Bioinformatics analysis of abnormal DNA methylation in muscle samples from monozygotic twins discordant for type 2 diabetes

Molecular Medicine Reports

Volumn 12, Issue 1, 2015, Pages 351-356

  Liu, Fei ^a   Sun, Qianqian ^a   Wang, Lingxiao ^b   Nie, Shuangshuang ^c   Li, Jun ^a  

^a SICHUAN UNIVERSITY   (China)

^b The Fifth People's Hospital of Chengdu   (China)

^c SICHUAN UNIVERSITY   (China)

Author keywords

Differentially methylated genes; Gene ontology enrichment analysis; Transcription factors; Type 2 diabetes

Indexed keywords

ACYLTRANSFERASE; HOMEODOMAIN PROTEIN; METHYL CPG BINDING PROTEIN 2; N ACETYLTRANSFERASE 6; PHOSPHOLIPASE A2 GROUP XIIB; PROTEIN; SIRTUIN 1; TFAP4 PROTEIN; TFEB PROTEIN; TRANSCRIPTION FACTOR NFAT; TRANSCRIPTION FACTOR RUNX1; UNCLASSIFIED DRUG; ZINC FINGER E BOX BINDING HOMEOBOX 1; BASIC HELIX LOOP HELIX LEUCINE ZIPPER TRANSCRIPTION FACTOR; REPIN1 PROTEIN, HUMAN; TFEB PROTEIN, HUMAN; TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; BIOINFORMATICS; CONTROLLED STUDY; DNA DETERMINATION; DNA METHYLATION; DNA RECOMBINATION; GENE IDENTIFICATION; GENETIC REASSORTMENT; HUMAN; HUMAN TISSUE; MONOZYGOTIC TWINS; NON INSULIN DEPENDENT DIABETES MELLITUS; PROMOTER REGION; TRANSCRIPTION INITIATION SITE; BIOLOGY; CHEMISTRY; CPG ISLAND; GENETIC DATABASE; GENETICS; METABOLISM; MUSCLE; PATHOLOGY;

BASIC HELIX-LOOP-HELIX LEUCINE ZIPPER TRANSCRIPTION FACTORS; BINDING SITES; COMPUTATIONAL BIOLOGY; CPG ISLANDS; DATABASES, GENETIC; DIABETES MELLITUS, TYPE 2; DNA METHYLATION; HUMANS; MUSCLES; PROMOTER REGIONS, GENETIC; TRANSCRIPTION FACTORS; TWINS, MONOZYGOTIC;

EID: 84926632671     PISSN: 17912997     EISSN: 17913004     Source Type: Journal    
DOI: 10.3892/mmr.2015.3452     Document Type: Article

References (31)

