| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
Advances in Brief |
The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland 21231-1000 [J. A. F., S. E., J. G. H., S. B. B.], and The Graduate Program in Cellular and Molecular Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231 [J. A. F., S. E., J. G. H., S. B. B.]
 |
ABSTRACT |
|---|
 Top ABSTRACT IntroductionMaterials and MethodsResultsDiscussionREFERENCES |
|---|
|
Introduction |
|---|
|
TopABSTRACTIntroductionMaterials and MethodsResultsDiscussionREFERENCES |
|---|
The above histone modifications have been widely hypothesized to determine active versus inactive gene expression status (4, 5, 6, 7, 8, 9) . Moreover, presence of methyl-H3-K9 has recently been shown to be essential for all or a subset of DNA methylation in Neurospora crassa (10) and Arabidopsis thaliana (11) , respectively. However, for hypermethylated tumor suppressor genes in human cancer, DNA hypermethylation appears to be dominant over at least the histone deacetylation part of the histone code for maintaining a silenced state (12) . In this regard, we have shown previously that the DNA demethylating agent 5-Aza-dC, but not the HDAC inhibitor TSA, reactivates the expression of such genes (12 , 13) . We now provide evidence that promoter DNA hypermethylation can control transcriptional silencing and, either directly or indirectly, the state of key elements of the histone code. At hMLH1, a mismatch repair gene often silenced with aberrant CpG island hypermethylation in colorectal cancers (14) , a zone of deacetylated H3 (deacetylated histone H3-K9 and -K14) plus methyl-H3-K9 (dimethyl-H3-K9) surrounds the hypermethylated, silenced promoter. This same promoter, when unmethylated and active, is embedded in methyl-H3-K4 (dimethyl-H3-K4) and acetylated H3 (acetylated histone H3-K9 and -K14). Treatment with TSA fails to reactivate the hypermethylated gene or dramatically alters the histone modifications examined. However, 5-Aza-dC treatment leads to initiation of demethylation by 12 h, appearance of transcription by 24 h, and full reversal of key elements of the histone code by 48 h. Thus, DNA hypermethylation, either directly or indirectly through suppressing transcription, appears to specify for repressive histone modifications at a tumor suppressor gene promoter. An important element of the findings is that the demethylating drug 5-Aza-dC appears to be a potent tool for dissecting the components of this DNA methylation-mediated transcriptional control and for potentially reversing their interaction for therapeutic purposes in cancer.
|
Materials and Methods |
|---|
|
TopABSTRACTIntroductionMaterials and MethodsResultsDiscussionREFERENCES |
|---|
5-Aza-dC and TSA Treatments.
Cells were treated with mock or 1 µM 5-Aza-dC (Sigma) for 12, 24, 48 h, or 5 days or with 300 nM TSA (Wako) for 24 h, as described previously (12
, 14)
.
ChIP.
We used the ChIP Assay Kit from Upstate Biotechnology and followed the manufacturer’s protocol with some modifications.
Briefly, proteins were cross-linked to DNA by addition of formaldehyde directly to the culture medium to a final concentration of 1% for 10 min at room temperature. The cross-linking reaction was quenched by adding glycine to a final concentration of 0.125 M for 5 min at room temperature. The medium was then removed and cells were washed with 1x PBS containing a combination of protease inhibitors (1 mM Pefabloc and 1x Complete protease inhibitor mixture; Roche Molecular Biochemicals). The PBS was removed and 0.2x trypsin was added to the cells. After a 5-min incubation at 37°C, ice-cold 1x PBS containing 10% FBS was added to stop trypsinization. The cells were scraped off the culture flask, pelleted, and washed twice with 1x PBS plus protease inhibitors as above. For each ChIP assay 
106 cells were used. The sonicated samples were precleared with 80 µl of salmon sperm DNA/Protein A and Protein G agarose beads (3:1 ratio of Protein A to Protein G; Upstate Biotechnology) for 1 h at 4°C with agitation. The soluble chromatin fraction was collected, and 5 µl of either anti-acetyl-Histone H3 (Lys 9 and Lys 14), anti-dimethyl-Histone H3 (Lys 4), anti-dimethyl-Histone H3 (Lys 9), or no antibody was added and incubated overnight with rotation (all antibodies from Upstate Biotechnology). Immune complexes were collected with 60 µl of the 3:1 salmon sperm DNA/Protein A and Protein G agarose beads. The beads were washed as recommended but were transferred to a new tube before each wash. After elution, the cross-links were reversed, and the samples were digested with proteinase K. DNA was recovered by phenol extraction, ethanol precipitated, and resuspended in 1x 10 mM Tris (pH 8)-1 mM EDTA buffer.
