This Article Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Pogribny, I. P. Articles by James, S. J. Search for Related Content PubMed PubMed Citation Articles by Pogribny, I. P. Articles by James, S. J.

Breaks in Genomic DNA and within the p53 Gene Are Associated with Hypomethylation in Livers of Folate/methyl-deficient Rats¹

National Center for Toxicological Research, Food and Drug Administration, Division of Nutritional Toxicology, Jefferson, Arkansas 72079

Male weanling Fischer 344 rats were fed either a semipurified diet deficient in the methyl donors methionine, choline, and folic acid or a supplemented control diet for a period of 9 weeks. At intervals of 2, 5, and 7 days, 3 weeks, and 9 weeks after initiation of the respective diets, the relative level of DNA strand breaks and the degree of cytosine methylation were quantified in high molecular weight DNA and also within the p53 gene in liver samples from these rats. Genome-wide strand break accumulation was associated with progressive genomic hypomethylation and increased DNA methyltransferase activity. With the use of quantitative PCR as a gene-specific DNA strand break assay, unique DNA strand breaks were detected in exon 5 but not in exons 6–8 of the p53 gene, and were accompanied by significant p53 gene hypomethylation. DNA hypomethylation has been shown to alter the conformation and stability of the chromatin structure, rendering affected regions more accessible to DNA-damaging agents. To determine whether methylation status alters the sensitivity of DNA to strand breakage, DNA in isolated nuclei was methylated in vitro and exposed to endogenous calcium/magnesium-dependent endonuclease activated under defined conditions. The incidence of enzyme-induced DNA strand breaks was decreased significantly with increased DNA methylation. In nuclei isolated from livers of methyl-deficient rats, the hypomethylated DNA was found to be more sensitive to enzyme- and oxidant-induced DNA strand break induction. Taken together, these results provide evidence that DNA strand breaks are induced in high molecular weight DNA and also within the p53 gene in liver tissue from methyl-deficient rats. The increased incidence of these strand breaks in DNA from methyl-deficient rats may be related to alterations in chromatin accessibility associated with DNA hypomethylation.

¹ Financial support for this work was provided by American Cancer Society Research Grant CN-73C (to S. J. J.) and by an appointment to the Postgraduate Research Program administered by the Oak Ridge Institute for Science and Education through an interagency agreement between the United States Department of Energy and the Food and Drug Administration (A. G. B., N. G. L.).

² To whom requests for reprints should be addressed.

Received 1/25/95. Accepted 3/ 7/95.

This article has been cited by other articles:

				L. S. Kristensen and A. Dobrovic Direct Genotyping of Single Nucleotide Polymorphisms in Methyl Metabolism Genes Using Probe-Free High-Resolution Melting Analysis Cancer Epidemiol. Biomarkers Prev., May 1, 2008; 17(5): 1240 - 1247. [Abstract] [Full Text] [PDF]

				S.S. Young, B. Eskenazi, F.M. Marchetti, G. Block, and A.J. Wyrobek The association of folate, zinc and antioxidant intake with sperm aneuploidy in healthy non-smoking men Hum. Reprod., May 1, 2008; 23(5): 1014 - 1022. [Abstract] [Full Text] [PDF]

				J. Kotsopoulos, K.-J. Sohn, and Y.-I. Kim Postweaning Dietary Folate Deficiency Provided through Childhood to Puberty Permanently Increases Genomic DNA Methylation in Adult Rat Liver J. Nutr., April 1, 2008; 138(4): 703 - 709. [Abstract] [Full Text] [PDF]

				X. Yin, E. O. Apostolov, S. V. Shah, X. Wang, K. V. Bogdanov, T. Buzder, A. G. Stewart, and A. G. Basnakian Induction of Renal Endonuclease G by Cisplatin Is Reduced in DNase I-Deficient Mice J. Am. Soc. Nephrol., September 1, 2007; 18(9): 2544 - 2553. [Full Text] [PDF]

