C-Jun binding site identification in K562 cells

Journal of Genetics and Genomics

Volumn 38, Issue 6, 2011, Pages 235-242

  Li, Minli ^a   Ge, Qinyu ^b   Wang, Wei ^a   Wang, Jinke ^a   Lu, Zuhong ^a,b  

^a SOUTHEAST UNIVERSITY   (China)

^b Southeast University   (China)

Author keywords

C Jun; ChIP Seq; Chromatin immunoprecipitation; DsDNA microarray

Indexed keywords

DOUBLE STRANDED DNA; PROTEIN C JUN;

ARTICLE; BINDING SITE; CELL STRAIN K 562; CONTROLLED STUDY; DNA MICROARRAY; GENE SEQUENCE; HUMAN; HUMAN CELL; HUMAN GENOME; MICROARRAY ANALYSIS; MICROCHIP ANALYSIS; MOLECULAR SIZE; PROTEIN BINDING; PROTEIN MOTIF; REGULATORY MECHANISM; TRANSCRIPTION REGULATION;

BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; ELECTROPHORETIC MOBILITY SHIFT ASSAY; GENOME, HUMAN; HUMANS; K562 CELLS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTO-ONCOGENE PROTEINS C-JUN; TRANSCRIPTION FACTOR AP-1;

EID: 79959377949     PISSN: 16738527     EISSN: 18735533     Source Type: Journal    
DOI: 10.1016/j.jgg.2011.05.004     Document Type: Article

References (53)

