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Mapping the HIF Transcription Factor in Cancer by ChIP-Seq Technology

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Abstract

Hypoxia-inducible factor (HIF) is the major transcriptional regulator mediating the cellular physiological response to reduced levels of oxygen (hypoxia). Upregulated as a consequence, both of intra-tumour hypoxia and through activation of oncogenic pathways, HIF has an important role in the pathogenesis of many cancers. However, activation of major physiological pathways in cancer upregulates pathways with both pro- and antitumorigenic actions and therefore confers a co-selection penalty. It is likely that both genetic and epigenetic factors alter the HIF-transcriptional response to favour a more tumorigenic profile. Mapping HIF transcription factor binding in cancer by ChIP-seq technology provides a framework for studying the mechanisms by which both genetic and epigenetic signatures associated with cancer may alter this HIF response.

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References

  1. Hindorff LA, MacArthur J, Wise A, Junkins HA, Hall PN, Klemm AK, et al. A Catalog of Published Genome-Wide Association Studies. Available from: http://www.genome.gov/gwastudies.

  2. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860–921. PubMed PMID: 11237011.

    Article  PubMed  CAS  Google Scholar 

  3. IHGS Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004;431(7011):931–45. PubMed PMID: 15496913. Epub 2004/10/22. eng.

    Article  Google Scholar 

  4. Freedman ML, Monteiro AN, Gayther SA, Coetzee GA, Risch A, Plass C, et al. Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet. 2011;43(6):513–8. PubMed PMID: 21614091. Pubmed Central PMCID: 3325768. Epub 2011/05/27. eng.

    Article  PubMed  CAS  Google Scholar 

  5. Pomerantz MM, Ahmadiyeh N, Jia L, Herman P, Verzi MP, Doddapaneni H, et al. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat Genet. 2009;41(8):882–4. PubMed PMID: 19561607. Pubmed Central PMCID: 2763485. Epub 2009/06/30. eng.

    Article  PubMed  CAS  Google Scholar 

  6. Jia L, Landan G, Pomerantz M, Jaschek R, Herman P, Reich D, et al. Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet. 2009;5(8):e1000597. PubMed PMID: 19680443. Pubmed Central PMCID: 2717370. Epub 2009/08/15. eng.

    Article  PubMed  Google Scholar 

  7. Schodel J, Bardella C, Sciesielski LK, Brown JM, Pugh CW, Buckle V, et al. Common genetic variants at the 11q13.3 renal cancer susceptibility locus influence binding of HIF to an enhancer of cyclin D1 expression. Nat Genet. 2012;44(4):420–5. Epub 11 Mar 2012.

    Article  PubMed  Google Scholar 

  8. Consortium EP, Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57–74. PubMed PMID: 22955616. Pubmed Central PMCID: 3439153.

    Article  Google Scholar 

  9. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, et al. High-resolution profiling of histone methylations in the human genome. Cell. 2007;129(4):823–37. PubMed PMID: 17512414. eng.

    Article  PubMed  CAS  Google Scholar 

  10. Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, et al. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol. 2012;13(9):R48. PubMed PMID: 22950945. Pubmed Central PMCID: 3491392.

    Article  PubMed  CAS  Google Scholar 

  11. Loenarz C, Coleman ML, Boleininger A, Schierwater B, Holland PW, Ratcliffe PJ, et al. The hypoxia-inducible transcription factor pathway regulates oxygen sensing in the simplest animal, Trichoplax adhaerens. EMBO Rep. 2011;12(1):63–70. PubMed PMID: 21109780. Pubmed Central PMCID: 3024122. Epub 2010/11/27. eng.

    Article  PubMed  CAS  Google Scholar 

  12. Kaelin Jr WG, Ratcliffe PJ. Oxygen sensing by metazoans: the central role of the HIF hydroxylase pathway. Mol Cell. 2008;30(4):393–402. PubMed PMID: 18498744. Epub 2008/05/24. eng.