PCR Amplification and Analysis.
Primer sets for PCR were designed to amplify overlapping fragments of 200 bp along the hMLH1 promoter. One primer set for GAPDH was designed to amplify a 128-bp fragment of the genomic sequence to serve as an internal control. All primers were purchased from Invitrogen or IDT. All PCR reactions were performed with JumpStart REDTaq DNA Polymerase (Sigma) in a total volume of 25 µl, using 1–2 µl of either immunoprecipitated (bound) DNA, a 1:10 dilution of nonimmunoprecipitated (input) DNA, or a no-antibody control. All reactions were optimized with input DNA to ensure that PCR products for both hMLH1 and GAPDH were in the linear range of amplification. Primer sequences and additional PCR conditions are available upon request. Ten µl of PCR product were size fractionated by PAGE and were quantified using Kodak Digital Science 1D Image Analysis software. Enrichment was calculated by taking the ratio between the net intensity of the hMLH1 PCR product from each primer set and the net intensity of the GAPDH PCR product for the bound sample and dividing this by the same ratio calculated for the input sample. Values for enrichment were calculated as the average from at least two independent ChIP experiments and multiple independent PCR analyses of each.
MSP.
Genomic DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega). The genomic DNA was modified by bisulfite treatment, as described previously (15)
. The primers used for MSP have been previously described (14)
and were purchased from Invitrogen. Primer sequences and additional PCR conditions are available upon request.
Reverse Transcriptase-PCR.
We isolated RNA with Trizol (Invitrogen), according to the manufacturer’s instructions. RNA was reverse transcribed using Superscript II Rnase H Reverse Transcriptase (Invitrogen). PCR was performed using 1 µl of cDNA and primers unambiguous for GAPDH or hMLH1 (Invitrogen). All PCR reactions were performed with JumpStart REDTaq DNA Polymerase (Sigma) in a total volume of 25 µl. Primer sequences and additional PCR conditions are available upon request.
|
Results |
|---|
|
TopABSTRACTIntroductionMaterials and MethodsResultsDiscussionREFERENCES |
|---|
. Overall, acetylated histone H3 was enriched throughout the unmethylated hMLH1 promoter; however, there was essentially no acetylation of these same sites along the hypermethylated promoter (Fig. 1, B and C)
. Virtually identical results were observed for methyl-H3-K4 at the two promoters (Fig. 1, D and E)
. In stark contrast, methyl-H3-K9 was enriched along the entire hypermethylated, silenced hMLH1 promoter, especially over a region where it was depleted to virtually undetectable levels along the unmethylated, transcriptionally active promoter (Fig. 1, F and G)
. Thus, it seems that key elements of the histone code surrounding an aberrantly hypermethylated tumor suppressor gene in human cancer resemble the histone modifications that may be necessary for proper genomic imprinting and gene expression along the X chromosome in other mammalian cells (6, 7, 8, 9)
and for defining large heterochromatic and euchromatic domains in chickens (4)
and yeast (5)
.
|
and essentially no change in methyl-H3-K4 (Fig. 2, C and D)
and methyl-H3-K9 (Fig. 2, E and F)
. These data show that in addition to being unable to reactivate expression of a hypermethylated, silenced hMLH1gene, TSA alone is unable to evoke obvious changes in key parameters of the histone code at this promoter.
|
, whereas methyl-H3-K9 levels were severely depleted (Fig. 3, E and F)
. Thus with 5-Aza-dC, we recapitulated in RKO cells the state of the unmethylated, expressed promoter originally observed in SW480 cells (compare Fig. 3, A, C, and E
to Fig. 1, B, D, and F
). This transformation of key parameters of the histone code upon inhibition of the DNMTs suggests that in human colorectal cancer cells, DNA hypermethylation, or another activity mediated by DNMTs, may be essential for maintaining a particular combination of histone modifications at gene promoters silenced with aberrant DNA hypermethylation. Furthermore, the observation that 5-Aza-dC, but not TSA, can both reactivate expression of the silenced hMLH1 gene and completely reverse key histone modifications surrounding the gene promoter strengthens the idea that there exists some interdependence between reversal of important histone code components and reactivation of a gene silenced with aberrant DNA hypermethylation.
