Role for tissue-dependent methylation differences in the expression of FOXE1 in nontumoral thyroid glands

Journal of Clinical Endocrinology and Metabolism

Volumn 99, Issue 6, 2014, Pages

  Abu Khudir, Rasha ^a,b   Magne, Fabien ^a   Chanoine, Jean Pierre ^c   Deal, Cheri ^a   Van Vliet, Guy ^a   Deladoëy, Johnny ^a,b  

^a UNIVERSITY OF MONTREAL   (Canada)

^b UNIVERSITÉ DE MONTRÉAL   (Canada)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; DNA SEQUENCE; ECTOPIC THYROID GLAND; FOXE1 GENE; GENE; GENE EXPRESSION; GENE MUTATION; HUMAN; HUMAN CELL; HUMAN TISSUE; IN VITRO STUDY; LEUKOCYTE; NKX2 1 GENE; NONHUMAN; PAX8 GENE; PRIORITY JOURNAL; PROMOTER REGION; RAT; THYROID GLAND; TISSUE SPECIFICITY; TRANSCRIPTION INITIATION SITE;

ANIMALS; CELLS, CULTURED; CPG ISLANDS; DNA METHYLATION; FORKHEAD TRANSCRIPTION FACTORS; GENE EXPRESSION REGULATION; HUMANS; K562 CELLS; LEUKOCYTES; ORGAN SPECIFICITY; PROMOTER REGIONS, GENETIC; RATS; THYROID GLAND;

EID: 84902324944     PISSN: 0021972X     EISSN: 19457197     Source Type: Journal    
DOI: 10.1210/jc.2013-4414     Document Type: Article

References (56)

