Abstract
Epigenetic alterations regulate the utilization of the genome by permitting or inhibiting access of transcription factors and associated complexes. Although there are several different types of epigenetic alterations, such as acetylation and methylation of histone tails, the one which has been the most extensively studied is DNA-methylation, wherein the cytosine residue in a CpG dinucleotide is methylated.
Luminometric Methylation Assay (LUMA) enables researchers to study global methylation by using methylation-sensitive restriction enzymes followed by Pyrosequencing® which quantitates the number of cuts in the genome relative to an internal standard. The relative measurement of global methylation levels is simple and enables up to 96 samples to be analyzed at the same time.
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References
Fraga, M. F., and Esteller, M. (2002) DNA methylation: a profile of methods and applications, Biotechniques 33: 632, 4, 6–49.
Cedar, H., Solage, A., Glaser, G., and Razin, A. (1979) Direct detection of methylated cytosine in DNA by use of the restriction enzyme MspI, Nucleic Acids Res 6: 2125–32.
Andersen, C. L., Koch, J., and Kjeldsen, E. (1998) CpG islands detected by self-primed in situ labeling (SPRINS), Chromosoma 107: 260–6.
Liang, G., Gonzalgo, M. L., Salem, C., and Jones, P. A. (2002) Identification of DNA methylation differences during tumorigenesis by methylation-sensitive arbitrarily primed polymerase chain reaction, Methods 27: 150–5.
Azhikina, T., Gainetdinov, I., Skvortsova, Y., Batrak, A., Dmitrieva, N., and Sverdlov, E. (2004) Non-methylated Genomic Sites Coincidence Cloning (NGSCC): an approach to large scale analysis of hypomethylated CpG patterns at predetermined genomic loci, Mol Genet Genomics 271: 22–32.
Yan, P. S., Wei, S. H., and Huang, T. H. (2002) Differential methylation hybridization using CpG island arrays, Methods Mol Biol 200: 87–100.
Chen, C. M., Chen, H. L., Hsiau, T. H., Hsiau, A. H., Shi, H., Brock, G. J., Wei, S. H., Caldwell, C. W., Yan, P. S., and Huang, T. H. (2003) Methylation target array for rapid analysis of CpG island hypermethylation in multiple tissue genomes, Am J Pathol 163: 37–45.
Ammerpohl, O., Martin-Subero, J. I., Richter, J., Vater, I., and Siebert, R. (2009) Hunting for the 5th base: Techniques for analyzing DNA methylation, Biochim Biophys Acta 1790: 847–62.
Pogribny, I., Yi, P., and James, S. J. (1999) A sensitive new method for rapid detection of abnormal methylation patterns in global DNA and within CpG islands, Biochem Biophys Res Commun 262: 624–8.
Fujiwara, H., and Ito, M. (2002) Nonisotopic cytosine extension assay: a highly sensitive method to evaluate CpG island methylation in the whole genome, Anal Biochem 307: 386–9.
Barres, R., Osler, M. E., Yan, J., Rune, A., Fritz, T., Caidahl, K., Krook, A., and Zierath, J. R. (2009) Non-CpG Methylation of the PGC-1 alpha Promoter through DNMT3B Controls Mitochondrial Density, Cell Metabolism 10: 189–98.
El-Maarri, O., Becker, T., Junen, J., Manzoor, S. S., Diaz-Lacava, A., Schwaab, R., Wienker, T., and Oldenburg, J. (2007) Gender specific differences in levels of DNA methylation at selected loci from human total blood: a tendency toward higher methylation levels in males, Human Genetics 122: 505–14.
El-Maarri, O., Kareta, M. S., Mikeska, T., Becker, T., Diaz-Lacava, A., Junen, J., Nusgen, N., Behne, F., Wienker, T., Waha, A., Oldenburg, J., and Chedin, F. (2009) A systematic search for DNA methyltransferase polymorphisms reveals a rare DNMT3L variant associated with subtelomeric hypomethylation, Human Molecular Genetics 18: 1755–68.