    Article  PubMed  CAS  Google Scholar 

  13. Wang GL, Jiang BH, Rue EA, Semenza GL. Hypoxia-inducible factor 1 is a basic-helix-loop-helix-PAS heterodimer regulated by cellular O2 tension. Proc Natl Acad Sci USA. 1995;92(12):5510–4. PubMed PMID: 7539918.

    Article  PubMed  CAS  Google Scholar 

  14. Gu YZ, Moran SM, Hogenesch JB, Wartman L, Bradfield CA. Molecular characterization and chromosomal localization of a third alpha-class hypoxia inducible factor subunit, HIF3alpha. Gene Expr. 1998;7(3):205–13. PubMed PMID: 9840812.

    PubMed  CAS  Google Scholar 

  15. Tian H, McKnight SL, Russell DW. Endothelial PAS domain protein 1 (EPAS1), a transcription factor selectively expressed in endothelial cells. Genes Dev. 1997;11(1):72–82. PubMed PMID: 9000051.

    Article  PubMed  CAS  Google Scholar 

  16. Schofield CJ, Ratcliffe PJ. Oxygen sensing by HIF hydroxylases. Nat Rev Mol Cell Biol. 2004;5(5):343–54. PubMed PMID: 15122348.

    Article  PubMed  CAS  Google Scholar 

  17. Lando D, Gorman JJ, Whitelaw ML, Peet DJ. Oxygen-dependent regulation of hypoxia-inducible factors by prolyl and asparaginyl hydroxylation. Eur J Biochem/FEBS. 2003;270(5):781–90. PubMed PMID: 12603311.

    Article  CAS  Google Scholar 

  18. PubMed PMID: 15063685. Epub 2004/04/06. eng

    Google Scholar 

  19. Talks KL, Turley H, Gatter KC, Maxwell PH, Pugh CW, Ratcliffe PJ, et al. The expression and distribution of the hypoxia-inducible factors HIF-1alpha and HIF-2alpha in normal human tissues, cancers, and tumor-associated macrophages. Am J Pathol. 2000;157(2):411–21. PubMed PMID: 10934146.

    Article  PubMed  CAS  Google Scholar 

  20. Zhong H, De Marzo AM, Laughner E, Lim M, Hilton DA, Zagzag D, et al. Overexpression of hypoxia-inducible factor 1alpha in common human cancers and their metastases. Cancer Res. 1999;59(22):5830–5. PubMed PMID: 10582706.

    PubMed  CAS  Google Scholar 

  21. Semenza GL. Defining the role of hypoxia-inducible factor 1 in cancer biology and therapeutics. Oncogene. 2010;29:625–34. PubMed PMID: 19946328. Epub 2009/12/01. Eng.

    Article  PubMed  CAS  Google Scholar 

  22. Laughner E, Taghavi P, Chiles K, Mahon PC, Semenza GL. HER2 (neu) signaling increases the rate of hypoxia-inducible factor 1alpha (HIF-1alpha) synthesis: novel mechanism for HIF-1-mediated vascular endothelial growth factor expression. Mol Cell Biol. 2001;21(12):3995–4004. PubMed PMID: 11359907.

    Article  PubMed  CAS  Google Scholar 

  23. Zhong H, Chiles K, Feldser D, Laughner E, Hanrahan C, Georgescu MM, et al. Modulation of hypoxia-inducible factor 1alpha expression by the epidermal growth factor/phosphatidylinositol 3-kinase/PTEN/AKT/FRAP pathway in human prostate cancer cells: implications for tumor angiogenesis and therapeutics. Cancer Res. 2000;60(6):1541–5. PubMed PMID: 10749120.

    PubMed  CAS  Google Scholar 

  24. Zundel W, Schindler C, Haas-Kogan D, Koong A, Kaper F, Chen E, et al. Loss of PTEN facilitates HIF-1-mediated gene expression. Genes Dev. 2000;14(4):391–6. PubMed PMID: 10691731Pubmed Central PMCID: 316386. Epub 2000/02/26. eng.

