Quantification of 5-methyl-2'-deoxycytidine in the DNA

• Authors: Małgorzata Giel-Pietraszuk , Małgorzata Insińska-Rak , Anna Golczak , Marek Sikorski , Mirosława Barciszewska , Jan Barciszewski
• Languages of publication: EN

Abstracts

EN

Methylation at position 5 of cytosine (Cyt) at the CpG sequences leading to formation of 5-methyl-cytosine (m5Cyt) is an important element of epigenetic regulation of gene expression. Modification of the normal methylation pattern, unique to each organism, leads to the development of pathological processes and diseases, including cancer. Therefore, quantification of the DNA methylation and analysis of changes in the methylation pattern is very important from a practical point of view and can be used for diagnostic purposes, as well as monitoring of the treatment progress. In this paper we present a new method for quantification of 5-methyl-2'deoxycytidine (m5C) in the DNA. The technique is based on conversion of m5C into fluorescent 3,N4-etheno-5-methyl-2'deoxycytidine (εm5C) and its identification by reversed-phase high-performance liquid chromatography (RP-HPLC). The assay was used to evaluate m5C concentration in DNA of calf thymus and peripheral blood of cows bred under different conditions. This approach can be applied for measuring of 5-methylcytosine in cellular DNA from different cells and tissues.

Keywords

EN

DNA methylation; 3,N4-etheno-5-methyl-2'deoxcytidine; fluorescence; RP-HPLC

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2015
• Volume: 62
• Issue: 2
• Pages: 281-286

Dates

published

2015

received

2015-02-09

revised

2015-04-29

accepted

2015-05-20

(unknown)