|
, which cover the region of greatest difference in histone modification observed between RKO and SW480 cells and also between 5-Aza-dC-treated and -untreated RKO cells at hMLH1 (Fig. 1, A, B, D, and F
; Fig. 3, A, C, and E
). At 12 and 24 h after the start of 5-Aza-dC treatment, there was no dramatic change in the histone code components examined (Fig. 4)
. By 48 h, acetylated H3 and methyl-H3-K4 showed dramatic enrichment in 5-Aza-dC-treated samples compared with mock-treated samples; at the same time, methyl-H3-K9 became depleted (Fig. 4)
. We next used MSP to examine the methylation status of the hMLH1 promoter after treatment with 5-Aza-dC. The region examined covers the area of greatest CpG density in the promoter and overlaps with the region examined by ChIP and PCR analysis in these time course studies (Fig. 1A)
. By 12 h, we observed demethylation of the promoter, which was maximal by 24 h and sustained until 5 days after the start of drug treatment (Fig. 5A)
. Finally, we examined reexpression of hMLH1 by 5-Aza-dC using reverse transcriptase-PCR. Transcriptional reactivation became apparent by 24 h after the start of 5-Aza-dC treatment, and gene expression continued throughout the time course (Fig. 5B)
. The observed sequence of events, then, is demethylation of the hMLH1 promoter by 12 h, appearance of hMLH1 transcript by 24 h, and complete reversal of all examined histone code components along the gene promoter by 48 h (Table 1)
.
|
|
|
|
Discussion |
|---|
|
TopABSTRACTIntroductionMaterials and MethodsResultsDiscussionREFERENCES |
|---|
In considering the mechanisms that underlie our observation that upon treatment with 5-Aza-dC, demethylation precedes reactivation of transcription, which precedes reversal of key histone code parameters, at least two scenarios may be considered. The first potential mechanism is one in which DNA methylation plays a direct role in both gene silencing and maintaining a repressive histone code at a hypermethylated gene promoter in cancer. We could speculate that the DNA modification itself, or components of the DNA methylating machinery such as the DNMTs or methyl-CpG binding proteins, could directly interact with histone methyltransferases or proteins that target them, directing them to regions containing DNA methylation and allowing them to set up a repressive histone code (18) . If this turns out to be the case, it would suggest a new paradigm, seeing that data from Neurospora (10) and Arabidopsis (11) suggest the opposite and point to a role for methyl-H3-K9 in targeting and maintaining DNA methylation. Our data stress the importance of identifying the enzymes responsible for modifying the histones in the setting of mammalian gene promoters and developing histone methyltransferase inhibitors to formally test relationships between histone modifications and DNA methylation in mammalian cells.
A second and more indirect mechanism may better fit the changes we have observed and relate to an important new view of relationships between histone code parameters and gene transcription (19, 20, 21) . In this scenario, DNA demethylation leads to gene reactivation, which in turn, leads to reversal of key elements of the histone code. This possibility is supported by our temporal data and by recent exciting findings in Arabidopsis (21) and Drosophila (20) by others. Johnson et al. (21) report that loss of DNA methylation itself does not lead to a decrease in methyl-H3-K9; rather, only at loci where reactivation of transcription occurs because of loss of DNA methylation does methyl-H3-K9 decrease. They postulate that methyl-H3-K9 may be replaced by replication-independent deposition of new nucleosomes containing variant histone H3.3 once transcription occurs (21) , a concept suggested by studies from Ahmad and Henikoff (20) in Drosophila. In light of these findings, our data could be interpreted as showing that 5-Aza-dC leads to demethylation of the DNA, which causes reactivation of hMLH1 gene transcription and, possibly, subsequent deposition of H3.3. The newly deposited variant histones would lack methyl-H3-K9 and could undergo posttranslational modification, including methylation at K4 or acetylation, resulting in a heritable histone code that supports active transcription at the hMLH1 promoter. This type of mechanism could also help to explain our previous findings that TSA alone cannot reactivate hypermethylated genes in cancer but can synergize with low doses of 5-Aza-dC to reactivate such genes (12 , 13) . In this model, TSA may be working by facilitating the acetylation of the newly deposited histones, thus helping to augment newly initiated transcription.