    PubMed  CAS  Google Scholar 

  25. Brugarolas JB, Vazquez F, Reddy A, Sellers WR, Kaelin WG. TSC2 regulates VEGF through mTOR-dependent and -independent pathways. Cancer Cell. 2003;4(2):147–58. PubMed PMID: 12957289.

    Article  PubMed  CAS  Google Scholar 

  26. Kondo S, Seo SY, Yoshizaki T, Wakisaka N, Furukawa M, Joab I, et al. EBV latent membrane protein 1 up-regulates hypoxia-inducible factor 1alpha through Siah1-mediated down-regulation of prolyl hydroxylases 1 and 3 in nasopharyngeal epithelial cells. Cancer Res. 2006;66(20):9870–7. PubMed PMID: 17047048. Epub 2006/10/19. eng.

    Article  PubMed  CAS  Google Scholar 

  27. Yoo YG, Cho S, Park S, Lee MO. The carboxy-terminus of the hepatitis B virus X protein is necessary and sufficient for the activation of hypoxia-inducible factor-1alpha. FEBS Lett. 2004;577(1–2):121–6. PubMed PMID: 15527772. Epub 2004/11/06. eng.

    Article  PubMed  CAS  Google Scholar 

  28. Tomita M, Semenza GL, Michiels C, Matsuda T, Uchihara JN, Okudaira T, et al. Activation of hypoxia-inducible factor 1 in human T-cell leukaemia virus type 1-infected cell lines and primary adult T-cell leukaemia cells. Biochem J. 2007;406(2):317–23. PubMed PMID: 17576198. Pubmed Central PMCID: 1948965. Epub 2007/06/20. eng.

    Article  PubMed  CAS  Google Scholar 

  29. Sodhi A, Montaner S, Patel V, Zohar M, Bais C, Mesri EA, et al. The Kaposi’s sarcoma-associated herpes virus G protein-coupled receptor up-regulates vascular endothelial growth factor expression and secretion through mitogen-activated protein kinase and p38 pathways acting on hypoxia-inducible factor 1alpha. Cancer Res. 2000;60(17):4873–80. PubMed PMID: 10987301. Epub 2000/09/15. eng.

    PubMed  CAS  Google Scholar 

  30. Shin YC, Joo CH, Gack MU, Lee HR, Jung JU. Kaposi’s sarcoma-associated herpesvirus viral IFN regulatory factor 3 stabilizes hypoxia-inducible factor-1 alpha to induce vascular endothelial growth factor expression. Cancer Res. 2008;68(6):1751–9. PubMed PMID: 18339855. Epub 2008/03/15. eng.

    Article  PubMed  CAS  Google Scholar 

  31. Nakamura M, Bodily JM, Beglin M, Kyo S, Inoue M, Laimins LA. Hypoxia-specific stabilization of HIF-1alpha by human papillomaviruses. Virology. 2009;387(2):442–8. PubMed PMID: 19321184. Pubmed Central PMCID: 2674135. Epub 2009/03/27. eng.

    Article  PubMed  CAS  Google Scholar 

  32. Selak MA, Armour SM, MacKenzie ED, Boulahbel H, Watson DG, Mansfield KD, et al. Succinate links TCA cycle dysfunction to oncogenesis by inhibiting HIF-alpha prolyl hydroxylase. Cancer Cell. 2005;7(1):77–85. PubMed PMID: 15652751.

    Article  PubMed  CAS  Google Scholar 

  33. Isaacs JS, Jung YJ, Mole DR, Lee S, Torres-Cabala C, Chung Y-L, et al. HIF overexpression correlates with biallelic loss of fumarate hydratase in renal cancer: Novel role of fumarate in regulation of HIF stability. Cancer Cell. 2005;8(2):143–53.