				B. F. Cole, J. A. Baron, R. S. Sandler, R. W. Haile, D. J. Ahnen, R. S. Bresalier, G. McKeown-Eyssen, R. W. Summers, R. I. Rothstein, C. A. Burke, et al. Folic Acid for the Prevention of Colorectal Adenomas: A Randomized Clinical Trial JAMA, June 6, 2007; 297(21): 2351 - 2359. [Abstract] [Full Text] [PDF]

				G. R. Wasson, A. P. McGlynn, H. McNulty, S. L. O'Reilly, V. J. McKelvey-Martin, G. McKerr, J. J. Strain, J. Scott, and C. S. Downes Global DNA and p53 Region-Specific Hypomethylation in Human Colonic Cells Is Induced by Folate Depletion and Reversed by Folate Supplementation J. Nutr., November 1, 2006; 136(11): 2748 - 2753. [Abstract] [Full Text] [PDF]

				K.-A. da Costa, M. D Niculescu, C. N Craciunescu, L. M Fischer, and S. H Zeisel Choline deficiency increases lymphocyte apoptosis and DNA damage in humans Am. J. Clinical Nutrition, July 1, 2006; 84(1): 88 - 94. [Abstract] [Full Text] [PDF]

				C. Torrens, L. Brawley, F. W. Anthony, C. S. Dance, R. Dunn, A. A. Jackson, L. Poston, and M. A. Hanson Folate Supplementation During Pregnancy Improves Offspring Cardiovascular Dysfunction Induced by Protein Restriction Hypertension, May 1, 2006; 47(5): 982 - 987. [Abstract] [Full Text] [PDF]

				H. J. Powers Interaction among Folate, Riboflavin, Genotype, and Cancer, with Reference to Colorectal and Cervical Cancer J. Nutr., December 1, 2005; 135(12): 2960S - 2966S. [Abstract] [Full Text] [PDF]

				C. M. Ulrich, K. Curtin, W. Samowitz, J. Bigler, J. D. Potter, B. Caan, and M. L. Slattery MTHFR Variants Reduce the Risk of G:C->A:T Transition Mutations within the p53 Tumor Suppressor Gene in Colon Tumors J. Nutr., October 1, 2005; 135(10): 2462 - 2467. [Abstract] [Full Text] [PDF]

				J. M. Stempak, K.-J. Sohn, E.-P. Chiang, B. Shane, and Y.-I. Kim Cell and stage of transformation-specific effects of folate deficiency on methionine cycle intermediates and DNA methylation in an in vitro model Carcinogenesis, May 1, 2005; 26(5): 981 - 990. [Abstract] [Full Text] [PDF]

				G. Poschl and H. K. Seitz ALCOHOL AND CANCER Alcohol Alcohol., May 1, 2004; 39(3): 155 - 165. [Abstract] [Full Text] [PDF]

				Y.-I. Kim Folate and DNA Methylation: A Mechanistic Link between Folate Deficiency and Colorectal Cancer? Cancer Epidemiol. Biomarkers Prev., April 1, 2004; 13(4): 511 - 519. [Abstract] [Full Text] [PDF]

				J. Han, S. E. Hankinson, S. M. Zhang, I. De Vivo, and D. J. Hunter Interaction between Genetic Variations in DNA Repair Genes and Plasma Folate on Breast Cancer Risk Cancer Epidemiol. Biomarkers Prev., April 1, 2004; 13(4): 520 - 524. [Abstract] [Full Text] [PDF]

				L. Brawley, C. Torrens, F. W. Anthony, S. Itoh, T. Wheeler, A. A. Jackson, G. F. Clough, L. Poston, and M. A. Hanson Glycine rectifies vascular dysfunction induced by dietary protein imbalance during pregnancy J. Physiol., January 15, 2004; 554(2): 497 - 504. [Abstract] [Full Text] [PDF]

				F. Esfandiari, R. Green, R. F. Cotterman, I. P. Pogribny, S. J. James, and J. W. Miller Methyl deficiency causes reduction of the methyl-CpG-binding protein, MeCP2, in rat liver Carcinogenesis, December 1, 2003; 24(12): 1935 - 1940. [Abstract] [Full Text] [PDF]