Although additional studies must continue to verify the above proposed sequence of events, our new findings are important to multiple aspects of abnormal, epigenetically mediated gene silencing in cancer. Pooling all of the available data, including ours and those from studies in Neurospora (10) and Arabidopsis (11 , 21) , the following sequence of events is a plausible model for DNA methylation-mediated silencing of tumor suppressor genes in cancer. Our extensive histone code map along the hMLH1 promoter in SW480 cells suggests that enrichment of acetylated H3 and methyl-H3-K4 within and upstream of promoter CpG islands could protect the islands at normally expressed mammalian genes from DNA hypermethylation, similar to the postulated methyl-H3-K4- and acetylation-mediated protection from transcriptional repression that has been suggested to occur in chickens (4) and yeast (5) . Such protection may be lost in some cancers at selected sites because these key components of the histone code break down, allowing histone deacetylation to occur, methyl-H3-K9 to spread into the promoter, and aberrant DNA hypermethylation of the CpG island and silencing to result. Our data suggest that DNA hypermethylation firmly maintains this new heritable silenced state by repressing transcription and, directly or indirectly, sustaining these key elements of a repressive histone code. Importantly, 5-Aza-dC is able to disrupt this established heritable state of the histones. These findings stress the usefulness of this drug for dissecting the basic relationships between DNA methylation and histone modifications for their contribution to gene expression patterns in normal and disease states, as well as the possibilities for reversing DNA hypermethylation and repressive components of the histone code for prevention and treatment of cancer.
|
ACKNOWLEDGMENTS |
|---|
|
FOOTNOTES |
|---|
1 Supported by NIH Grant CA43318 from the National Cancer Institute and ES11858 from the National Institute of Environmental Health Sciences. 
2 J. G. H. and S. B. B. are consultants to Tibotec-Virco. Under licensing agreement between the Johns Hopkins University and Tibotec-Virco, MSP was licensed to Tibotec-Virco, and they are entitled to a share of the royalties received by the University from sales of the licensed technology. The terms of these arrangements are being managed by the University in accordance with its conflict of interest policies.
3 These authors contributed equally to this work.
4 To whom requests for reprints should be addressed, at The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Tumor Biology Laboratory, The Bunting-Blaustein Cancer Research Building, 1650 Orleans Street, Room 541, Baltimore, MD 21231-1000. Phone: (410) 955-8506; Fax: (410) 614-9884; E-mail: sbaylin{at}jhmi.edu
5 The abbreviations used are: methyl-H3-K4, methylated histone H3-lysine 4; methyl-H3-K9, methylated histone H3-lysine 9; DNMT, DNA methyltransferase; HDAC, histone deacetylase; 5-Aza-dC, 5-Aza-2'deoxycytidine; TSA, Trichostatin A; ChIP, chromatin immunoprecipitation; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; MSP, methylation-specific PCR.
Received 11/11/02. Accepted 11/11/02.
