Allele-specific, age-dependent and BMI-associated DNA methylation of human MCHR1

PLoS ONE

Volumn 6, Issue 5, 2011, Pages

  Stepanow, Stefanie ^a   Reichwald, Kathrin ^a   Huse, Klaus ^a   Gausmann, Ulrike ^a   Nebel, Almut ^b   Rosenstiel, Philip ^b   Wabitsch, Martin ^c   Fischer Posovszky, Pamela ^c   Platzer, Matthias ^a  

^a FRITZ LIPMANN INSTITUTE   (Germany)

^b UNIVERSITY OF KIEL   (Germany)

^c UNIVERSITY OF ULM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

5 AZA 2' DEOXYCYTIDINE; BISULFITE; MELANIN CONCENTRATING HORMONE RECEPTOR 1; AZACITIDINE; MCHR1 PROTEIN, HUMAN; MESSENGER RNA; SOMATOSTATIN RECEPTOR;

ADULT; ALLELE; ARTICLE; BODY MASS; CLINICAL ARTICLE; CPG ISLAND; DNA METHYLATION; FEMALE; GENE; GENE EXPRESSION; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC REGULATION; HAPLOTYPE; HETEROZYGOSITY; HUMAN; HUMAN CELL; LYMPHOBLASTOID CELL; MALE; MCHR1 GENE; NUCLEOTIDE SEQUENCE; OBESITY; PHENOTYPE; AGED; AGING; CELL LINE; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETICS; HUMAN GENOME; METABOLISM; MIDDLE AGED;

RODENTIA;

ADULT; AGED; AGING; ALLELES; AZACITIDINE; BODY MASS INDEX; CELL LINE; CPG ISLANDS; DNA METHYLATION; GENE EXPRESSION REGULATION; GENOME, HUMAN; HUMANS; MALE; MIDDLE AGED; RECEPTORS, SOMATOSTATIN; RNA, MESSENGER; YOUNG ADULT;

EID: 79957551879     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0017711     Document Type: Article

References (57)