Fish, J. E., Yan, M. S., Matouk, C. C., Bernard, R. S., Ho, J. J. D., Gavryushova, A., Srivastava, D., and Marsden, P. A. (2010) Hypoxic Repression of Endothelial Nitric-oxide Synthase Transcription Is Coupled with Eviction of Promoter Histones, Journal of Biological Chemistry 285: 810–26.
Perisic, T., Zimmermann, N., Kirmeier, T., Asmus, M., Tuorto, F., Uhr, M., Holsboer, F., Rein, T., and Zschocke, J. (2010) Valproate and Amitriptyline Exert Common and Divergent Influences on Global and Gene Promoter-Specific Chromatin Modifications in Rat Primary Astrocytes, Neuropsychopha-rmacology 35: 792–805.
Pilsner, J. R., Lazarus, A. L., Nam, D. H., Letcher, R. J., Sonne, C., Dietz, R., and Basu, N. (2010) Mercury-associated DNA hypomethylation in polar bear brains via the LUminometric Methylation Assay: a sensitive method to study epigenetics in wildlife, Molecular Ecology 19: 307–14.
Romermann, D., Hasemeier, B., Metzig, K., Gohring, G., Schlegelberger, B., Langer, F., Kreipe, H., and Lehmann, U. (2008) Global increase in DNA methylation in patients with myelodysplastic syndrome, Leukemia 22: 1954–6.
Sadeghi, R. N., Zojaji, H., Mohebbi, S. R., Chiani, M., Vahedi, M., Mirsattari, D., Molaei, M., Mashayekhi, R., and Zali, M. R. (2009) Evaluation of Global Genome Methylation in Gastritis Lesion and its Correlation With Clinicopatological Findings, Oncology Research 17: 549–58.
Thompson, R. F., Atzmon, G., Gheorghe, C., Liang, H. Q., Lowes, C., Greally, J. M., and Barzilai, N. (2010) Tissue-specific dysregulation of DNA methylation in aging, Aging Cell 9: 506–18.
Thompson, R. F., Fazzari, M. J., and Greally, J. M. (2010) Experimental approaches to the study of epigenomic dysregulation in ageing, Experimental Gerontology 45: 255–68.
Zechner, U., Nolte, J., Wolf, M., Shirneshan, K., El Hajj, N., Weise, D., Kaltwasser, B., Zovoilis, A., Haaf, T., and Engel, W. (2009) Comparative methylation profiles and telomerase biology of mouse multipotent adult germline stem cells and embryonic stem cells, Molecular Human Reproduction 15: 345–53.
Karimi, M., Johansson, S., and Ekstrom, T. J. (2006) Using LUMA: a Luminometric-based assay for global DNA-methylation, Epigenetics 1: 45–8.
Ronaghi, M. (2001) Pyrosequencing sheds light on DNA sequencing, Genome Res 11: 3–11.
Bjornsson, H. T., Sigurdsson, M. I., Fallin, M. D., Irizarry, R. A., Aspelund, T., Cui, H., Yu, W., Rongione, M. A., Ekström, T. J., Harris, T. B., Launer, L. J., Eiriksdottir, G., Leppert, M. F., Sapienza, C., Gudnason, V., and Feinberg, A. P. (2008) Intra-individual change over time in DNA methylation with familial clustering, JAMA 299: 2877–83.
Fazzari, M. J., and Greally, J. M. (2004) Epigenomics: beyond CpG islands, Nat Rev Genet 5: 446–55.
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Karimi, M., Luttropp, K., Ekström, T.J. (2011). Global DNA Methylation Analysis Using the Luminometric Methylation Assay. In: Tollefsbol, T. (eds) Epigenetics Protocols. Methods in Molecular Biology, vol 791. Humana Press. https://doi.org/10.1007/978-1-61779-316-5_11
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DOI: https://doi.org/10.1007/978-1-61779-316-5_11
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