    Article  PubMed  CAS  Google Scholar 

  34. Maxwell PH, Wiesener MS, Chang GW, Clifford SC, Vaux EC, Cockman ME, et al. The tumour suppressor protein VHL targets hypoxia-inducible factors for oxygen-dependent proteolysis. Nature. 1999;399(6733):271–5. PubMed PMID: 10353251.

    Article  PubMed  CAS  Google Scholar 

  35. Ravi R, Mookerjee B, Bhujwalla ZM, Sutter CH, Artemov D, Zeng Q, et al. Regulation of tumor angiogenesis by p53-induced degradation of hypoxia-inducible factor 1alpha. Genes Dev. 2000;14(1):34–44. PubMed PMID: 10640274.

    PubMed  CAS  Google Scholar 

  36. Shackelford DB, Vasquez DS, Corbeil J, Wu S, Leblanc M, Wu CL, et al. mTOR and HIF-1alpha-mediated tumor metabolism in an LKB1 mouse model of Peutz-Jeghers syndrome. Proc Natl Acad Sci USA. 2009;106(27):11137–42. PubMed PMID: 19541609. Pubmed Central PMCID: 2708689. Epub 2009/06/23. eng.

    Article  PubMed  CAS  Google Scholar 

  37. Zhao S, Lin Y, Xu W, Jiang W, Zha Z, Wang P, et al. Glioma-derived mutations in IDH1 dominantly inhibit IDH1 catalytic activity and induce HIF-1alpha. Science. 2009;324(5924):261–5. Med PMID: 19359588. Pubmed Central PMCID: 3251015. Epub 2009/04/11. eng.

    Article  PubMed  CAS  Google Scholar 

  38. PubMed PMID: 20061373. Pubmed Central PMCID: 2853119. Epub 2010/01/12. eng

    Google Scholar 

  39. Semenza GL. Hypoxia-inducible factors: mediators of cancer progression and targets for cancer therapy. Trends Pharmacol Sci. 2012;33(4):207–14. PubMed PMID: 22398146. Epub 2012/03/09. Eng.

    Article  PubMed  CAS  Google Scholar 

  40. Wenger RH, Stiehl DP, Camenisch G. Integration of oxygen signaling at the consensus HRE. Sci STKE. 2005;2005(306):re12. PubMed PMID: 16234508. eng.

    PubMed  Google Scholar 

  41. Elvidge GP, Glenny L, Appelhoff RJ, Ratcliffe PJ, Ragoussis J, Gleadle JM. Concordant regulation of gene expression by hypoxia and 2-oxoglutarate-dependent dioxygenase inhibition: the role of HIF-1alpha, HIF-2alpha, and other pathways. J Biol Chem. 2006;281(22):15215–26. PubMed PMID: 16565084.

    Article  PubMed  CAS  Google Scholar 

  42. Manalo DJ, Rowan A, Lavoie T, Natarajan L, Kelly BD, Ye SQ, et al. Transcriptional regulation of vascular endothelial cell responses to hypoxia by HIF-1. Blood. 2005;105(2):659–69. PubMed PMID: 15374877. eng.

    Article  PubMed  CAS  Google Scholar 

  43. Hu CJ, Iyer S, Sataur A, Covello KL, Chodosh LA, Simon MC. Differential regulation of the transcriptional activities of hypoxia-inducible factor 1 alpha (HIF-1alpha) and HIF-2alpha in stem cells. Mol Cell Biol. 2006;26(9):3514–26. PubMed PMID: 16611993. eng.

    Article  PubMed  CAS  Google Scholar 

  44. Hu CJ, Wang LY, Chodosh LA, Keith B, Simon MC. Differential roles of hypoxia-inducible factor 1alpha (HIF-1alpha) and HIF-2alpha in hypoxic gene regulation. Mol Cell Biol. 2003;23(24):9361–74. PubMed PMID: 14645546. eng.

    Article  PubMed  CAS  Google Scholar 

  45. Greijer AE, van der Groep P, Kemming D, Shvarts A, Semenza GL, Meijer GA, et al. Up-regulation of gene expression by hypoxia is mediated predominantly by hypoxia-inducible factor 1 (HIF-1). J Pathol. 2005;206(3):291–304. PubMed PMID: 15906272. eng.