1. Bird A, (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16: 6-21.
2. Robertson KD, (2005) DNA methylation and human disease. Nat Rev Genet 6: 597-610.
3. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
4. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. (2001) The sequence of the human genome. Science 291: 1304-1351.
5. Jones PA, Takai D, (2001) The role of DNA methylation in mammalian epigenetics. Science 293: 1068-1070.
6. Coulondre C, Miller JH, Farabaugh PJ, Gilbert W, (1978) Molecular basis of base substitution hotspots in Escherichia coli. Nature 274: 775-780.
7. Bird A, Taggart M, Frommer M, Miller OJ, Macleod D, (1985) A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 40: 91-99.
8. Cross SH, Bird AP, (1995) CpG islands and genes. Curr Opin Genet Dev 5: 309-314.
9. Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, et al. (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27: 361-368.
10. Ferguson-Smith AC, Surani MA, (2001) Imprinting and the epigenetic asymmetry between parental genomes. Science 293: 1086-1089.
11. Tilghman SM, (1999) The sins of the fathers and mothers: genomic imprinting in mammalian development. Cell 96: 185-193.
12. Heard E, Disteche CM, (2006) Dosage compensation in mammals: fine-tuning the expression of the X chromosome. Genes Dev 20: 1848-1867.
13. Kerkel K, Spadola A, Yuan E, Kosek J, Jiang L, et al. (2008) Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat Genet 40: 904-908.
14. Yamada Y, Watanabe H, Miura F, Soejima H, Uchiyama M, et al. (2004) A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q. Genome Res 14: 247-266.
15. Zhang Y, Rohde C, Reinhardt R, Voelcker-Rehage C, Jeltsch A, (2009) Non-imprinted allele-specific DNA methylation on human autosomes. Genome Biol 10: R138.
16. Zhang Y, Rohde C, Tierling S, Jurkowski TP, Bock C, et al. (2009) DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution. PLoS Genet 5: e1000438.
17. Schalkwyk LC, Meaburn EL, Smith R, Dempster EL, Jeffries AR, et al. Allelic skewing of DNA methylation is widespread across the genome. Am J Hum Genet 86: 196-212.
18. Gimelbrant A, Hutchinson JN, Thompson BR, Chess A, (2007) Widespread monoallelic expression on human autosomes. Science 318: 1136-1140.
19. Serre D, Gurd S, Ge B, Sladek R, Sinnett D, et al. (2008) Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet 4: e1000006.
20. Zakharova IS, Shevchenko AI, Zakian SM, (2009) Monoallelic gene expression in mammals. Chromosoma 118: 279-290.
21. Mill J, Tang T, Kaminsky Z, Khare T, Yazdanpanah S, et al. (2008) Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet 82: 696-711.
22. Esteller M, (2008) Epigenetics in cancer. N Engl J Med 358: 1148-1159.
23. Bjornsson HT, Sigurdsson MI, Fallin MD, Irizarry RA, Aspelund T, et al. (2008) Intra-individual change over time in DNA methylation with familial clustering. Jama 299: 2877-2883.
24. Christensen BC, Houseman EA, Marsit CJ, Zheng S, Wrensch MR, et al. (2009) Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet 5: e1000602.
25. Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, et al. (2005) Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci U S A 102: 10604-10609.
26. Fraga MF, Esteller M, (2007) Epigenetics and aging: the targets and the marks. Trends Genet 23: 413-418.
27. Gravina S, Vijg J, (2010) Epigenetic factors in aging and longevity. Pflugers Arch 459: 247-258.
28. Abbott CR, Kennedy AR, Wren AM, Rossi M, Murphy KG, et al. (2003) Identification of hypothalamic nuclei involved in the orexigenic effect of melanin-concentrating hormone. Endocrinology 144: 3943-3949.
29. Borowsky B, Durkin MM, Ogozalek K, Marzabadi MR, DeLeon J, et al. (2002) Antidepressant, anxiolytic and anorectic effects of a melanin-concentrating hormone-1 receptor antagonist. Nat Med 8: 825-830.
30. Luthin DR, (2007) Anti-obesity effects of small molecule melanin-concentrating hormone receptor 1 (MCHR1) antagonists. Life Sci 81: 423-440.
31. Marsh DJ, Weingarth DT, Novi DE, Chen HY, Trumbauer ME, et al. (2002) Melanin-concentrating hormone 1 receptor-deficient mice are lean, hyperactive, and hyperphagic and have altered metabolism. Proc Natl Acad Sci U S A 99: 3240-3245.
32. Bell CG, Meyre D, Samson C, Boyle C, Lecoeur C, et al. (2005) Association of melanin-concentrating hormone receptor 1 5′ polymorphism with early-onset extreme obesity. Diabetes 54: 3049-3055.
33. Gibson WT, Pissios P, Trombly DJ, Luan J, Keogh J, et al. (2004) Melanin-concentrating hormone receptor mutations and human obesity: functional analysis. Obes Res 12: 743-749.
34. Kring SLL II, Holst C, Toubro S, Hansen T, Astrup A, et al. (2008) Genotype-Phenotype Associations in Obesity Dependent on Definition of the Obesity Phenotype. Obesity Facts 1: 138-145.
35. Wermter AK, Reichwald K, Buch T, Geller F, Platzer C, et al. (2005) Mutation analysis of the MCHR1 gene in human obesity. Eur J Endocrinol 152: 851-862.
36. Rutanen J, Pihlajamaki J, Vanttinen M, Salmenniemi U, Ruotsalainen E, et al. (2007) Single nucleotide polymorphisms of the MCHR1 gene do not affect metabolism in humans. Obesity (Silver Spring) 15: 2902-2907.
37. Ling C, Poulsen P, Simonsson S, Ronn T, Holmkvist J, et al. (2007) Genetic and epigenetic factors are associated with expression of respiratory chain component NDUFB6 in human skeletal muscle. J Clin Invest 117: 3427-3435.
38. Gardiner-Garden M, Frommer M, (1987) CpG islands in vertebrate genomes. J Mol Biol 196: 261-282.
39. Dausset J, Cann H, Cohen D, Lathrop M, Lalouel JM, et al. (1990) Centre d'etude du polymorphisme humain (CEPH): collaborative genetic mapping of the human genome. Genomics 6: 575-577.
40. Bradley RL, Kokkotou EG, Maratos-Flier E, Cheatham B, (2000) Melanin-concentrating hormone regulates leptin synthesis and secretion in rat adipocytes. Diabetes 49: 1073-1077.
41. Morison IM, Paton CJ, Cleverley SD, (2001) The imprinted gene and parent-of-origin effect database. Nucleic Acids Res 29: 275-276.
42. Bennett-Baker PE, Wilkowski J, Burke DT, (2003) Age-associated activation of epigenetically repressed genes in the mouse. Genetics 165: 2055-2062.
43. Boks MP, Derks EM, Weisenberger DJ, Strengman E, Janson E, et al. (2009) The relationship of DNA methylation with age, gender and genotype in twins and healthy controls. PLoS One 4: e6767.
44. Knight JC, (2004) Allele-specific gene expression uncovered. Trends Genet 20: 113-116.
45. Klose RJ, Bird AP, (2006) Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 31: 89-97.
46. Chen Y, Hu C, Hsu CK, Zhang Q, Bi C, et al. (2002) Targeted disruption of the melanin-concentrating hormone receptor-1 results in hyperphagia and resistance to diet-induced obesity. Endocrinology 143: 2469-2477.
47. Bradley RL, Mansfield JP, Maratos-Flier E, Cheatham B, (2002) Melanin-concentrating hormone activates signaling pathways in 3T3-L1 adipocytes. Am J Physiol Endocrinol Metab 283: E584-592.
48. Schwartz MW, Woods SC, Porte D Jr, Seeley RJ, Baskin DG, (2000) Central nervous system control of food intake. Nature 404: 661-671.
49. Krawczak M, Nikolaus S, von Eberstein H, Croucher PJ, El Mokhtari NE, et al. (2006) PopGen: population-based recruitment of patients and controls for the analysis of complex genotype-phenotype relationships. Community Genet 9: 55-61.
50. Ewing B, Green P, (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
51. Ewing B, Hillier L, Wendl MC, Green P, (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185.
52. Bonfield JK, Smith K, Staden R, (1995) A new DNA sequence assembly program. Nucleic Acids Res 23: 4992-4999.
53. Takai D, Jones PA, (2003) The CpG island searcher: a new WWW resource. In Silico Biol 3: 235-240.
54. Li LC, Dahiya R, (2002) MethPrimer: designing primers for methylation PCRs. Bioinformatics 18: 1427-1431.
55. Bock C, Reither S, Mikeska T, Paulsen M, Walter J, et al. (2005) BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics 21: 4067-4068.
56. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG, (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
57. Bain BJ, England JM, (1975) Normal Haematological Values: Sex Differences in Neutrophil Count. British Medical Journal 1: 306-309.