				S. J. James, I. P. Pogribny, M. Pogribna, B. J. Miller, S. Jernigan, and S. Melnyk Mechanisms of DNA Damage, DNA Hypomethylation, and Tumor Progression in the Folate/Methyl-Deficient Rat Model of Hepatocarcinogenesis J. Nutr., November 1, 2003; 133(11): 3740S - 3747. [Abstract] [Full Text] [PDF]

				J. B. Mason Biomarkers of Nutrient Exposure and Status in One-Carbon (Methyl) Metabolism J. Nutr., March 1, 2003; 133(3): 941S - 947. [Abstract] [Full Text] [PDF]

				J. Trasler, L. Deng, S. Melnyk, I. Pogribny, F. Hiou-Tim, S. Sibani, C. Oakes, E. Li, S. J. James, and R. Rozen Impact of Dnmt1 deficiency, with and without low folate diets, on tumor numbers and DNA methylation in Min mice Carcinogenesis, January 1, 2003; 24(1): 39 - 45. [Abstract] [Full Text] [PDF]

				K.-J. Sohn, J. M. Stempak, S. Reid, S. Shirwadkar, J. B. Mason, and Y.-I. Kim The effect of dietary folate on genomic and p53-specific DNA methylation in rat colon Carcinogenesis, January 1, 2003; 24(1): 81 - 90. [Abstract] [Full Text] [PDF]

				X. Miao, D. Xing, W. Tan, J. Qi, W. Lu, and D. Lin Susceptibility to Gastric Cardia Adenocarcinoma and Genetic Polymorphisms in Methylenetetrahydrofolate Reductase in an At-Risk Chinese Population Cancer Epidemiol. Biomarkers Prev., November 1, 2002; 11(11): 1454 - 1458. [Abstract] [Full Text] [PDF]

				S. F. Choumenkovitch, J. Selhub, P. J. Bagley, N. Maeda, M. R. Nadeau, D. E. Smith, and S.-W. Choi In the Cystathionine {beta}-Synthase Knockout Mouse, Elevations in Total Plasma Homocysteine Increase Tissue S-Adenosylhomocysteine, but Responses of S-Adenosylmethionine and DNA Methylation Are Tissue Specific J. Nutr., August 1, 2002; 132(8): 2157 - 2160. [Abstract] [Full Text] [PDF]

				S. J. James, S. Melnyk, M. Pogribna, I. P. Pogribny, and M. A. Caudill Elevation in S-Adenosylhomocysteine and DNA Hypomethylation: Potential Epigenetic Mechanism for Homocysteine-Related Pathology J. Nutr., August 1, 2002; 132(8): 2361S - 2366. [Abstract] [Full Text] [PDF]

				S. Friso and S.-W. Choi Gene-Nutrient Interactions and DNA Methylation J. Nutr., August 1, 2002; 132(8): 2382S - 2387. [Abstract] [Full Text] [PDF]

				C. A. Cooney, A. A. Dave, and G. L. Wolff Maternal Methyl Supplements in Mice Affect Epigenetic Variation and DNA Methylation of Offspring J. Nutr., August 1, 2002; 132(8): 2393S - 2400. [Abstract] [Full Text] [PDF]

				B. C. Richardson Role of DNA Methylation in the Regulation of Cell Function: Autoimmunity, Aging and Cancer J. Nutr., August 1, 2002; 132(8): 2401S - 2405. [Abstract] [Full Text] [PDF]

				S.-W. Choi and J. B. Mason Folate Status: Effects on Pathways of Colorectal Carcinogenesis J. Nutr., August 1, 2002; 132(8): 2413S - 2418. [Abstract] [Full Text] [PDF]

				M. Ehrlich DNA Hypomethylation, Cancer, the Immunodeficiency, Centromeric Region Instability, Facial Anomalies Syndrome and Chromosomal Rearrangements J. Nutr., August 1, 2002; 132(8): 2424S - 2429. [Abstract] [Full Text] [PDF]