|
REFERENCES |
|---|
|
TopABSTRACTIntroductionMaterials and MethodsResultsDiscussionREFERENCES |
|---|
This article has been cited by other articles:
|
|
 |
|
  V. J. Bailey, H. Easwaran, Y. Zhang, E. Griffiths, S. A. Belinsky, J. G. Herman, S. B. Baylin, H. E. Carraway, and T.-H. Wang MS-qFRET: A quantum dot-based method for analysis of DNA methylation Genome Res., August 1, 2009; 19(8): 1455 - 1461. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Derks, L. J.W. Bosch, H. E.C. Niessen, P. T.M. Moerkerk, S. M. van den Bosch, B. Carvalho, S. Mongera, J.W. Voncken, G. A. Meijer, A. P. de Bruine, et al. Promoter CpG island hypermethylation- and H3K9me3 and H3K27me3-mediated epigenetic silencing targets the deleted in colon cancer (DCC) gene in colorectal carcinogenesis without affecting neighboring genes on chromosomal region 18q21 Carcinogenesis, June 1, 2009; 30(6): 1041 - 1048. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Shikauchi, A. Saiura, T. Kubo, Y. Niwa, J. Yamamoto, Y. Murase, and H. Yoshikawa SALL3 Interacts with DNMT3A and Shows the Ability To Inhibit CpG Island Methylation in Hepatocellular Carcinoma Mol. Cell. Biol., April 1, 2009; 29(7): 1944 - 1958. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. M. Yi, H.-C. Tsai, S. C. Glockner, S. Lin, J. E. Ohm, H. Easwaran, C. D. James, J. F. Costello, G. Riggins, C. G. Eberhart, et al. Abnormal DNA Methylation of CD133 in Colorectal and Glioblastoma Tumors Cancer Res., October 1, 2008; 68(19): 8094 - 8103. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. S.M. Li, M. K.Y. Siu, HuiJuan Zhang, E. S.Y. Wong, K. Y.K. Chan, H. Y.S. Ngan, and A. N.Y. Cheung Hypermethylation of SOX2 Gene in Hydatidiform Mole and Choriocarcinoma Reproductive Sciences, September 1, 2008; 15(7): 735 - 744. [Abstract] [PDF]
|
|
|
|
|
|
W. Ji, L. Yang, L. Yu, J. Yuan, D. Hu, W. Zhang, J. Yang, Y. Pang, W. Li, J. Lu, et al. Epigenetic silencing of O6-methylguanine DNA methyltransferase gene in NiS-transformed cells Carcinogenesis, June 1, 2008; 29(6): 1267 - 1275. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B.-G. Jeon, G. Coppola, S. D Perrault, G.-J. Rho, D. H Betts, and W A. King S-adenosylhomocysteine treatment of adult female fibroblasts alters X-chromosome inactivation and improves in vitro embryo development after somatic cell nuclear transfer Reproduction, June 1, 2008; 135(6): 815 - 828. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L.-P. Wu, X. Wang, L. Li, Y. Zhao, S. Lu, Y. Yu, W. Zhou, X. Liu, J. Yang, Z. Zheng, et al. Histone Deacetylase Inhibitor Depsipeptide Activates Silenced Genes through Decreasing both CpG and H3K9 Methylation on the Promoter Mol. Cell. Biol., May 15, 2008; 28(10): 3219 - 3235. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Maguire, P. C. Nield, T. Devling, R. E. Jenkins, B. K. Park, R. Polanski, N. Vlatkovic, and M. T. Boyd MDM2 Regulates Dihydrofolate Reductase Activity through Monoubiquitination Cancer Res., May 1, 2008; 68(9): 3232 - 3242. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Sadikovic, J. Andrews, D. Carter, J. Robinson, and D. I. Rodenhiser Genome-wide H3K9 Histone Acetylation Profiles Are Altered in Benzopyrene-treated MCF7 Breast Cancer Cells J. Biol. Chem., February 15, 2008; 283(7): 4051 - 4060. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Li, L. Da, H. Tang, T. Li, and M. Zhao CpG methylation plays a vital role in determining tissue- and cell-specific expression of the human cell-death-inducing DFF45-like effector A gene through the regulation of Sp1/Sp3 binding Nucleic Acids Res., January 17, 2008; 36(1): 330 - 341. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. R. Fantin and V. M. Richon Mechanisms of Resistance to Histone Deacetylase Inhibitors and Their Therapeutic Implications Clin. Cancer Res., December 15, 2007; 13(24): 7237 - 7242. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Kholod, J. Boniver, and P. Delvenne A New Dimethyl Sulfoxide-Based Method for Gene Promoter Methylation Detection J. Mol. Diagn., November 1, 2007; 9(5): 574 - 581. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Watanabe, M. Toyota, Y. Kondo, H. Suzuki, T. Imai, M. Ohe-Toyota, R. Maruyama, M. Nojima, Y. Sasaki, Y. Sekido, et al. PRDM5 Identified as a Target of Epigenetic Silencing in Colorectal and Gastric Cancer Clin. Cancer Res., August 15, 2007; 13(16): 4786 - 4794. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. V. Jacinto and M. Esteller Mutator pathways unleashed by epigenetic silencing in human cancer Mutagenesis, July 1, 2007; 22(4): 247 - 253. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. M. McGarvey, E. Greene, J. A. Fahrner, T. Jenuwein, and S. B. Baylin DNA Methylation and Complete Transcriptional Silencing of Cancer Genes Persist after Depletion of EZH2 Cancer Res., June 1, 2007; 67(11): 5097 - 5102. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Huang, E. Greene, T. Murray Stewart, A. C. Goodwin, S. B. Baylin, P. M. Woster, and R. A. Casero Jr Inhibition of lysine-specific demethylase 1 by polyamine analogues results in reexpression of aberrantly silenced genes PNAS, May 8, 2007; 104(19): 8023 - 8028. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Wu, A. Starzinski-Powitz, and S.-W. Guo Trichostatin A, a Histone Deacetylase Inhibitor, Attenuates Invasiveness and Reactivates E-Cadherin Expression in Immortalized Endometriotic Cells Reproductive Sciences, May 1, 2007; 14(4): 374 - 382. [Abstract] [PDF]
|
|
|
|
|
|
K. Kawamoto, S. T. Okino, R. F. Place, S. Urakami, H. Hirata, N. Kikuno, T. Kawakami, Y. Tanaka, D. Pookot, Z. Chen, et al. Epigenetic Modifications of RASSF1A Gene through Chromatin Remodeling in Prostate Cancer Clin. Cancer Res., May 1, 2007; 13(9): 2541 - 2548. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Strathdee, A. Sim, R. Soutar, T. L. Holyoake, and R. Brown HOXA5 is targeted by cell-type-specific CpG island methylation in normal cells and during the development of acute myeloid leukaemia Carcinogenesis, February 1, 2007; 28(2): 299 - 309. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Li, M. Papworth, M. Minczuk, C. Rohde, Y. Zhang, S. Ragozin, and A. Jeltsch Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes Nucleic Acids Res., January 12, 2007; 35(1): 100 - 112. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. L. Zinn, K. Pruitt, S. Eguchi, S. B. Baylin, and J. G. Herman hTERT Is Expressed in Cancer Cell Lines Despite Promoter DNA Methylation by Preservation of Unmethylated DNA and Active Chromatin around the Transcription Start Site Cancer Res., January 1, 2007; 67(1): 194 - 201. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J J L Wong, N J Hawkins, and R L Ward Colorectal cancer: a model for epigenetic tumorigenesis Gut, January 1, 2007; 56(1): 140 - 148. [Full Text] [PDF]
|
|
|
|
 |
|
 A. H. Ting, K. M. McGarvey, and S. B. Baylin The cancer epigenome--components and functional correlates Genes & Dev., December 1, 2006; 20(23): 3215 - 3231. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. M.E.I. Hellebrekers, K. Castermans, E. Vire, R. P.M. Dings, N. T.H. Hoebers, K. H. Mayo, M. G.A. oude Egbrink, G. Molema, F. Fuks, M. van Engeland, et al. Epigenetic Regulation of Tumor Endothelial Cell Anergy: Silencing of Intercellular Adhesion Molecule-1 by Histone Modifications. Cancer Res., November 15, 2006; 66(22): 10770 - 10777. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Verdone, E. Agricola, M. Caserta, and E. Di Mauro Histone acetylation in gene regulation Brief Funct Genomic Proteomic, September 1, 2006; 5(3): 209 - 221. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Tzao, G.-H. Sun, H.-J. Tung, H.-S. Hsu, W.-H. Hsu, Y.-C. Wang, Y.-L. Cheng, and S.-C. Lee Reduced Acetylated Histone H4 is Associated With Promoter Methylation of the Fragile Histidine Triad Gene in Resected Esophageal Squamous Cell Carcinoma Ann. Thorac. Surg., August 1, 2006; 82(2): 396 - 401. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Li, T. Rauch, Z.