Development and Evaluation of Epigenetic Regulation of Sucrose Metabolism in Saccharomyces cerevisiae by Using COBRA Technique and Selected CpG Islands in HXT10 and SUC2 genes

Abstract

Epigenetics mostly focuses on heritable changes in gene expression that does not contain changes to the underlying primary DNA sequences; an alteration in phenotype without an alteration in genotype. Among various cellular mechanisms, especially DNA methylation plays a central role in many epigenetic processes. Therefore, it has been the most studied epigenetic mechanism and many special techniques for assessment of changes in DNA methylation patterns have been developed. Combined bisulfite restriction analysis (COBRA) is one of these commonly used techniques. Although many studies have been conducted to get information about epigenetic regulation mechanisms in mammalian cell by using COBRA, there is still limited information on the the epigenetic programs and related pathways in other organisms.  

Keywords

• COBRA,DNA methylation

References

1. [1] FREİDBERG, J. (2007). Plasma Physics and Fusion Energy. Cambridge university press. 25-30.
2. [2] Ho S, Tang W, 2007. Techiques used in studies of epigenome dysregulation due to aberrant DNA methylation: An emphasis on fetal-based adult diseases. Reproductive Toxicology. 23: 267-282.
3. [3] Dalton VS, Kolshus E, McLoughlin DM, 2014. Epigenetics and depression: return of the repressed. Journal of Affective Disorders. 155: 1-12.
4. [4] Gulluce M, Alaylar B, Koc TY, Karadayi M, 2014. Epigenetics: An Innovative Approach for Biotechnology and Food Science. Internetional Journal of Bioscience, Biochemistry and Bioinformatics. 4(3): 195-199.
5. [5] Choi SW, Friso S, 2010. Epigenetics: A New Bridge between Nutrition and Health. Advances in Nutrition An International Review Journal. 1: 8-16.
6. [6] Tollefsbol TO, 2011. Chapter 1:Epigenetics: The New Science of Genetics. Handbook of Epigenetics: The New Molecular and Medical Genetics, Ed: T.O. Tollefsbol. Academic Press, San Diego. 1-6.
7. [7] Bird A, 2002. DNA methylation patterns and epigenetic memory. Cold Spring Harbor Laboratory Press. 6-21.
8. [8] Holliday R, 2006. Epigenetics: A Historical overview. Epigenetics, 1: 76-80.

9. [9] İzmirli M, 2013. Epigenetic Mechanisms and Approaches in Cancer Treatments. Van Medical Journal. 20(1): 48-51.
10. [10] Janitz K, Janitz M, 2011. Chapter 12: Assessing Epigenetic Information. Handbook of Epigenetics: The New Molecular and Medical Genetics, Ed: T.O. Tollefsbol. Academic Press, San Diego. 173-181.
11. [11] Taherzadeh MJ, Fox M, Hjorth H, Edebo L, 2003. Production of mycelium biomass and ethanol from paper pulp sulfite liquor by Rhizopus oryzae. Bioresource Technology. 88: 167-177.
12. [12] Alaylar B, 2014. Determination of epigenetic changes depending on presence of sucrose and glucuse in related gene regions of Saccharomyces cerevisiae. Master Thesis, Atatürk University Institute of Natural and Applied Sciences. 1-58.
13. [13] Egger G, Liang G, Aparicio A, Jones PA, 2004. Epigenetics in human disease and prospects for epigenetic therapy. Nature. 429: 457-463.
14. [14] Taylor KH, Kramer RS, Davis JW, Guo J, Duff DJ, Xu D, Caldwell CW, Shi H, 2007. Ultradeep Bisulfite Sequencing Analysis of DNA Methylation Patterns in Multiple Gene Promoters by 454 Sequencing. Cancer Research. 67: 8511-8518.
15. [15] Kristensen LS, Hansen LL, 2009. PCR-Based Methods for Detecting Single-Locus DNA Methylation Biomarkers in Cancer Diagnostics, Prognostics and Response to Treatment. Clinical Chemistry. 55(8): 1471-1483.
16. [16] Karpinski P, Szmida E, Misiak B, Ramsey D, Leszczynski P, Bebenek M, Sedziak T, Grzebieniak Z, Jonkisz A, Lebioda A, Sasiadek MM, 2012. Assessment of Three Epigenotypes in Colorectal Cancer by Combined Bisulfite Restriction Analysis. Molecular Carcinogenesis. 51: 1003-1008.
17. [17] Xiong Z, Laird PW, 1997. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Research. 25(12): 2532-2534.
18. [18] Eads CA, Laird PW, 2002. Chapter 7: Combined Bisülfite Restriction Analysis (COBRA). Methods in Molecular Biology: DNA Methylation Protocols, Ed: K.I.Mills and B.H. Ramsahoye. Humana Press Inc. 200: 71-85.
19. [19] Fraga MF, Esteller M, 2002. DNA Methylation: A profile of Methods and Applications. Biotechniques. 33: 632-649.
20. [20] Brena RM, Auer H, Kornacker K, Hackanson B, Raval A, Byrd JC, Plass C, 2006. Accurate quantification of DNA methylation using combined bisulfite restriction analysis coupled with the Agilent 2100 Bioanalyser platform. Nucleic Acid Research. 34(3): 1-8.