				S. J. Duthie, S. Narayanan, G. M. Brand, L. Pirie, and G. Grant Impact of Folate Deficiency on DNA Stability J. Nutr., August 1, 2002; 132(8): 2444S - 2449. [Abstract] [Full Text] [PDF]

				C. H. Halsted, J. A. Villanueva, A. M. Devlin, O. Niemela, S. Parkkila, T. A. Garrow, L. M. Wallock, M. K. Shigenaga, S. Melnyk, and S. J. James Folate deficiency disturbs hepatic methionine metabolism and promotes liver injury in the ethanol-fed micropig PNAS, July 23, 2002; 99(15): 10072 - 10077. [Abstract] [Full Text] [PDF]

				F Stickel, D Schuppan, E G Hahn, and H K Seitz Cocarcinogenic effects of alcohol in hepatocarcinogenesis Gut, July 1, 2002; 51(1): 132 - 139. [Abstract] [Full Text] [PDF]

				D. E. Epner Can Dietary Methionine Restriction Increase the Effectiveness of Chemotherapy in Treatment of Advanced Cancer? J. Am. Coll. Nutr., October 1, 2001; 20(90005): 443S - 449. [Abstract] [Full Text]

				H. TSUKAMOTO and S. C. LU Current concepts in the pathogenesis of alcoholic liver injury FASEB J, June 1, 2001; 15(8): 1335 - 1349. [Abstract] [Full Text] [PDF]

				C. A. Cooney Dietary Selenium and Arsenic Affect DNA Methylation J. Nutr., June 1, 2001; 131(6): 1871 - 1871. [Full Text]

				J. F Costello and C. Plass Methylation matters J. Med. Genet., May 1, 2001; 38(5): 285 - 303. [Abstract] [Full Text]

				K. Woodson, J. Mason, S.-W. Choi, T. Hartman, J. Tangrea, J. Virtamo, P. R. Taylor, and D. Albanes Hypomethylation of p53 in Peripheral Blood DNA Is Associated with the Development of Lung Cancer Cancer Epidemiol. Biomarkers Prev., January 1, 2001; 10(1): 69 - 74. [Abstract] [Full Text]

				C. D. Davis, E. O. Uthus, and J. W. Finley Dietary Selenium and Arsenic Affect DNA Methylation In Vitro in Caco-2 Cells and In Vivo in Rat Liver and Colon J. Nutr., December 1, 2000; 130(12): 2903 - 2909. [Abstract] [Full Text] [PDF]

				J E Klaunig, L M Kamendulis, and Y. Xu Epigenetic mechanisms of chemical carcinogenesis Human and Experimental Toxicology, October 1, 2000; 19(10): 543 - 555. [Abstract] [PDF]

				L. L. Stern, J. B. Mason, J. Selhub, and S.-W. Choi Genomic DNA Hypomethylation, a Characteristic of Most Cancers, Is Present in Peripheral Leukocytes of Individuals Who Are Homozygous for the C677T Polymorphism in the Methylenetetrahydrofolate Reductase Gene Cancer Epidemiol. Biomarkers Prev., August 1, 2000; 9(8): 849 - 853. [Abstract] [Full Text]

				S. C. Lu, Z.-Z. Huang, H. Yang, J. M. Mato, M. A. Avila, and H. Tsukamoto Changes in methionine adenosyltransferase and S-adenosylmethionine homeostasis in alcoholic rat liver Am J Physiol Gastrointest Liver Physiol, July 1, 2000; 279(1): G178 - G185. [Abstract] [Full Text] [PDF]

				W. D. Rees, S. M. Hay, D. S. Brown, C. Antipatis, and R. M. Palmer Maternal Protein Deficiency Causes Hypermethylation of DNA in the Livers of Rat Fetuses J. Nutr., July 1, 2000; 130(7): 1821 - 1826. [Abstract] [Full Text]

				J. Song, K.-J. Sohn, A. Medline, C. Ash, S. Gallinger, and Y.-I. Kim Chemopreventive Effects of Dietary Folate on Intestinal Polyps in Apc+/- Msh2-/- Mice Cancer Res., June 1, 2000; 60(12): 3191 - 3199. [Abstract] [Full Text]