-X. Chen, P. E. Szabo, A. D. Riggs, and G. P. Pfeifer The Histone Methyltransferase SETDB1 and the DNA Methyltransferase DNMT3A Interact Directly and Localize to Promoters Silenced in Cancer Cells J. Biol. Chem., July 14, 2006; 281(28): 19489 - 19500. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. D. Gore, S. Baylin, E. Sugar, H. Carraway, C. B. Miller, M. Carducci, M. Grever, O. Galm, T. Dauses, J. E. Karp, et al. Combined DNA methyltransferase and histone deacetylase inhibition in the treatment of myeloid neoplasms. Cancer Res., June 15, 2006; 66(12): 6361 - 6369. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. M. McGarvey, J. A. Fahrner, E. Greene, J. Martens, T. Jenuwein, and S. B. Baylin Silenced tumor suppressor genes reactivated by DNA demethylation do not return to a fully euchromatic chromatin state. Cancer Res., April 1, 2006; 66(7): 3541 - 3549. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. S. Kassis, M. Zhao, J. A. Hong, G. A. Chen, D. M. Nguyen, and D. S. Schrump Depletion of DNA methyltransferase 1 and/or DNA methyltransferase 3b mediates growth arrest and apoptosis in lung and esophageal cancer and malignant pleural mesothelioma cells J. Thorac. Cardiovasc. Surg., February 1, 2006; 131(2): 298 - 306. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Saxonov, P. Berg, and D. L. Brutlag A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters PNAS, January 31, 2006; 103(5): 1412 - 1417. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Hernandez-Munoz, P. Taghavi, C. Kuijl, J. Neefjes, and M. van Lohuizen Association of BMI1 with Polycomb Bodies Is Dynamic and Requires PRC2/EZH2 and the Maintenance DNA Methyltransferase DNMT1 Mol. Cell. Biol., December 15, 2005; 25(24): 11047 - 11058. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. J. Noh, E. R. Jang, G. Jeong, Y. M. Lee, C. K. Min, and J.-S. Lee Methyl CpG-Binding Domain Protein 3 Mediates Cancer-Selective Cytotoxicity by Histone Deacetylase Inhibitors via Differential Transcriptional Reprogramming in Lung Cancer Cells Cancer Res., December 15, 2005; 65(24): 11400 - 11410. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H.-W. Chan, J. S. Miller, M. B. Moore, and C. T. Lutz Epigenetic Control of Highly Homologous Killer Ig-Like Receptor Gene Alleles J. Immunol., November 1, 2005; 175(9): 5966 - 5974. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Pogribny, I. Koturbash, V. Tryndyak, D. Hudson, S. M.L. Stevenson, O. Sedelnikova, W. Bonner, and O. Kovalchuk Fractionated Low-Dose Radiation Exposure Leads to Accumulation of DNA Damage and Profound Alterations in DNA and Histone Methylation in the Murine Thymus Mol. Cancer Res., October 1, 2005; 3(10): 553 - 561. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zhang, N. Fatima, and M. L. Dufau Coordinated Changes in DNA Methylation and Histone Modifications Regulate Silencing/Derepression of Luteinizing Hormone Receptor Gene Transcription Mol. Cell. Biol., September 15, 2005; 25(18): 7929 - 7939. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. N. Bhalla Epigenetic and Chromatin Modifiers As Targeted Therapy of Hematologic Malignancies J. Clin. Oncol., June 10, 2005; 23(17): 3971 - 3993. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. W. Laird Cancer epigenetics Hum. Mol. Genet., April 15, 2005; 14(suppl_1): R65 - R76. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J.G. HERMAN Epigenetic Changes in Cancer and Preneoplasia Cold Spring Harb Symp Quant Biol, January 1, 2005; 70(0): 329 - 333. [Abstract] [PDF]
|
|
|
|
|
|
S.B. BAYLIN and W.Y. CHEN Aberrant Gene Silencing in Tumor Progression: Implications for Control of Cancer Cold Spring Harb Symp Quant Biol, January 1, 2005; 70(0): 427 - 433. [Abstract] [PDF]
|
|
|
|
|
|