1. Parving H-H, Brenner BM, McMurray JJ, et al; ALTITUDE Investigators: Cardiorenal end points in a trial of aliskiren for type 2 diabetes. N Engl J Med 367: 2204-2213, 2012.
2. Kitada M and Koya D: SIRT1 in type 2 diabetes: Mechanisms and therapeutic potential. Diabetes Metab J 37: 315-325, 2013.
3. Kahn SE: The relative contributions of insulin resistance and beta-cell dysfunction to the pathophysiology of Type 2 diabetes. Diabetologia 46: 3-19, 2003.
4. Spranger J, Kroke A, Möhlig M, et al: Adiponectin and protection against type 2 diabetes mellitus. Lancet 361: 226-228, 2003.
5. Hofsø D, Jenssen T, Hager H, Røislien J and Hjelmesaeth J: Fasting plasma glucose in the screening for type 2 diabetes in morbidly obese subjects. Obes Surg 20: 302-307, 2010.
6. Zhang P, Zhang X, Brown J, et al: Global healthcare expenditure on diabetes for 2010 and 2030. Diabetes Res Clin Pract 87: 293-301, 2010.
7. Liebl A, Mata M and Eschwège E; ODE-2 Advisory Board: Evaluation of risk factors for development of complications in Type II diabetes in Europe. Diabetologia 45: S23-S28, 2002.
8. Sjöström L, Lindroos A-K, Peltonen M, et al; Swedish Obese Subjects Study Scientific Group: Lifestyle, diabetes, and cardiovascular risk factors 10 years after bariatric surgery. N Engl J Med 351: 2683-2693, 2004.
9. Barres R and Zierath JR: DNA methylation in metabolic disorders. Am J Clin Nutr 93: 897S-900S, 2011.
10. Takizawa T, Nakashima K, Namihira M, et al: DNA methylation is a critical cell-intrinsic determinant of astrocyte differentiation in the fetal brain. Dev Cell 1: 749-758, 2001.
11. Robertson KD: DNA methylation and human disease. Nat Rev Genet 6: 597-610, 2005.
12. Rönn T, Poulsen P, Hansson O, et al: Age influences DNA methylation and gene expression of COX7A1 in human skeletal muscle. Diabetologia 51: 1159-1168, 2008.
13. Ling C, Poulsen P, Carlsson E, et al: Multiple environmental and genetic factors influence skeletal muscle PGC-1α and PGC-1β gene expression in twins. J Clin Invest 114: 1518-1526, 2004.
14. Ling C, Poulsen P, Simonsson S, et al: Genetic and epigenetic factors are associated with expression of respiratory chain component NDUFB6 in human skeletal muscle. J Clin Invest 117: 3427-3435, 2007.
15. Jensen CB, Storgaard H, Madsbad S, Richter EA and Vaag AA: Altered skeletal muscle fiber composition and size precede whole-body insulin resistance in young men with low birth weight. J Clin Endocrinol Metab 92: 1530-1534, 2007.
16. Barrett T, Wilhite SE, Ledoux P, et al: NCBI GEO: archive for functional genomics data sets - update. Nucleic Acids Res 41: D991-D995, 2013.
17. Du P, Zhang X, Huang CC, et al: Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics 11: 587, 2010.
18. Da Wei Huang BTS, Sherman BT and Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57, 2009.
19. Dubchak I, Munoz M, Poliakov A, et al: Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data. Bioinformatics 29: 2059-2061, 2013.
20. Wingender E, Dietze P, Karas H, and Knüppel R: TRANSFAC: A database on transcription factors and their DNA binding sites. Nucleic Acids Res 24: 238-241, 1996.
21. Kume S, Uzu T, Kashiwagi A and Koya D: SIRT1, a calorie restriction mimetic, in a new therapeutic approach for type 2 diabetes mellitus and diabetic vascular complications. Endocr Metab Immune Disord Drug Targets 10: 16-24, 2010.
22. Sharma S, Misra CS, Arumugam S, et al: Antidiabetic activity of resveratrol, a known SIRT1 activator in a genetic model for type 2 diabetes. Phytother Res 25: 67-73, 2011.
23. Bordone L, Motta MC, Picard F, et al: Sirt1 regulates insulin secretion by repressing UCP2 in pancreatic β cells. PLoS Biol 4: e31, 2006.
24. Bhakta S, Besra GS, Upton AM, et al: Arylamine N-acetyltransferase is required for synthesis of mycolic acids and complex lipids in Mycobacterium bovis BCG and represents a novel drug target. J Exp Med 199: 1191-1199, 2004.
25. Aljakna A, Choi S, Savage H, et al: Pla2g12b and Hpn are genes identified by mouse ENU mutagenesis that affect HDL cholesterol. PLoS One 7: e43139, 2012.
26. Blum M, Grant DM, Mcbride W, Heim M and Meyer UA: Human arylamine N-acetyltransferase genes: isolation, chromosomal localization, and functional expression. DNA Cell Biol 9: 193-203, 1990.
27. Heit JJ, Apelqvist AA, Gu X, et al: Calcineurin/NFAT signalling regulates pancreatic β -cell growth and function. Nature 443: 345-349, 2006.
28. Papadopoulou V, Postigo A, Sánchez-Tilló E, Porter AC and Wagner SD: ZEB1 and CtBP form a repressive complex at a distal promoter element of the BCL6 locus. Biochem J 427: 541-550, 2010.
29. Karnik SK, Chen H, McLean GW, et al: Menin controls growth of pancreatic β-cells in pregnant mice and promotes gestational diabetes mellitus. Science 318: 806-809, 2007.
30. Nan X, Ng HH, Johnson CA, et al: Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393: 386-389, 1998.
31. Li E, Beard C and Jaenisch R: Role for DNA methylation in genomic imprinting. Nature 366: 362-365, 1993.