1. Arts J., Grimbergen J., Toet K., Kooistra T. On the role of c-Jun in the induction of PAI-1 gene expression by phorbol ester, serum, and IL-1alpha in HepG2 cells. Arterioscler. Thromb. Vasc. Biol. 1999, 19:39-46.
2. Bakiri L., Lallemand D., Bossy-Wetzel E., Yaniv M. Cell cycle-dependent variations in c-Jun and JunB phosphorylation: a role in the control of cyclin D1 expression. EMBO J. 2000, 19:2056-2068.
3. Borde-Chiche P., Diederich M., Morceau F., Wellman M., Dicato M. Phorbol ester responsiveness of the glutathione S-transferase P1 gene promoter involves an inducible c-Jun binding in human K562 leukemia cells. Leuk. Res. 2001, 25:241-247.
4. Bulyk M.L., Huang X., Choo Y., Church G.M. Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. USA 2001, 98:7158-7163.
5. Bulyk M.L., Johnson P.L., Church G.M. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res. 2002, 30:1255-1261.
6. Carroll J.S., Liu X.S., Brodsky A.S., Li W., Meyer C.A., Szary A.J., Eeckhoute J., Shao W., Hestermann E.V., Geistlinger T.R., Fox E.A., Silver P.A., Brown M. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 2005, 122:33-43.
7. Chen J., Panchanathan R., Choubey D. Stimulation of T cells up-regulates expression of Ifi202, an interferon-inducible lupus susceptibility gene, through activation of JNK/c-Jun pathway. Immunol. Lett. 2008, 118:13-20.
8. Chen X., Xu H., Yuan P., Fang F., Huss M., Vega V.B., Wong E., Orlov Y.L., Zhang W., Jiang J., Loh Y.H., Yeo H.C., Yeo Z.X., Narang V., Govindarajan K.R., Leong B., Shahab A., Ruan Y., Bourque G., Sung W.K., Clarke N.D., Wei C.L., Ng H.H. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008, 133:1106-1117.
9. Chen K.C., Chiou Y.L., Chang L.S. JNK1/c-Jun and p38 alpha MAPK/ATF-2 pathways are responsible for upregulation of Fas/FasL in human chronic myeloid leukemia K562 cells upon exposure to Taiwan cobra phospholipase A2. J. Cell Biochem. 2009, 108:612-620.
10. Chinenov Y., Kerppola T.K. Close encounters of many kinds: fos-Jun interactions that mediate transcription regulatory specificity. Oncogene 2001, 20:2438-2452.
11. Cooper S.J., Trinklein N.D., Anton E.D., Nguyen L., Myers R.M. Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res. 2006, 16:1-10.
12. Daubeuf S., Duvoix A., Wellman-Rousseau M., Diederich M., Visvikis A. Phorbol ester regulation of the human gamma-glutamyltransferase gene promoter. Biochem. Biophys. Res. Commun. 2004, 313:300-307.
13. Dong L.Y., Wang X.N., Song Z.G., Guo D., Zhao Y.Y., An W. Identification of human hepatic stimulator substance gene promoter and demonstration of dual regulation of AP1/AP4 cis-acting element in different cell lines. Int. J. Biochem. Cell Biol. 2007, 39:181-196.
14. Elagib K.E., Xiao M., Hussaini I.M., Delehanty L.L., Palmer L.A., Racke F.K., Birrer M.J., Shanmugasundaram G., McDevitt M.A., Goldfarb A.N. Jun blockade of erythropoiesis: role for repression of GATA-1 by HERP2. Mol. Cell. Biol. 2004, 24:7779-7794.
15. Eriksson M., Arminen L., Karjalainen-Lindsberg M.L., Leppa S. AP-1 regulates alpha2beta1 integrin expression by ERK-dependent signals during megakaryocytic differentiation of K562 cells. Exp. Cell Res. 2005, 304:175-186.
16. Farnham P.J. Insights from genomic profiling of transcription factors. Nat. Rev. Genet. 2009, 10:605-616.
17. Gu Q., Tan M., Sun Y. SAG/ROC2/Rbx2 is a novel activator protein-1 target that promotes c-Jun degradation and inhibits 12-O-tetradecanoylphorbol-13-acetate-induced neoplastic transformation. Cancer Res. 2007, 67:3616-3625.
18. Hatzis P., van der Flier L.G., van Driel M.A., Guryev V., Nielsen F., Denissov S., Nijman I.J., Koster J., Santo E.E., Welboren W., Versteeg R., Cuppen E., van de Wetering M., Clevers H., Stunnenberg H.G. Genome-wide pattern of TCF7L2/TCF4 chromatin occupancy in colorectal cancer cells. Mol. Cell. Biol. 2008, 28:2732-2744.
19. Humbert O., Achour I., Lautier D., Laurent G., Salles B. hMSH2 expression is driven by AP1-dependent regulation through phorbol-ester exposure. Nucleic Acids Res. 2003, 31:5627-5634.
20. Ivanov V.N., Bhoumik A., Krasilnikov M., Raz R., Owen-Schaub L.B., Levy D., Horvath C.M., Ronai Z. Cooperation between STAT3 and c-Jun suppresses Fas transcription. Mol. Cell 2001, 7:517-528.
21. Johnson D.S., Mortazavi A., Myers R.M., Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007, 316:1497-1502.
22. Kasibhatla S., Brunner T., Genestier L., Echeverri F., Mahboubi A., Green D.R. DNA damaging agents induce expression of Fas ligand and subsequent apoptosis in T lymphocytes via the activation of NF-kappa B and AP-1. Mol. Cell 1998, 1:543-551.
23. Klampfer L., Lee T.H., Hsu W., Vilcek J., Chen-Kiang S. NF-IL6 and AP-1 cooperatively modulate the activation of the TSG-6 gene by tumor necrosis factor alpha and interleukin-1. Mol. Cell. Biol. 1994, 14:6561-6569.
24. Kovacic-Milivojevic B., Gardner D.G. Divergent regulation of the human atrial natriuretic peptide gene by c-Jun and c-fos. Mol. Cell. Biol. 1992, 12:292-301.
25. Lamb R.F., Hennigan R.F., Turnbull K., Katsanakis K.D., MacKenzie E.D., Birnie G.D., Ozanne B.W. AP-1-mediated invasion requires increased expression of the hyaluronan receptor CD44. Mol. Cell. Biol. 1997, 17:963-976.
26. Lee T.I., Johnstone S.E., Young R.A. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat. Protoc. 2006, 1:729-748.
27. Macpherson P., Humbert O., Karran P. Frameshift mismatch recognition by the human MutS alpha complex. Mutat. Res. 1998, 408:55-66.
28. Miao Z.H., Ding J. Transcription factor c-Jun activation represses mdr-1 gene expression. Cancer Res. 2003, 63:4527-4532.
