Transcriptional and Epigenetic Regulation of KIAA1199 Gene Expression in Human Breast Cancer

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Kuscu, Cem ^a   Evensen, Nikki ^a   Kim, Deborah ^a   Hu, You Jun ^a   Zucker, Stanley ^a,b   Cao, Jian ^a  

^a STONY BROOK UNIVERSITY   (United States)

^b Veterans Affair Medical Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; TRANSCRIPTION FACTOR AP 1; TRANSCRIPTION FACTOR TWIST; TRANSCRIPTION FACTOR TWIST 1; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; BIOINFORMATICS; BREAST CANCER; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; CPG ISLAND; DNA FLANKING REGION; DNA METHYLATION; DNA SEQUENCE; EPIGENETICS; GEL MOBILITY SHIFT ASSAY; GENE EXPRESSION; GENE EXPRESSION REGULATION; HUMAN; HUMAN CELL; HUMAN TISSUE; KIAA1199 GENE; PROMOTER REGION; REGULATORY MECHANISM; REGULATORY SEQUENCE; SITE DIRECTED MUTAGENESIS; TATA BOX; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION;

BASE SEQUENCE; BREAST NEOPLASMS; DNA; EPIGENESIS, GENETIC; FEMALE; GENE SILENCING; HUMANS; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS, GENETIC; PROTEINS; REAL-TIME POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY, NUCLEIC ACID; TRANSCRIPTION, GENETIC;

EID: 84866075905     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0044661     Document Type: Article

References (47)

