Global profiling of histone and DNA methylation reveals epigenetic-based regulation of gene expression during epithelial to mesenchymal transition in prostate cells

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Ke, Xi Song ^a,e   Qu, Yi ^a   Cheng, Yang ^b   Li, Wen Cheng ^a,c   Rotter, Varda ^d   Øyan, Anne M ^a,e   Kalland, Karl Henning ^a,e  

^a UNIVERSITY OF BERGEN   (Norway)

^b Huazhong University of Science and Technology ^*  (Germany)

^c HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^d WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^e HAUKELAND UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; FIBROBLAST GROWTH FACTOR RECEPTOR; HISTONE; CADHERIN; LYSINE;

ARTICLE; CELL JUNCTION; CELL LINE; CONTROLLED STUDY; DNA METHYLATION; DNA MODIFICATION; EPIGENETICS; EPITHELIAL MESENCHYMAL TRANSITION; EPITHELIUM CELL; GENE EXPRESSION REGULATION; GENE REPRESSION; GENE SILENCING; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; PROSTATE; PROTEIN METHYLATION; CELL TRANSFORMATION; GENE EXPRESSION PROFILING; GENETIC EPIGENESIS; GENETICS; HUMAN GENOME; MALE; METABOLISM; PATHOLOGY;

CADHERINS; CELL LINE; CELL TRANSFORMATION, NEOPLASTIC; DNA METHYLATION; EPIGENESIS, GENETIC; EPITHELIAL-MESENCHYMAL TRANSITION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE SILENCING; GENOME, HUMAN; HISTONES; HUMANS; LYSINE; MALE; PROSTATE; RECEPTORS, FIBROBLAST GROWTH FACTOR; TRANSCRIPTION, GENETIC;

EID: 78649328949     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-669     Document Type: Article

References (34)