2015-06-22

Contributors

author

Małgorzata Giel-Pietraszuk

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

author

Małgorzata Insińska-Rak

• Faculty of Chemistry, Adam Mickiewicz University in Poznan, Poznań, Poland

author

Anna Golczak

• Faculty of Chemistry, Adam Mickiewicz University in Poznan, Poznań, Poland

author

Marek Sikorski

• Faculty of Chemistry, Adam Mickiewicz University in Poznan, Poznań, Poland

author

Mirosława Barciszewska

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

author

Jan Barciszewski

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

References

• Armstrong KM, Bermingham EN, Bassett SA, Treloar BP, Roy NC, Barnett MP (2011) Global DNA methylation measurement by HPLC using low amounts of DNA. Biotechnol J 6: 113-117.
• Ballestar E (2011) An introduction to epigenetics. Adv Exp Med Biol 711: 1-11.
• Barciszewska AM, Murawa D, Gawronska I, Murawa P, Nowak S, Barciszewska MZ (2007) Analysis of 5-methylcytosine in DNA of breast and colon cancer tissues. IUBMB Life 59: 765-770.
• Barrio JR, Sattsangi PD, Gruber BA, Dammann LG, Leonard NJ (1976) Species responsible for the fluorescence of 3,N4-ethenocytidine. J Am Chem Soc 98: 7408-7414.
• Barrio JR, Secrist JA 3rd, Leonard NJ (1972) Fluorescent adenosine and cytidine derivatives. Biochem Biophys Res Commun 46: 597-604.
• Bedell MA, Dyroff MC, Doerjer G, Swenberg JA (1986) Quantitation of etheno adducts by fluorescence detection. IARC Sci Publ 70: 425-436.
• Bezy V, Morin P, Couerbe P, Leleu G, Agrofoglio L (2005) Simultaneous analysis of several antiretroviral nucleosides in rat-plasma by high-performance liquid chromatography with UV using acetic acid/hydroxylamine buffer Test of this new volatile medium-pH for HPLC-ESI-MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 821: 132-143.
• Biernat J, Ciesiołka J, Górnicki P, Adamiak RW, Kryzosiak WJ, Wiewiórowski M (1978) New observations concerning the chloroacetaldehyde reaction with some tRNA constituents. Stable intermediates, kinetics and selectivity of the reaction. Nucleic Acids Res 5: 789-804.
• Feinberg AP, Tycko B (2004) The history of cancer epigenetics. Nat Rev Cancer 4: 143-153.
• Feinberg AP, Vogelstein B (1983) Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301: 89-92.
• Fraga MF, Agrelo R, Esteller M (2007) Cross-talk between aging and cancer: the epigenetic language. Ann NY Acad Sci 1100: 60-74.
• Fraga MF, Uriol E, Borja Diego L, Berdasco M, Esteller M, Canal MJ, Rodriguez R (2002) High-performance capillary electrophoretic method for the quantification of 5'-methyl 2'-deoxycytidine in genomic DNA: application to plant, animal and human cancer tissues. Electrophoresis 23: 1677-1681.
• Friso S, Choi SW, Dolnikowski GG, Selhub J (2002) A method to assess genomic DNA methylation using high-performance liquid chromatography/electrospray ionisation mass spectrometry. Anal Chem 74: 4526-4531.
• Gehrke CW, McCune RA, Gama-Sosa MA, Ehrlich M, Kuo KC (1984) Quantitative reversed-phase high-performance liquid chromatography of major and modified nucleosides in DNA. J Chromatogr 301: 199-219.
• Hermann A, Goyal R, Jeltsch A (2004) The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites. J Biol Chem 279: 48350-48359.
• Johnston JW, Harding K, Bremner DH, Souch G, Green J, Lynch PT, Grout B, Benson EE (2005) HPLC analysis of plant DNA methylation: a study of critical methodological factors. Plant Physiol Biochem 43: 844-853.
• Jones P, Baylin S (2002) The fundamental role of epigenetic events in cancer. Nat Rev Genet 3: 415-428.
• Jones PA (1996) DNA methylation errors and cancer. Cancer Res 56: 2463-2467.
• Jones PA, Takai D (2001) The role of DNA methylation in mammalian epigenetics. Science 293: 1068-1070.
• Kim JK, Samaranayake M, Pradhan S (2009) Epigenetic mechanisms in mammals. Cell Mol Life Sci 66: 596-612.
• Kochetkov NK, Shibaev VN, Kost AA (1971) New reaction of adenine and cytosine derivatives, potentially useful for nucleic acids modification. Tetrahedron Lett 12: 1993-1996.
• Kremer D, Metzger S, Kolb-Bachofen V, Kremer D (2012) Quantitative measurement of genome-wide DNA methylation by a reliable and cost-efficient enzyme-linked immunosorbent assay technique. Anal Biochem 422: 74-78.
• Krzyzosiak WJ, Biernat J, Ciesiołka J, Gulewicz K, Wiewiórowski M (1981) The reaction of adenine and cytosine residues in tRNA with chloroacetaldehyde. Nucleic Acids Res 9: 2841-2851.
• Kulis M, Esteller M (2010) DNA methylation and cancer. Adv Genet 70: 27-56.
• Kusmierek JT, Singer B (1982) Chloroacetaldehyde-treated ribo- and deoxyribopolynucleotides. 1. Reaction products. Biochemistry 21: 5717-5722
• Laird PW, Jaenisch R (1994) DNA methylation and cancer. Hum Mol Genet 3: 1487-1495.
• Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11: 204-220.
• Liu L, Wylie RC, Andrews LG, Tollefsbol TO (2003) Aging, cancer and nutrition: the DNA methylation connection. Mech Ageing Dev 124: 989-998.
• Ma H, Zhang W, Hu J, Yu Z, Chen Y, Luo Q, Shi X, Zhang Y, Song R, Zhou Z, Shen G, Fu J (2009) Analysis of global DNA methylation levels in human blood high performance liquid chromatography/tandem electrospray ionisation mass spectrometry. Eur J Mass Spectrom (Chichester, Eng) 15: 555-561.
• Magaña AA, Wrobel K, Caudillo YA, Zaina S, Lund G, Wrobel K (2008) High-performance liquid chromatography determination of 5-methyl-2'-deoxycytidine, 2'-deoxycytidine, and other deoxynucleosides and nucleosides in DNA digests. Anal Biochem 374: 378-385.
• Miller SA, Dykes DD, Polesky HF (1988) A simple salting out procedure for extracting DNA from nucleated cells. Nucleic Acids Res 16: 1215.
• Oakeley EJ (1999) DNA methylation analysis: a review of current methodologies. Pharmacol Ther 84: 389-400.
• Oakeley EJ, Podestà A, Jost JP (1997) Developmental changes in DNA methylation of the two tobacco pollen nuclei during mutation. Proc Natl Acad Sci USA 94: 11721-11725.
• Oakeley EJ, Schmitt F, Jost JP (1999) Quantification of 5-methylcytosine in DNA by the chloroacetaldehyde reaction. Biotechniques 27: 744-746, 748-750, 752.
• San Romerio A, Fiorillo G, Terruzzi I, Senesi P, Testolin G, Battezzati A (2005) Measurement of DNA methylation using stable isotope dilution and gas chromatography-mass spectrometry. Anal Biochem 336: 158-163.
• Spencer RD, Weber G, Tolman GL, Barrio JR, Leonard NJ (1974) Species responsible for the fluorescence of 1:N6-ethenoadenosine. Eur J Biochem 45: 425-429.
• Wagner I, Capesius I (1981) Determination of 5-methylcytosine from plant DNA by high-performance liquid chromatography. Biochim Biophys Acta 654: 52-56.
• Wilson VL, Smith RA, Autrup H, Krokan H, Musci DE, Le NN, Longoria J, Ziska D, Harris CC (1986) Genomic 5-methylcytosine determination by 32P-postlabeling analysis. Anal Biochem 152: 275-284.
• Yanez Barrientos E, Wrobel K, Lopez Torres A, Gutiérrez Corona F, Wrobel K (2013) Application of reversed-phase high-performance liquid chromatography with fluorimetric detection for simultaneous assessment of global DNA and total RNA methylation in Lepidium sativum: effect of plant exposure to Cd(II) and Se(IV). Anal Bioanal Chem 405: 2397-2404.

Identifiers

DOI

10.18388/abp.2015_988