29. Oka T., Rairkar A., Chen J.H. Structural and functional analysis of the regulatory sequences of the ets-1 gene. Oncogene 1991, 6:2077-2083.
30. Okazaki M., Maeda G., Chiba T., Doi T., Imai K. Identification of GATA3 binding sites in Jurkat cells. Gene 2009, 445:17-25.
31. Paliogianni F., Raptis A., Ahuja S.S., Najjar S.M., Boumpas D.T. Negative transcriptional regulation of human interleukin 2 (IL-2) gene by glucocorticoids through interference with nuclear transcription factors AP-1 and NF-AT. J. Clin. Invest. 1993, 91:1481-1489.
32. Park J.M., Adam R.M., Peters C.A., Guthrie P.D., Sun Z., Klagsbrun M., Freeman M.R. AP-1 mediates stretch-induced expression of HB-EGF in bladder smooth muscle cells. Am. J. Physiol. 1999, 277:294-301.
33. Qian X.X., Mata-Greenwood E., Liao W.X., Zhang H., Zheng J., Chen D.B. Transcriptional regulation of endothelial nitric oxide synthase expression in uterine artery endothelial cells by c-Jun/AP-1. Mol. Cell. Endocrinol. 2007, 279:39-51.
34. Rabinovich A., Jin V.X., Rabinovich R., Xu X., Farnham P.J. E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. Genome Res. 2008, 18:1763-1777.
35. Rebollo A., Dumoutier L., Renauld J.C., Zaballos A., Ayllon V., Martinez A.C. Bcl-3 expression promotes cell survival following interleukin-4 deprivation and is controlled by AP1 and AP1-like transcription factors. Mol. Cell. Biol. 2000, 20:3407-3416.
36. Robertson G., Hirst M., Bainbridge M., Bilenky M., Zhao Y., Zeng T., Euskirchen G., Bernier B., Varhol R., Delaney A., Thiessen N., Griffith O.L., He A., Marra M., Snyder M., Jones S. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 2007, 4:651-657.
37. Sark M.W., Fischer D.F., de Meijer E., van de Putte P., Backendorf C. AP-1 and ets transcription factors regulate the expression of the human SPRR1A keratinocyte terminal differentiation marker. J. Biol. Chem. 1998, 273:24683-24692.
38. Schreiber M., Kolbus A., Piu F., Szabowski A., Mohle-Steinlein U., Tian J., Karin M., Angel P., Wagner E.F. Control of cell cycle progression by c-Jun is p53 dependent. Genes Dev. 1999, 13:607-619.
39. Shaulian E., Schreiber M., Piu F., Beeche M., Wagner E.F., Karin M. The mammalian UV response: c-Jun induction is required for exit from p53-imposed growth arrest. Cell 2000, 103:897-907.
40. Sprowles A., Robinson D., Wu Y.M., Kung H.J., Wisdom R. c-Jun controls the efficiency of MAP kinase signaling by transcriptional repression of MAP kinase phosphatases. Exp. Cell Res. 2005, 308:459-468.
41. Szabowski A., Maas-Szabowski N., Andrecht S., Kolbus A., Schorpp-Kistner M., Fusenig N.E., Angel P. C-Jun and JunB antagonistically control cytokine-regulated mesenchymal-epidermal interaction in skin. Cell 2000, 103:745-755.
42. Takahashi H., Asano K., Kinouchi M., Ishida-Yamamoto A., Wuepper K.D., Iizuka H. Structure and transcriptional regulation of the human cystatin A gene. The 12-O-tetradecanoylphorbol-13-acetate (TPA) responsive element-2 site (-272 to -278) on cystatin A gene is critical for TPA-dependent regulation. J. Biol. Chem. 1998, 273:17375-17380.
43. Takahashi S., Harigae H., Yokoyama H., Kaku M., Sasaki T. Genomic structure and regulation of a novel human gene, Klp1. Biochim. Biophys. Acta 2001, 1522:207-211.
44. Toft D.J., Rosenberg S.B., Bergers G., Volpert O., Linzer D.I. Reactivation of proliferin gene expression is associated with increased angiogenesis in a cell culture model of fibrosarcoma tumor progression. Proc. Natl. Acad. Sci. USA 2001, 98:13055-13059.
45. Tseng P.C., Hsu H.C., Janmanchi D., Lin C.H., Kuo Y.H., Chou C.K., Yeh S.F. Helioxanthin inhibits interleukin-1 beta-induced MIP-1 beta production by reduction of c-jun expression and binding of the c-jun/CREB1 complex to the AP-1/CRE site of the MIP-1 beta promoter in Huh7 cells. Biochem. Pharmacol. 2008, 76:1121-1133.
46. Ukon K., Tanimoto K., Shimokuni T., Noguchi T., Hiyama K., Tsujimoto H., Fukushima M., Toge T., Nishiyama M. Activator protein accelerates dihydropyrimidine dehydrogenase gene transcription in cancer cells. Cancer Res. 2005, 65:1055-1062.
47. Valouev A., Johnson D.S., Sundquist A., Medina C., Anton E., Batzoglou S., Myers R.M., Sidow A. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods 2008, 5:829-834.
48. Wang J.K., Li T.X., Bai Y.F., Lu Z.H. Evaluating the binding affinities of NF-kappaB p50 homodimer to the wild-type and single-nucleotide mutant Ig-kappaB sites by the unimolecular dsDNA microarray. Anal. Biochem. 2003, 316:192-201.
49. Wederell E.D., Bilenky M., Cullum R., Thiessen N., Dagpinar M., Delaney A., Varhol R., Zhao Y.J., Zeng T., Bernier B., Ingham M., Hirst M., Robertson G., Marra M.A., Jones S., Hoodless P.A. Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res. 2008, 36:4549-4564.
50. Whitfield J., Neame S.J., Paquet L., Bernard O., Ham J. Dominant-negative c-Jun promotes neuronal survival by reducing BIM expression and inhibiting mitochondrial cytochrome c release. Neuron 2001, 29:629-643.
51. Yang A., Zhu Z., Kapranov P., McKeon F., Church G.M., Gingeras T.R., Struhl K. Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol. Cell 2006, 24:593-602.
52. Yu X., Luo A., Zhou C., Ding F., Wu M., Zhan Q., Liu Z. Differentiation-associated genes regulated by TPA-induced c-Jun expression via a PKC/JNK pathway in KYSE450 cells. Biochem. Biophys. Res. Commun. 2006, 342:286-292.
53. Zenz R., Scheuch H., Martin P., Frank C., Eferl R., Kenner L., Sibilia M., Wagner E.F. C-Jun regulates eyelid closure and skin tumor development through EGFR signaling. Dev. Cell 2003, 4:879-889.