Brd4 coactivates transcriptional activation of NF-kappaB via specific binding to acetylated RelA. Mol. Cell. Biol. 29, 1375–1387 (2009).

    Article  CAS  Google Scholar 

  38. 38.

    Schuermann, M., Jooss, K. & Muller, R. fosB is a transforming gene encoding a transcriptional activator. Oncogene 6, 567–576 (1991).

    CAS  Google Scholar 

  39. 39.

    Miyamoto, M. et al. Regulated expression of a gene encoding a nuclear factor, IRF-1, that specifically binds to IFN-beta gene regulatory elements. Cell 54, 903–913 (1988).

    Article  CAS  Google Scholar 

  40. 40.

    Bossone, S.A., Asselin, C., Patel, A.J. & Marcu, K.B. MAZ, a zinc finger protein, binds to c-MYC and C2 gene sequences regulating transcriptional initiation and termination. Proc. Natl. Acad. Sci. U S A 89, 7452–7456 (1992).

    Article  CAS  Google Scholar 

  41. 41.

    Koues, O.I., Dudley, R.K., Mehta, N.T. & Greer, S.F. The 19S proteasome positively regulates histone methylation at cytokine inducible genes. Biochim. Biophys. Acta 1789, 691–701 (2009).

    Article  CAS  Google Scholar 

  42. 42.

    Morton, G.J. & Schwartz, M.W. Leptin and the central nervous system control of glucose metabolism. Physiol. Rev. 91, 389–411 (2011).

    Article  CAS  Google Scholar 

  43. 43.

    White, V. et al. Leptin modulates nitric oxide production and lipid metabolism in human placenta. Reprod. Fertil. Dev. 18, 425–432 (2006).

    Article  CAS  Google Scholar 

  44. 44.

    Chutkow, W.A. & Lee, R.T. Thioredoxin regulates adipogenesis through thioredoxin-interacting protein (Txnip) protein stability. J. Biol. Chem. 286, 29139–29145 (2011).

    Article  CAS  Google Scholar 

  45. 45.

    Saleh, M.C., Wheeler, M.B. & Chan, C.B. Uncoupling protein-2: evidence for its function as a metabolic regulator. Diabetologia 45, 174–187 (2002).

    Article  CAS  Google Scholar 

  46. 46.

    Benirschke, R.C. et al. Molecular basis for the association of human E4B U box ubiquitin ligase with E2-conjugating enzymes UbcH5c and Ubc4. Structure 18, 955–965 (2010).

    Article  CAS  Google Scholar 

  47. 47.

    Zhu, T. et al. JWA as a novel molecule involved in oxidative stress-associated signal pathway in myelogenous leukemia cells. J. Toxicol. Environ. Health A 69, 1399–1411 (2006).

    Article  CAS  Google Scholar 

  48. 48.

    Faustin, B. et al. Reconstituted NALP1 inflammasome reveals two-step mechanism of caspase-1 activation. Mol. Cell 25, 713–724 (2007).

    Article  CAS  Google Scholar 

  49. 49.

    Seve, M., Chimienti, F., Devergnas, S. & Favier, A. In silico identification and expression of SLC30 family genes: an expressed sequence tag data mining strategy for the characterization of zinc transporters’ tissue expression. BMC Genomics 5, 32 (2004).

    Article  Google Scholar 

  50. 50.

    World, C., Spindel, O.N. & Berk, B.C. Thioredoxininteracting protein mediates TRX1 translocation to the plasma membrane in response to tumor necrosis factor-alpha: a key mechanism for vascular endothelial growth factor receptor-2 transactivation by reactive oxygen species. Arterioscler. Thromb. Vasc. Biol. 31, 1890–1897 (2011).

    Article  CAS  Google Scholar 

Download references

Author information



Corresponding author

Correspondence to Yi Xie.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Sun, Y., Zheng, D., Gu, S. et al. Gene expression profile of NFκB repressing factor (NKRF) knockdown cells by microarray analysis. BioChip J 6, 247–253 (2012).

Download citation


  • NKRF
  • RNAi
  • Microarray
  • Gene expression profile