    Article  PubMed  CAS  Google Scholar 

  46. Imamura T, Kikuchi H, Herraiz MT, Park DY, Mizukami Y, Mino-Kenduson M, et al. HIF-1alpha and HIF-2alpha have divergent roles in colon cancer. Int J Cancer. 2009;124(4):763–71. PubMed PMID: 19030186. Epub 2008/11/26. eng.

    Article  PubMed  CAS  Google Scholar 

  47. Wang V, Davis DA, Haque M, Huang LE, Yarchoan R. Differential gene up-regulation by hypoxia-inducible factor-1alpha and hypoxia-inducible factor-2alpha in HEK293T cells. Cancer Res. 2005;65(8):3299–306. PubMed PMID: 15833863. eng.

    PubMed  CAS  Google Scholar 

  48. Sung FL, Hui EP, Tao Q, Li H, Tsui NB, Dennis Lo YM, et al. Genome-wide expression analysis using microarray identified complex signaling pathways modulated by hypoxia in nasopharyngeal carcinoma. Cancer Lett. 2007;253(1):74–88. PubMed PMID: 17320280. Epub 2007/02/27. eng.

    Article  PubMed  CAS  Google Scholar 

  49. discussion 7. PubMed PMID: 17486380. eng

    Google Scholar 

  50. Choi SM, Oh H, Park H. Microarray analyses of hypoxia-regulated genes in an aryl hydrocarbon receptor nuclear translocator (Arnt)-dependent manner. FEBS J. 2008;275(22):5618–34. PubMed PMID: 18959748. Epub 2008/10/31. eng.

    Article  PubMed  CAS  Google Scholar 

  51. Oikawa M, Abe M, Kurosawa H, Hida W, Shirato K, Sato Y. Hypoxia induces transcription factor ETS-1 via the activity of hypoxia-inducible factor-1. Biochem Biophys Res Commun. 2001;289(1):39–43. PubMed PMID: 11708773. Epub 2001/11/16. eng.

    Article  PubMed  CAS  Google Scholar 

  52. Laderoute KR, Calaoagan JM, Gustafson-Brown C, Knapp AM, Li GC, Mendonca HL, et al. The response of c-jun/AP-1 to chronic hypoxia is hypoxia-inducible factor 1 alpha dependent. Mol Cell Biol. 2002;22(8):2515–23. PubMed PMID: 11909946. eng.

    Article  PubMed  CAS  Google Scholar 

  53. PubMed PMID: 12354771. Epub 2002/10/02. eng

    Google Scholar 

  54. Koshiji M, Kageyama Y, Pete EA, Horikawa I, Barrett JC, Huang LE. HIF-1alpha induces cell cycle arrest by functionally counteracting Myc. EMBO J. 2004;23(9):1949–56. PubMed PMID: 15071503. eng.

    Article  PubMed  CAS  Google Scholar 

  55. Gordan JD, Lal P, Dondeti VR, Letrero R, Parekh KN, Oquendo CE, et al. HIF-alpha effects on c-Myc distinguish two subtypes of sporadic VHL-deficient clear cell renal carcinoma. Cancer Cell. 2008;14(6):435–46. PubMed PMID: 19061835. Epub 2008/12/09. eng.

    Article  PubMed  CAS  Google Scholar 

  56. Gustafsson MV, Zheng X, Pereira T, Gradin K, Jin S, Lundkvist J, et al. Hypoxia requires notch signaling to maintain the undifferentiated cell state. Dev Cell. 2005;9(5):617–28. PubMed PMID: 16256737. Epub 2005/11/01. eng.

    Article  PubMed  CAS  Google Scholar 

  57. Kaidi A, Williams AC, Paraskeva C. Interaction between beta-catenin and HIF-1 promotes cellular adaptation to hypoxia. Nat Cell Biol. 2007;9(2):210–7. PubMed PMID: 17220880. Epub 2007/01/16. eng.