				C. M. Ulrich, E. Kampman, J. Bigler, S. M. Schwartz, C. Chen, R. Bostick, L. Fosdick, S. A. A. Beresford, Y. Yasui, and J. D. Potter Lack of Association between the C677T MTHFR Polymorphism and Colorectal Hyperplastic Polyps Cancer Epidemiol. Biomarkers Prev., April 1, 2000; 9(4): 427 - 433. [Abstract] [Full Text]

				I. P. Pogribny, M. Pogribna, J. K. Christman, and S. J. James Single-Site Methylation within the p53 Promoter Region Reduces Gene Expression in a Reporter Gene Construct: Possible in Vivo Relevance during Tumorigenesis Cancer Res., February 1, 2000; 60(3): 588 - 594. [Abstract] [Full Text]

				S.-W. Choi, F. Stickel, H. W. Baik, Y.-I. Kim, H. K. Seitz, and J. B. Mason Chronic Alcohol Consumption Induces Genomic but Not p53-Specific DNA Hypomethylation in Rat Colon J. Nutr., November 1, 1999; 129(11): 1945 - 1950. [Abstract] [Full Text]

				S J. James, M. Pogribna, I. P Pogribny, S. Melnyk, R J. Hine, J. B Gibson, P. Yi, D. L Tafoya, D. H Swenson, V. L Wilson, et al. Abnormal folate metabolism and mutation in the methylenetetrahydrofolate reductase gene may be maternal risk factors for Down syndrome Am. J. Clinical Nutrition, October 1, 1999; 70(4): 495 - 501. [Abstract] [Full Text] [PDF]

				C. M. Ulrich, E. Kampman, J. Bigler, S. M. Schwartz, C. Chen, R. Bostick, L. Fosdick, S. A. A. Beresford, Y. Yasui, and J. D. Potter Colorectal Adenomas and the C677T MTHFR Polymorphism: Evidence for Gene-Environment Interaction? Cancer Epidemiol. Biomarkers Prev., August 1, 1999; 8(8): 659 - 668. [Abstract] [Full Text]

				T. Minamoto, M. Mai, and Z.'e. Ronai Environmental factors as regulators and effectors of multistep carcinogenesis Carcinogenesis, April 1, 1999; 20(4): 519 - 527. [Abstract] [Full Text] [PDF]

				R.-F. S. Huang, Y.-H. Ho, H.-L. Lin, J.-S. Wei, and T.-Z. Liu Folate Deficiency Induces a Cell Cycle-Specific Apoptosis in HepG2 Cells J. Nutr., January 1, 1999; 129(1): 25 - 31. [Abstract] [Full Text] [PDF]

				S. J. Duthie and A. Hawdon DNA instability (strand breakage, uracil misincorporation, and defective repair) is increased by folic acid depletion in human lymphocytes in vitro FASEB J, November 1, 1998; 12(14): 1491 - 1497. [Abstract] [Full Text]

				R. A. Jacob, D. M. Gretz, P. C. Taylor, S. J. James, I. P. Pogribny, B. J. Miller, S. M. Henning, and M. E. Swendseid Moderate Folate Depletion Increases Plasma Homocysteine and Decreases Lymphocyte DNA Methylation in Postmenopausal Women J. Nutr., July 1, 1998; 128(7): 1204 - 1212. [Abstract] [Full Text] [PDF]

				C. D. Jackson, C. Weis, B. J. Miller, and S. J. James Dietary Nucleotides: Effects on Cell Proliferation Following Partial Hepatectomy in Rats Fed NIH-31, AIN-76A, or Folate/Methyl-Deficient Diets J. Nutr., May 1, 1997; 127 (5): 834S - 834S. [Abstract] [Full Text] [PDF]

				G. L. WOLFF, D. W. ROBERTS, and K. G. MOUNTJOY Physiological consequences of ectopic agouti gene expression: the yellow obese mouse syndrome Physiol Genomics, November 11, 1999; 1(3): 151 - 163. [Abstract] [Full Text] [PDF]