1. Thiery JP. Epithelial-mesenchymal transitions in tumour progression. Nat Rev Cancer 2002, 2(6):442-454. 10.1038/nrc822, 12189386.
2. Thiery JP, Sleeman JP. Complex networks orchestrate epithelial-mesenchymal transitions. Nat Rev Mol Cell Biol 2006, 7(2):131-142. 10.1038/nrm1835, 16493418.
3. Yang J, Weinberg RA. Epithelial-mesenchymal transition: at the crossroads of development and tumor metastasis. Dev Cell 2008, 14(6):818-829. 10.1016/j.devcel.2008.05.009, 18539112.
4. Ke XS, Qu Y, Goldfinger N, Rostad K, Hovland R, Akslen LA, Rotter V, Oyan AM, Kalland KH. Epithelial to Mesenchymal Transition of a Primary Prostate Cell Line with Switches of Cell Adhesion Modules but without Malignant Transformation. PloS ONE 2008, 3(10):1-11.
5. Ke XS, Li WC, Hovland R, Qu Y, Liu RH, McCormack E, Thorsen F, Olsen JR, Molven A, Kogan-Sakin I, et al. Reprogramming of cell junction modules during stepwise epithelial to mesenchymal transition and accumulation of malignant features in vitro in a prostate cell model. Exp Cell Res 2011, 317:234-247.
6. Cedar H, Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet 2009, 10(5):295-304. 10.1038/nrg2540, 19308066.
7. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 2006, 125(2):315-326. 10.1016/j.cell.2006.02.041, 16630819.
8. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448(7153):553-560. 10.1038/nature06008, 2921165, 17603471.
9. Pan G, Tian S, Nie J, Yang C, Ruotti V, Wei H, Jonsdottir GA, Stewart R, Thomson JA. Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell 2007, 1(3):299-312. 10.1016/j.stem.2007.08.003, 18371364.
10. Zhao XD, Han X, Chew JL, Liu J, Chiu KP, Choo A, Orlov YL, Sung WK, Shahab A, Kuznetsov VA, et al. Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 2007, 1(3):286-298. 10.1016/j.stem.2007.08.004, 18371363.
11. Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, Cui K, Kanno Y, Roh TY, Watford WT, et al. Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Immunity 2009, 30(1):155-167. 10.1016/j.immuni.2008.12.009, 2722509, 19144320.
12. Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 2009, 4(1):80-93. 10.1016/j.stem.2008.11.011, 2785912, 19128795.
13. Ke XS, Qu Y, Rostad K, Li WC, Lin B, Halvorsen OJ, Haukaas SA, Jonassen I, Petersen K, Goldfinger N, et al. Genome-wide profiling of histone h3 lysine 4 and lysine 27 trimethylation reveals an epigenetic signature in prostate carcinogenesis. PLoS ONE 2009, 4(3):e4687. 10.1371/journal.pone.0004687, 2650415, 19262738.
14. Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schubeler D. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007, 39(4):457-466. 10.1038/ng1990, 17334365.
15. Gal-Yam EN, Egger G, Iniguez L, Holster H, Einarsson S, Zhang X, Lin JC, Liang G, Jones PA, Tanay A. Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line. Proc Natl Acad Sci USA 2008, 105(35):12979-12984. 10.1073/pnas.0806437105, 2529074, 18753622.
16. Komashko VM, Acevedo LG, Squazzo SL, Iyengar SS, Rabinovich A, O'Geen H, Green R, Farnham PJ. Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells. Genome Res 2008, 18(4):521-532. 10.1101/gr.074609.107, 2279240, 18347325.
17. Yoshiura K, Kanai Y, Ochiai A, Shimoyama Y, Sugimura T, Hirohashi S. Silencing of the E-cadherin invasion-suppressor gene by CpG methylation in human carcinomas. Proc Natl Acad Sci USA 1995, 92(16):7416-7419. 10.1073/pnas.92.16.7416, 41350, 7543680.
18. Yang X, Pursell B, Lu S, Chang TK, Mercurio AM. Regulation of beta 4-integrin expression by epigenetic modifications in the mammary gland and during the epithelial-to-mesenchymal transition. J Cell Sci 2009, 122(Pt 14):2473-2480. 10.1242/jcs.049148, 2704882, 19549682.
19. Jarrard DF, Paul R, van Bokhoven A, Nguyen SH, Bova GS, Wheelock MJ, Johnson KR, Schalken J, Bussemakers M, Isaacs WB. P-Cadherin is a basal cell-specific epithelial marker that is not expressed in prostate cancer. Clin Cancer Res 1997, 3(11):2121-2128.
20. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 2004, 101(16):6062-6067. 10.1073/pnas.0400782101, 395923, 15075390.
21. Eisenberg E, Levanon EY. Human housekeeping genes are compact. Trends Genet 2003, 19(7):362-365. 10.1016/S0168-9525(03)00140-9, 12850439.
22. She X, Rohl CA, Castle JC, Kulkarni AV, Johnson JM, Chen R. Definition, conservation and epigenetics of housekeeping and tissue-enriched genes. BMC Genomics 2009, 10:269. 10.1186/1471-2164-10-269, 2706266, 19534766.
23. Esteller M. Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 2007, 8(4):286-298. 10.1038/nrg2005, 17339880.
24. Richiardi L, Fiano V, Vizzini L, De Marco L, Delsedime L, Akre O, Tos AG, Merletti F. Promoter methylation in APC, RUNX3, and GSTP1 and mortality in prostate cancer patients. J Clin Oncol 2009, 27(19):3161-3168. 10.1200/JCO.2008.18.2485, 19470943.
25. Acevedo VD, Gangula RD, Freeman KW, Li R, Zhang Y, Wang F, Ayala GE, Peterson LE, Ittmann M, Spencer DM. Inducible FGFR-1 activation leads to irreversible prostate adenocarcinoma and an epithelial-to-mesenchymal transition. Cancer Cell 2007, 12(6):559-571. 10.1016/j.ccr.2007.11.004, 18068632.
26. Jang JH. Reciprocal relationship in gene expression between FGFR1 and FGFR3: implication for tumorigenesis. Oncogene 2005, 24(5):945-948. 10.1038/sj.onc.1208254, 15558020.
27. Warzecha CC, Sato TK, Nabet B, Hogenesch JB, Carstens RP. ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing. Mol Cell 2009, 33(5):591-601. 10.1016/j.molcel.2009.01.025, 2702247, 19285943.
28. Fouse SD, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, Fan G. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell 2008, 2(2):160-169. 10.1016/j.stem.2007.12.011, 18371437.
29. Li X, Wang X, He K, Ma Y, Su N, He H, Stolc V, Tongprasit W, Jin W, Jiang J, et al. High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell 2008, 20(2):259-276. 10.1105/tpc.107.056879, 2276441, 18263775.
30. Bloushtain-Qimron N, Yao J, Snyder EL, Shipitsin M, Campbell LL, Mani SA, Hu M, Chen H, Ustyansky V, Antosiewicz JE, et al. Cell type-specific DNA methylation patterns in the human breast. Proc Natl Acad Sci USA 2008, 105(37):14076-14081. 10.1073/pnas.0805206105, 2532972, 18780791.
31. Shann YJ, Cheng C, Chiao CH, Chen DT, Li PH, Hsu MT. Genome-wide mapping and characterization of hypomethylated sites in human tissues and breast cancer cell lines. Genome Res 2008, 18(5):791-801. 10.1101/gr.070961.107, 2336806, 18256232.
32. Keshet I, Schlesinger Y, Farkash S, Rand E, Hecht M, Segal E, Pikarski E, Young RA, Niveleau A, Cedar H, et al. Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet 2006, 38(2):149-153. 10.1038/ng1719, 16444255.
33. Cao Q, Yu J, Dhanasekaran SM, Kim JH, Mani RS, Tomlins SA, Mehra R, Laxman B, Cao X, Kleer CG, et al. Repression of E-cadherin by the polycomb group protein EZH2 in cancer. Oncogene 2008, 27(58):7274-7284. 10.1038/onc.2008.333, 2690514, 18806826.
34. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19(2):185-193. 10.1093/bioinformatics/19.2.185, 12538238.