P. M. Das and R. Singal DNA Methylation and Cancer J. Clin. Oncol., November 15, 2004; 22(22): 4632 - 4642. [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. Ushmorov, O. Ritz, M. Hummel, F. Leithauser, P. Moller, H. Stein, and T. Wirth Epigenetic silencing of the immunoglobulin heavy-chain gene in classical Hodgkin lymphoma-derived cell lines contributes to the loss of immunoglobulin expression Blood, November 15, 2004; 104(10): 3326 - 3334. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Stirzaker, J. Z. Song, B. Davidson, and S. J. Clark Transcriptional Gene Silencing Promotes DNA Hypermethylation through a Sequential Change in Chromatin Modifications in Cancer Cells Cancer Res., June 1, 2004; 64(11): 3871 - 3877. [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]
|
|
|
|
|
|
G. Narayan, H. Arias-Pulido, S. V. Nandula, K. Basso, D. D. Sugirtharaj, H. Vargas, M. Mansukhani, J. Villella, L. Meyer, A. Schneider, et al. Promoter Hypermethylation of FANCF: Disruption of Fanconi Anemia-BRCA Pathway in Cervical Cancer Cancer Res., May 1, 2004; 64(9): 2994 - 2997. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Deng, G.-A. Song, E. Pong, M. Sleisenger, and Y. S. Kim Promoter Methylation Inhibits APC Gene Expression by Causing Changes in Chromatin Conformation and Interfering with the Binding of Transcription Factor CCAAT-Binding Factor Cancer Res., April 15, 2004; 64(8): 2692 - 2698. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. P. Kimura, S. A. Liebhaber, and N. E. Cooke Epigenetic Modifications at the Human Growth Hormone Locus Predict Distinct Roles for Histone Acetylation and Methylation in Placental Gene Activation Mol. Endocrinol., April 1, 2004; 18(4): 1018 - 1032. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. G. Herman and S. B. Baylin Gene Silencing in Cancer in Association with Promoter Hypermethylation N. Engl. J. Med., November 20, 2003; 349(21): 2042 - 2054. [Full Text] [PDF]
|
|
|
|
|
|
K.-C. Kim, L. Geng, and S. Huang Inactivation of a Histone Methyltransferase by Mutations in Human Cancers Cancer Res., November 15, 2003; 63(22): 7619 - 7623. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. S. Yan, H. Shi, F. Rahmatpanah, T. H-C. Hsiau, A. H-A. Hsiau, Y.-W. Leu, J. C. Liu, and T. H.-M. Huang Differential Distribution of DNA Methylation within the RASSF1A CpG Island in Breast Cancer Cancer Res., October 1, 2003; 63(19): 6178 - 6186. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. N. Carnell and J. I. Goodman The Long (LINEs) and the Short (SINEs) of It: Altered Methylation as a Precursor to Toxicity Toxicol. Sci., October 1, 2003; 75(2): 229 - 235. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Nimmanapalli, L. Fuino, P. Bali, M. Gasparetto, M. Glozak, J. Tao, L. Moscinski, C. Smith, J. Wu, R. Jove, et al. Histone Deacetylase Inhibitor LAQ824 Both Lowers Expression and Promotes Proteasomal Degradation of Bcr-Abl and Induces Apoptosis of Imatinib Mesylate-sensitive or -refractory Chronic Myelogenous Leukemia-Blast Crisis Cells Cancer Res., August 15, 2003; 63(16): 5126 - 5135. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Fahrner and S. B. Baylin Heterochromatin: stable and unstable invasions at home and abroad Genes & Dev., August 1, 2003; 17(15): 1805 - 1812. [Full Text] [PDF]
|
|
|
|
|
|
Y. Kondo and J.-P. J. Issa Enrichment for Histone H3 Lysine 9 Methylation at Alu Repeats in Human Cells J. Biol. Chem., July 18, 2003; 278(30): 27658 - 27662. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Lachner, R. J. O'Sullivan, and T. Jenuwein An epigenetic road map for histone lysine methylation J. Cell Sci., June 1, 2003; 116(11): 2117 - 2124. [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 |
represent data from SW480. 
represent data from RKO. C, E, and G, representative PCR analyses of ChIP on RKO and SW480 from areas typical of enrichment for acetylated H3, methyl-H3-K4, and methyl-H3-K9, respectively. Multiplex PCR was performed on bound (B) immunoprecipitated DNA and input (I) nonimmunoprecipitated DNA with each hMLH1 primer set.
represents enrichment in RKO cells treated with TSA. 
represents data from untreated RKO cells. Points on each graph represent data from the corresponding DNA fragment amplified by PCR, as illustrated in Fig. 1A
