| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
Molecular Biology and Genetics |
Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia, Missouri 65203 [H. S., S. H. W., Y-W. L., F. R., J. C. L., P. S. Y., T. H-M. H.]; Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana 47405 [K. P. N.]; and Departments of Cellular and Integrative Physiology, and Obstetrics and Gynecology, Indiana University Cancer Center, Indianapolis, Indiana, 46202 [K. P. N.]
We developed a novel microarray system to assess gene expression, DNA methylation, and histone acetylation in parallel, and to dissect the complex hierarchy of epigenetic changes in cancer. An integrated microarray panel consisting of 1507 short CpG island tags located at the 5'-end regions (including the first exons) was used to assess effects of epigenetic treatments on a human epithelial ovarian cancer cell line. Treatment with methylation (5-aza-2'-deoxycytidine) or deacetylation (trichostatin A) inhibitors alone resulted in up-regulation of 1.9 or 1.1% of the genes analyzed; however, the combined treatment resulted in synergistic reactivation of more genes (10.4%; P < 0.001 versus either treatment alone). On the basis of either primary or secondary responses to the treatments, genes were identified as methylation-dependent or -independent. Synergistic reactivation of the methylation-dependent genes by 5-aza-2'-deoxycytidine plus trichostatin A revealed a functional interaction between methylated promoters and deacetylated histones. Increased expression of some methylation-independent genes was associated with enhanced histone acetylation, but up-regulation of most of the genes identified using this technology was because of events downstream of the epigenetic cascade. We demonstrate proof of principle for using the triple microarray system in analyzing the dynamic relationship between transcription factors and promoter targets in cancer genomes.
This article has been cited by other articles:
|
|
 |
|
  N. Yamada, Y. Nishida, H. Tsutsumida, T. Hamada, M. Goto, M. Higashi, M. Nomoto, and S. Yonezawa MUC1 Expression Is Regulated by DNA Methylation and Histone H3 Lysine 9 Modification in Cancer Cells Cancer Res., April 15, 2008; 68(8): 2708 - 2716. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Ripperger, N. von Neuhoff, K. Kamphues, M. Emura, U. Lehmann, M. Tauscher, M. Schraders, P. Groenen, B. Skawran, C. Rudolph, et al. Promoter methylation of PARG1, a novel candidate tumor suppressor gene in mantle cell lymphomas Haematologica, April 1, 2007; 92(4): 460 - 468. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Shi, J. Guo, D. J. Duff, F. Rahmatpanah, R. Chitima-Matsiga, M. Al-Kuhlani, K. H. Taylor, O. Sjahputera, M. Andreski, J. E. Wooldridge, et al. Discovery of novel epigenetic markers in non-Hodgkin's lymphoma Carcinogenesis, January 1, 2007; 28(1): 60 - 70. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Rauch, H. Li, X. Wu, and G. P. Pfeifer MIRA-Assisted Microarray Analysis, a New Technology for the Determination of DNA Methylation Patterns, Identifies Frequent Methylation of Homeodomain-Containing Genes in Lung Cancer Cells Cancer Res., August 15, 2006; 66(16): 7939 - 7947. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Wu, L. T. Smith, C. Plass, and T. H-M. Huang ChIP-chip Comes of Age for Genome-wide Functional Analysis. Cancer Res., July 15, 2006; 66(14): 6899 - 6902. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. J. Lee and B. T. Zhu Inhibition of DNA methylation by caffeic acid and chlorogenic acid, two common catechol-containing coffee polyphenols Carcinogenesis, February 1, 2006; 27(2): 269 - 277. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Schumacher, P. Kapranov, Z. Kaminsky, J. Flanagan, A. Assadzadeh, P. Yau, C. Virtanen, N. Winegarden, J. Cheng, T. Gingeras, et al. Microarray-based DNA methylation profiling: technology and applications Nucleic Acids Res., January 20, 2006; 34(2): 528 - 542. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. WANG, J. HAYAKAWA, F. LONG, Q. YU, A. H. CHO, G. RONDEAU, J. WELSH, S. MITTAL, I. DE BELLE, E. ADAMSON, et al. "Promoter Array" Studies Identify Cohorts of Genes Directly Regulated by Methylation, Copy Number Change, or Transcription Factor Binding in Human Cancer Cells Ann. N.Y. Acad. Sci., November 1, 2005; 1058(1): 162 - 185. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. M. Gallagher, O. E. Bergin, M. Rafferty, Z. D. Kelly, I.-M. Nolan, E. J.P. Fox, A. C. Culhane, L. McArdle, M. F. Fraga, L. Hughes, et al. Multiple markers for melanoma progression regulated by DNA methylation: insights from transcriptomic studies Carcinogenesis, November 1, 2005; 26(11): 1856 - 1867. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Balch, P. Yan, T. Craft, S. Young, D. G. Skalnik, T. H-M. Huang, and K. P. Nephew Antimitogenic and chemosensitizing effects of the methylation inhibitor zebularine in ovarian cancer Mol. Cancer Ther., October 1, 2005; 4(10): 1505 - 1514. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. J. Lee, J.-Y. Shim, and B. T. Zhu Mechanisms for the Inhibition of DNA Methyltransferases by Tea Catechins and Bioflavonoids Mol. Pharmacol., October 1, 2005; 68(4): 1018 - 1030. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Takai, N. Kawamata, C. S. Walsh, S. Gery, J. C. Desmond, S. Whittaker, J. W. Said, L. M. Popoviciu, P. A. Jones, I. Miyakawa, et al. Discovery of Epigenetically Masked Tumor Suppressor Genes in Endometrial Cancer Mol. Cancer Res., May 1, 2005; 3(5): 261 - 269. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. W. Laird Cancer epigenetics Hum. Mol. Genet., April 15, 2005; 14(suppl_1): R65 - R76. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Mori, J. Kim, T. Yamano, H. Takeuchi, S. Huang, N. Umetani, K. Koyanagi, and D. S.B. Hoon Epigenetic Up-regulation of C-C Chemokine Receptor 7 and C-X-C Chemokine Receptor 4 Expression in Melanoma Cells Cancer Res., March 1, 2005; 65(5): 1800 - 1807. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Chang and C. S. Pikaard Transcript Profiling in Arabidopsis Reveals Complex Responses to Global Inhibition of DNA Methylation and Histone Deacetylation J. Biol. Chem., January 7, 2005; 280(1): 796 - 804. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. R. Russanova, T. H. Hirai, and B. H. Howard Semirandom Sampling to Detect Differentiation-Related and Age-Related Epigenome Remodeling J. Gerontol. A Biol. Sci. Med. Sci., December 1, 2004; 59(12): 1221 - 1233. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Nouzova, N. Holtan, M. M. Oshiro, R. B. Isett, J. L. Munoz-Rodriguez, A. F. List, M. L. Narro, S. J. Miller, N. C. Merchant, and B. W. Futscher Epigenomic Changes during Leukemia Cell Differentiation: Analysis of Histone Acetylation and Cytosine Methylation Using CpG Island Microarrays J. Pharmacol. Exp. Ther., December 1, 2004; 311(3): 968 - 981. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-W. Leu, P. S. Yan, M. Fan, V. X. Jin, J. C. Liu, E. M. Curran, W. V. Welshons, S. H. Wei, R. V. Davuluri, C. Plass, et al. Loss of Estrogen Receptor Signaling Triggers Epigenetic Silencing of Downstream Targets in Breast Cancer Cancer Res., November 15, 2004; 64(22): 8184 - 8192. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Kirmizis and P. J. Farnham Genomic Approaches That Aid in the Identification of Transcription Factor Target Genes Experimental Biology and Medicine, September 1, 2004; 229(8): 705 - 721. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Kondo, L. Shen, P. S. Yan, T. H.-M. Huang, and J.-P. J. Issa Chromatin immunoprecipitation microarrays for identification of genes silenced by histone H3 lysine 9 methylation PNAS, May 11, 2004; 101(19): 7398 - 7403. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. C. Lindsey, M. E. Lusher, J. A. Anderton, S. Bailey, R. J. Gilbertson, A. D.J. Pearson, D. W. Ellison, and S. C. Clifford Identification of tumour-specific epigenetic events in medulloblastoma development by hypermethylation profiling Carcinogenesis, May 1, 2004; 25(5): 661 - 668. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. A. Ross, P. R. Srinivas, A. J. Clifford, S. C. Lee, M. A. Philbert, and R. L. Hettich New Technologies for Nutrition Research J. Nutr., March 1, 2004; 134(3): 681 - 685. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Diagnostic Arrays for Epigenetic Markers: YU-WEI LEU AND TIM H.-M. HUANG, Human Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center, Medical Research Facility, Columbus, Ohio 43210 Toxicol Pathol, January 1, 2004; 32(1): 139 - 139. [PDF]
|
|
|
|
|
|
M. Z. Fang, Y. Wang, N. Ai, Z. Hou, Y. Sun, H. Lu, W. Welsh, and C. S. Yang Tea Polyphenol (-)-Epigallocatechin-3-Gallate Inhibits DNA Methyltransferase and Reactivates Methylation-Silenced Genes in Cancer Cell Lines Cancer Res., November 15, 2003; 63(22): 7563 - 7570. [Abstract] [Full Text] [PDF]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| Cancer Research | Clinical Cancer Research |
| Cancer Epidemiology Biomarkers & Prevention | Molecular Cancer Therapeutics |
| Molecular Cancer Research | Cancer Prevention Research |
| Cancer Prevention Journals Portal | Cancer Reviews Online |
| Annual Meeting Education Book | Meeting Abstracts Online |