    Article  PubMed  CAS  Google Scholar 

  58. Semenza GL, Traystman MD, Gearhart JD, Antonarakis SE. Polycythemia in transgenic mice expressing the human erythropoietin gene. Proc Natl Acad Sci USA. 1989;86(7):2301–5. PubMed PMID: 2928334. eng.

    Article  PubMed  CAS  Google Scholar 

  59. Semenza GL, Dureza RC, Traystman MD, Gearhart JD, Antonarakis SE. Human erythropoietin gene expression in transgenic mice: multiple transcription initiation sites and cis-acting regulatory elements. Mol Cell Biol. 1990;10(3):930–8. PubMed PMID: 2304468. eng.

    PubMed  CAS  Google Scholar 

  60. Levy NS, Goldberg MA, Levy AP. Sequencing of the human vascular endothelial growth factor (VEGF) 3' untranslated region (UTR): conservation of five hypoxia-inducible RNA-protein binding sites. Biochim Biophys Acta. 1997;1352(2):167–73. PubMed PMID: 9199248.

    Article  PubMed  CAS  Google Scholar 

  61. Pugh CW, Tan CC, Jones RW, Ratcliffe PJ. Functional analysis of an oxygen-regulated transcriptional enhancer lying 3' to the mouse erythropoietin gene. Proc Natl Acad Sci USA. 1991;88(23):10553–7. PubMed PMID: 1961720. eng.

    Article  PubMed  CAS  Google Scholar 

  62. Pugh CW, Ebert BL, Ebrahim O, Maxwell PH, Ratcliffe PJ. Analysis of cis-acting sequences required for operation of the erythropoietin 3' enhancer in different cell lines. Ann N Y Acad Sci. 1994;718:31–9. discussion 9-40. PubMed PMID: 8185238. eng.

    Article  PubMed  CAS  Google Scholar 

  63. Semenza GL, Nejfelt MK, Chi SM, Antonarakis SE. Hypoxia-inducible nuclear factors bind to an enhancer element located 3' to the human erythropoietin gene. Proc Natl Acad Sci USA. 1991;88(13):5680–4. PubMed PMID: 2062846. eng.

    Article  PubMed  CAS  Google Scholar 

  64. Firth JD, Ebert BL, Ratcliffe PJ. Hypoxic regulation of lactate dehydrogenase A. Interaction between hypoxia-inducible factor 1 and cAMP response elements. J Biol Chem. 1995;270(36):21021–7. PubMed PMID: 7673128. Epub 1995/09/08. eng.

    Article  PubMed  CAS  Google Scholar 

  65. Dimova EY, Moller U, Herzig S, Fink T, Zachar V, Ebbesen P, et al. Transcriptional regulation of plasminogen activator inhibitor-1 expression by insulin-like growth factor-1 via MAP kinases and hypoxia-inducible factor-1 in HepG2 cells. Thromb Haemost. 2005;93(6):1176–84. PubMed PMID: 15968405.

    PubMed  CAS  Google Scholar 

  66. Schodel J, Oikonomopoulos S, Ragoussis J, Pugh CW, Ratcliffe PJ, Mole DR. High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq. Blood. 2011;117(23):e207–17. PubMed PMID: 21447827. Epub 2011/03/31. eng.

    Article  PubMed  CAS  Google Scholar 

  67. O'Neill LP, Turner BM. Immunoprecipitation of chromatin. Methods Enzymol. 1996;274:189–97. PubMed PMID: 8902805. Epub 1996/01/01. eng.

    Article  PubMed  Google Scholar 

  68. Collas P. The current state of chromatin immunoprecipitation. Mol Biotechnol. 2010;45(1):87–100. PubMed PMID: 20077036. Epub 2010/01/16. eng.