1. Jemal A, Siegel R, Xu J, Ward E, (2010) Cancer statistics, 2010. CA Cancer J Clin 60: 277-300.
2. Nakayama M, Kikuno R, Ohara O, (2002) Protein-protein interactions between large proteins: two-hybrid screening using a functionally classified library composed of long cDNAs. Genome Res 12: 1773-1784.
3. Abe S, Usami S, Nakamura Y, (2003) Mutations in the gene encoding KIAA1199 protein, an inner-ear protein expressed in Deiters' cells and the fibrocytes, as the cause of nonsyndromic hearing loss. J Hum Genet 48: 564-570.
4. Matsuzaki S, Tanaka F, Mimori K, Tahara K, Inoue H, et al. (2009) Clinicopathologic significance of KIAA1199 overexpression in human gastric cancer. Ann Surg Oncol 16: 2042-2051.
5. Sabates-Bellver J, Van der Flier LG, de Palo M, Cattaneo E, Maake C, et al. (2007) Transcriptome profile of human colorectal adenomas. Mol Cancer Res 5: 1263-1275.
6. Birkenkamp-Demtroder K, Maghnouj A, Mansilla F, Thorsen K, Andersen CL, et al. (2011) Repression of KIAA1199 attenuates Wnt-signalling and decreases the proliferation of colon cancer cells. Br J Cancer 105: 552-561.
7. Michishita E, Garces G, Barrett JC, Horikawa I, (2006) Upregulation of the KIAA1199 gene is associated with cellular mortality. Cancer Lett 239: 71-77.
8. He QY, Liu XH, Li Q, Studholme DJ, Li XW, et al. (2006) G8: a novel domain associated with polycystic kidney disease and non-syndromic hearing loss. Bioinformatics 22: 2189-2191.
9. Guo J, Cheng H, Zhao S, Yu L, (2006) GG: a domain involved in phage LTF apparatus and implicated in human MEB and non-syndromic hearing loss diseases. FEBS Lett 580: 581-584.
10. Esteller M, (2002) CpG island hypermethylation and tumor suppressor genes: a booming present, a brighter future. Oncogene 21: 5427-5440.
11. Saxonov S, Berg P, Brutlag DL, (2006) A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A 103: 1412-1417.
12. Kawaji H, Kasukawa T, Fukuda S, Katayama S, Kai C, et al. (2006) CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. Nucleic Acids Res 34: D632-636.
13. Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, et al. (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A 100: 15776-15781.
14. Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, et al. (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38: 626-635.
15. Huber MA, Azoitei N, Baumann B, Grunert S, Sommer A, et al. (2004) NF-kappaB is essential for epithelial-mesenchymal transition and metastasis in a model of breast cancer progression. J Clin Invest 114: 569-581.
16. Yang MH, Hsu DS, Wang HW, Wang HJ, Lan HY, et al. (2010) Bmi1 is essential in Twist1-induced epithelial-mesenchymal transition. Nat Cell Biol 12: 982-992.
17. Gardiner-Garden M, Frommer M, (1987) CpG islands in vertebrate genomes. J Mol Biol 196: 261-282.
18. Broadbent S, van der Woude M, Aziz N, (2010) Accurate and simple sizing of primer extension products using a non-radioactive approach facilitates identification of transcription initiation sites. J Microbiol Methods 81: 256-258.
19. Suzuki S, Takeda T, Liu RT, Hashizume K, DeGroot LJ, (1995) Importance of the most proximal GC box for activity of the promoter of human thyroid hormone receptor beta 1. Mol Endocrinol 9: 1288-1296.
20. Miyajima A, Furihata T, Chiba K, (2009) Functional analysis of GC Box and its CpG methylation in the regulation of CYP1A2 gene expression. Drug Metab Pharmacokinet 24: 269-276.
21. Muckenfuss H, Kaiser JK, Krebil E, Battenberg M, Schwer C, et al. (2007) Sp1 and Sp3 regulate basal transcription of the human APOBEC3G gene. Nucleic Acids Res 35: 3784-3796.
22. Sakai DD, Helms S, Carlstedt-Duke J, Gustafsson JA, Rottman FM, et al. (1988) Hormone-mediated repression: a negative glucocorticoid response element from the bovine prolactin gene. Genes Dev 2: 1144-1154.
23. Hasegawa H, Senga T, Ito S, Iwamoto T, Hamaguchi M, (2009) A role for AP-1 in matrix metalloproteinase production and invadopodia formation of v-Crk-transformed cells. Exp Cell Res 315: 1384-1392.
24. Kornberg RD, (2007) The molecular basis of eukaryotic transcription. Proc Natl Acad Sci U S A 104: 12955-12961.
25. Ponticos M, Harvey C, Ikeda T, Abraham D, Bou-Gharios G, (2009) JunB mediates enhancer/promoter activity of COL1A2 following TGF-beta induction. Nucleic Acids Res 37: 5378-5389.
26. Vaiopoulos AG, Papachroni KK, Papavassiliou AG, (2010) Colon carcinogenesis: Learning from NF-kappaB and AP-1. Int J Biochem Cell Biol 42: 1061-1065.
27. Sandoval J, Heyn HA, Moran S, Serra-Musach J, Pujana MA, et al. (2011) Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics 6: 692-702.
28. Fatemi M, Pao MM, Jeong S, Gal-Yam EN, Egger G, et al. (2005) Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level. Nucleic Acids Res 33: e176.
29. Ko YG, Park HJ, Yun J, Koh PO, Min W, et al. (2010) DNA methylation contributes to the tissue-specific expression of the rPL-Iv gene. Placenta 31: 969-975.
30. Watt F, Molloy PL, (1988) Cytosine methylation prevents binding to DNA of a HeLa cell transcription factor required for optimal expression of the adenovirus major late promoter. Genes Dev 2: 1136-1143.
31. Rupon JW, Wang SZ, Gaensler K, Lloyd J, Ginder GD, (2006) Methyl binding domain protein 2 mediates gamma-globin gene silencing in adult human betaYAC transgenic mice. Proc Natl Acad Sci U S A 103: 6617-6622.
32. Hanada M, Delia D, Aiello A, Stadtmauer E, Reed JC, (1993) bcl-2 gene hypomethylation and high-level expression in B-cell chronic lymphocytic leukemia. Blood 82: 1820-1828.
33. Watt PM, Kumar R, Kees UR, (2000) Promoter demethylation accompanies reactivation of the HOX11 proto-oncogene in leukemia. Genes Chromosomes Cancer 29: 371-377.
34. Zhou H, Chen WD, Qin X, Lee K, Liu L, et al. (2001) MMTV promoter hypomethylation is linked to spontaneous and MNU associated c-neu expression and mammary carcinogenesis in MMTV c-neu transgenic mice. Oncogene 20: 6009-6017.
35. Honda T, Tamura G, Waki T, Kawata S, Terashima M, et al. (2004) Demethylation of MAGE promoters during gastric cancer progression. Br J Cancer 90: 838-843.
36. Nishigaki M, Aoyagi K, Danjoh I, Fukaya M, Yanagihara K, et al. (2005) Discovery of aberrant expression of R-RAS by cancer-linked DNA hypomethylation in gastric cancer using microarrays. Cancer Res 65: 2115-2124.
37. Tabu K, Sasai K, Kimura T, Wang L, Aoyanagi E, et al. (2008) Promoter hypomethylation regulates CD133 expression in human gliomas. Cell Res 18: 1037-1046.
38. Jun HJ, Woolfenden S, Coven S, Lane K, Bronson R, et al. (2009) Epigenetic regulation of c-ROS receptor tyrosine kinase expression in malignant gliomas. Cancer Res 69: 2180-2184.
39. Smith IM, Glazer CA, Mithani SK, Ochs MF, Sun W, et al. (2009) Coordinated activation of candidate proto-oncogenes and cancer testes antigens via promoter demethylation in head and neck cancer and lung cancer. PLoS One 4: e4961.
40. Harbeck N, Nimmrich I, Hartmann A, Ross JS, Cufer T, et al. (2008) Multicenter study using paraffin-embedded tumor tissue testing PITX2 DNA methylation as a marker for outcome prediction in tamoxifen-treated, node-negative breast cancer patients. J Clin Oncol 26: 5036-5042.
41. Radvanyi L, Singh-Sandhu D, Gallichan S, Lovitt C, Pedyczak A, et al. (2005) The gene associated with trichorhinophalangeal syndrome in humans is overexpressed in breast cancer. Proc Natl Acad Sci U S A 102: 11005-11010.
42. Skrzypczak M, Goryca K, Rubel T, Paziewska A, Mikula M, et al. (2010) Modeling oncogenic signaling in colon tumors by multidirectional analyses of microarray data directed for maximization of analytical reliability. PLoS One 5.
43. D'Errico M, de Rinaldis E, Blasi MF, Viti V, Falchetti M, et al. (2009) Genome-wide expression profile of sporadic gastric cancers with microsatellite instability. Eur J Cancer 45: 461-469.
44. Hou J, Aerts J, den Hamer B, van Ijcken W, den Bakker M, et al. (2010) Gene expression-based classification of non-small cell lung carcinomas and survival prediction. PLoS One 5: e10312.
45. Ginos MA, Page GP, Michalowicz BS, Patel KJ, Volker SE, et al. (2004) Identification of a gene expression signature associated with recurrent disease in squamous cell carcinoma of the head and neck. Cancer Res 64: 55-63.
46. Adib TR, Henderson S, Perrett C, Hewitt D, Bourmpoulia D, et al. (2004) Predicting biomarkers for ovarian cancer using gene-expression microarrays. Br J Cancer 90: 686-692.
47. Grutzmann R, Pilarsky C, Ammerpohl O, Luttges J, Bohme A, et al. (2004) Gene expression profiling of microdissected pancreatic ductal carcinomas using high-density DNA microarrays. Neoplasia 6: 611-622.