    Article  PubMed  CAS  Google Scholar 

  69. Lau KW, Tian YM, Raval RR, Ratcliffe PJ, Pugh CW. Target gene selectivity of hypoxia-inducible factor-alpha in renal cancer cells is conveyed by post-DNA-binding mechanisms. Br J Cancer. 2007;96(8):1284–92. PubMed PMID: 17387348. eng.

    Article  PubMed  CAS  Google Scholar 

  70. Mole DR, Blancher C, Copley RR, Pollard PJ, Gleadle JM, Ragoussis J, et al. Genome-wide association of hypoxia-inducible factor (HIF)-1{alpha} and HIF-2{alpha} DNA binding with expression profiling of hypoxia-inducible transcripts. J Biol Chem. 2009;284(25):16767–75. PubMed PMID: 19386601. Pubmed Central PMCID: 2719312. Epub 2009/04/24. eng.

    Article  PubMed  CAS  Google Scholar 

  71. Xia X, Kung AL. Preferential binding of HIF-1 to transcriptionally active loci determines cell-type specific response to hypoxia. Genome Biol. 2009;10(10):R113. PubMed PMID: 19828020. Epub 2009/10/16. Eng.

    Article  PubMed  Google Scholar 

  72. Xia X, Lemieux ME, Li W, Carroll JS, Brown M, Liu XS, et al. Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis. Proc Natl Acad Sci USA. 2009;106(11):4260–5. PubMed PMID: 19255431. Eng.

    Article  PubMed  CAS  Google Scholar 

  73. Krieg AJ, Rankin EB, Chan D, Razorenova O, Fernandez S, Giaccia AJ. Regulation of the histone demethylase JMJD1A by hypoxia-inducible factor 1 alpha enhances hypoxic gene expression and tumor growth. Mol Cell Biol. 2010;30(1):344–53. PubMed PMID: 19858293. Pubmed Central PMCID: 2798291. Epub 2009/10/28. eng.

    Article  PubMed  CAS  Google Scholar 

  74. Tanimoto K, Tsuchihara K, Kanai A, Arauchi T, Esumi H, Suzuki Y, et al. Genome-wide identification and annotation of HIF-1alpha binding sites in two cell lines using massively parallel sequencing. Hugo J. 2010;4(1–4):35–48. PubMed PMID: 22132063. Pubmed Central PMCID: 3051044. Epub 2011/12/02. eng.

    Article  PubMed  Google Scholar 

  75. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. PubMed PMID: 18798982. Pubmed Central PMCID: 2592715. Epub 2008/09/19. eng.

    Article  PubMed  Google Scholar 

  76. Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol. 2008;26(11):1293–300. PubMed PMID: 18978777. eng.

    Article  PubMed  CAS  Google Scholar 

  77. Koshiji M, To KK, Hammer S, Kumamoto K, Harris AL, Modrich P, et al. HIF-1alpha induces genetic instability by transcriptionally downregulating MutSalpha expression. Mol Cell. 2005;17(6):793–803. PubMed PMID: 15780936. Epub 2005/03/23. eng.

    Article  PubMed  CAS  Google Scholar 

  78. Hankinson O. The aryl hydrocarbon receptor complex. Annu Rev Pharmacol Toxicol. 1995;35:307–40. PubMed PMID: 7598497.

    Article  PubMed  CAS  Google Scholar 

  79. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005;102(43):15545–50. PubMed PMID: 16199517. Pubmed Central PMCID: 1239896. Epub 2005/10/04. eng.

    Article  PubMed  CAS  Google Scholar 

  80. Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34(3):267–73. PubMed PMID: 12808457. Epub 2003/06/17. eng.

    Article  PubMed  CAS  Google Scholar 

  81. Maienschein-Cline M, Zhou J, White KP, Sciammas R, Dinner AR. Discovering transcription factor regulatory targets using gene expression and binding data. Bioinformatics. 2012;28(2):206–13. PubMed PMID: 22084256. Pubmed Central PMCID: 3259433.

    Article  PubMed  CAS  Google Scholar 

  82. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1):57–63. PubMed PMID: 19015660. Pubmed Central PMCID: 2949280.

    Article  PubMed  CAS  Google Scholar 

  83. Ozsolak F, Platt AR, Jones DR, Reifenberger JG, Sass LE, McInerney P, et al. Direct RNA sequencing. Nature. 2009;461(7265):814–8. PubMed PMID: 19776739.

    Article  PubMed  CAS  Google Scholar 

  84. Gumz ML, Zou H, Kreinest PA, Childs AC, Belmonte LS, LeGrand SN, et al. Secreted frizzled-related protein 1 loss contributes to tumor phenotype of clear cell renal cell carcinoma. Clin Cancer Res. 2007;13(16):4740–9. PubMed PMID: 17699851. Epub 2007/08/19. eng.

    Article  PubMed  CAS  Google Scholar 

  85. Cao Q, Qin C, Meng X, Ju X, Ding Q, Wang M, et al. Genetic polymorphisms in APE1 are associated with renal cell carcinoma risk in a Chinese population. Mol Carcinog. 2011;50(11):863–70. PubMed PMID: 21538578. Epub 2011/05/04. eng.

    Article  PubMed  CAS  Google Scholar 

  86. COSMIC. Catalogue Of Somatic Mutations In Cancer 2012. Available from: http://www.sanger.ac.uk/genetics/CGP/cosmic/.

  87. van Haaften G, Dalgliesh GL, Davies H, Chen L, Bignell G, Greenman C, et al. Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer. Nat Genet. 2009;41(5):521–3. PubMed PMID: 19330029. Epub 2009/03/31. eng.

    Article  PubMed  Google Scholar 

  88. Dalgliesh GL, Furge K, Greenman C, Chen L, Bignell G, Butler A, et al. Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature. 2010;463(7279):360–3. PubMed PMID: 20054297. Pubmed Central PMCID: 2820242. Epub 2010/01/08. eng.

    Article  PubMed  CAS  Google Scholar 

  89. Varela I, Tarpey P, Raine K, Huang D, Ong CK, Stephens P, et al. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature. 2011;469(7331):539–42. PubMed PMID: 21248752. Pubmed Central PMCID: 3030920. Epub 2011/01/21. eng.

    Article  PubMed  CAS  Google Scholar 

  90. Duns G, Hofstra RM, Sietzema JG, Hollema H, van Duivenbode I, Kuik A, et al. Targeted exome sequencing in clear cell renal cell carcinoma tumors suggests aberrant chromatin regulation as a crucial step in ccRCC development. Hum Mutat. 2012;33(7):1059–62. PubMed PMID: 22461374. Epub 2012/03/31. eng.

    Article  PubMed  CAS  Google Scholar 

  91. Duns G, van den Berg E, van Duivenbode I, Osinga J, Hollema H, Hofstra RM, et al. Histone methyltransferase gene SETD2 is a novel tumor suppressor gene in clear cell renal cell carcinoma. Cancer Res. 2010;70(11):4287–91. PubMed PMID: 20501857. Epub 2010/05/27. eng.

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Nephrology and Hypertension, Friedrich-Alexander-University Erlangen-Nuremberg, Ulmenweg 18, 91054, Erlangen, Germany

    Johannes Schödel

  2. Henry Wellcome Building for Molecular Physiology, University of Oxford, Roosevelt Drive, OX3 7BN, Oxford, UK

    David R. Mole

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  1. Johannes Schödel
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  2. David R. Mole
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Correspondence to David R. Mole .

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Editors and Affiliations

  1. Dept. Pathology & Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada

    Wei Wu

  2. The Wellcome Trust Centre for Human Gene, University of Oxford, Oxford, United Kingdom

    Hani Choudhry

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Schödel, J., Mole, D.R. (2013). Mapping the HIF Transcription Factor in Cancer by ChIP-Seq Technology. In: Wu, W., Choudhry, H. (eds) Next Generation Sequencing in Cancer Research. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7645-0_5

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