1. Dathan N, Parlato R, Rosica A, De Felice M, Di Lauro R. Distribution of the titf2/foxe1 gene product is consistent with an important role in the development of foregut en doderm, palate, and hair. Dev Dyn. 2002;224:450-456.
2. De Felice M, Ovitt C, Biffali E, et al. A mouse model for hereditary thyroid dysgenesis and cleft palate. Nat Genet. 1998;19:395-398.
3. Bamforth JS, Hughes IA, Lazarus JH, Weaver CM, Harper PS. Congenital hypothyroidism, spiky hair, and cleft palate. J Med Genet. 1989;26:49-51.
4. Clifton-Bligh RJ, Wentworth JM, Heinz P, et al. Mutation of the gene encoding human TTF-2 associated with thyroid agenesis, cleft palate and choanal atresia. Nat Genet. 1998;19:399-401.
5. Castanet M, Park SM, Smith A, et al. A novel loss-of-function mutation in TTF-2 is associated with congenital hypothyroidism, thyroid agenesis and cleft palate. Hum Mol Genet. 2002;11:2051-2059.
6. Parlato R,Rosica A,Rodriguez-Mallon A,et al An integrated regulatory network controlling survival and migration in thyroid organogenesis Dev Biol. 2004 276 464-475.
7. Delado ey J, Ruel J, Giguere Y, Van Vliet G. Is the incidence of congenital hypothyroidism really increasing? A 20-year retrospective population-based study in Quebec. J Clin Endocrinol Metab. 2011;96:2422-2429.
8. Pohlenz J, Dumitrescu A, Zundel D, et al. Partial deficiency of thyroid transcription factor 1 produces predominantly neurological defects in humans and mice. J Clin Invest. 2002;109:469-473.
9. Krude H, Schutz B, Biebermann H, et al. Choreoathetosis, hypothyroidism, and pulmonary alterations due to human NKX2-1 haploinsufficiency. J Clin Invest. 2002;109:475-480.
10. Macchia PE, Lapi P, Krude H, et al.PAX8mutations associated with congenital hypothyroidism caused by thyroid dysgenesis. Nat Genet. 1998;19:83-86.
11. Dentice M, Cordeddu V, Rosica A, et al. Missense mutation in the transcription factor NKX2-5: a novel molecular event in the pathogenesis of thyroid dysgenesis. J Clin Endocrinol Metab. 2006;91: 1428-1433.
12. Narumi S, Muroya K, Asakura Y, Adachi M, Hasegawa T. Transcription factor mutations and congenital hypothyroidism: systematic genetic screening of a population-based cohort of Japanese patients. J Clin Endocrinol Metab. 2010;95:1981-1985.
13. CastanetM,Sura-Trueba S, Chauty A, et al. Linkage and mutational analysis of familial thyroid dysgenesis demonstrate genetic heterogeneity implicating novel genes. Eur J Hum Genet. 2005;13:232-239.
14. Castanet M, Lyonnet S, Bonaiti-Pellie C, Polak M, Czernichow P, Leger J. Familial forms of thyroid dysgenesis among infants with congenital hypothyroidism. N Engl J Med. 2000; 343:441-442.
15. Perry R, Heinrichs C, Bourdoux P, et al. Discordance of monozygotic twins for thyroid dysgenesis: implications for screening and for molecular pathophysiology. J Clin Endocrinol Meta b. 2002;87: 4072-4077.
16. Stoppa-Vaucher S, Van Vliet G, Deladoey J. Variation by ethnicity in the prevalence of congenital hypothyroidism due to thyroid dysgenesis. Thyroid. 2011;21:13-18.
17. Varley KE, Gertz J, Bowling KM, et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res. 2013;23: 555-567.
18. Venza I, Visalli M, Tripodo B, et al. FOXE1 is a target for aberrant methylation in cutaneous squamous cell carcinoma. Br J Dermatol. 2010;162:1093-1097.
19. Sato N, Fuku shima N, Maitra A, et al. Discovery of novel targets for aberrant methylation in pancreatic carcinoma using high-throughput microarrays. Cancer Res. 2003;63:3735-3742.
20. Weisenberger DJ, Trinh BN, Campan M, et al. DNA methylation analysis by digital bisulfite genomic sequencing and digital Methy-Light. Nucleic Acids Res. 2008;36:4689-4698.
21. Abu-Khudir R, Paquette J, Lefort A, et al. Transcriptome, methylomeand genomic variations analysis of ectopic thyroid glands.PLoS One. 2010;5:e13420.
22. Beaudet AL, Jiang YH. A rheostat model for a rapid and reversible form of imprinting-dependent evolution. Am J Hum Genet. 2002; 70:1389-1397.
23. Cooper DN, Mort M, Stenson PD, Ball EV, Chuzhanova NA. Methylation-mediated deamination of 5-methylcytosine appears to give ris e to mutations causing human inherited disease in CpNpG trinucleotides, as well as in CpG dinucleotides.HumGenomics. 2010; 4:406-410.
24. Weber M, Davies JJ, Wittig D, et al. Chromosome-wide and prom oter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet. 2005;37: 853-862.
25. McGowan PO, Sasaki A, D 'Alessio AC, et al. Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abuse. Nat Neurosci. 2009;12:342-348.
26. van Staveren WC, Solis DW, Delys L, et al. Human thyroid tumor cell l ines derived from different tumor types present a common dedifferentiated phenotype. Cancer Res. 2007;67:8113-8120.
27. Deng G,Chen A,Pong E,Kim YS Methylation inhMLH1promoter interferes with its binding to transcription factor CBF and inhibits gene expression Oncogene. 2001,20,7120-7127.
28. DiNardo DN, Butcher DT, Robinson DP, Archer TK, Rodenhiser DI. Functional analysis ofCpGmethylation in theBRCA1promoter region. Oncogene. 2001;20:5331-5340.
29. Futscher BW, Oshiro MM, Wozniak RJ, et al. Role for DNA methylation in the control of cell type specific maspin expression. Nat Genet. 2002;31:175-179.
30. Ching TT, Maunakea AK, Jun P, et al. Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3. Nat Genet. 2005;37:645-651.
31. Song F, Smith JF, Kimura MT, et al. Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression. Proc Natl Acad Sci U SA. 2005;102:3336-3341.
32. Eckhardt F, Lewin J, Cortese R, et al. DNA methylation profiling of human chromosomes 6, 20 and Nat Genet. 2006;38:1378-1385.
33. Khulan B, Thompson RF, Ye K, et al. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 2006;16:1046-1055.
34. Kitamura E, Igarashi J, Morohashi A, et al. Analysis of tissue-specific differentially methylated regions (TDMs) in humans. Genomics. 2007;89:326-337.
35. Illingworth R, Kerr A, Desousa D, et al. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 2008;6:e22.
36. Maunakea AK, Nagarajan RP, Bilenky M, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010;466:253-257.
37. Ohgane J, Yagi S, Shiota K. Epigenetics: the DNA methylation profile of tissue-dependent and differentially methylated regions in cells. Placenta. 2008;29(suppl A):S29-S35.
38. Zhang B, Zhou Y, Lin N, et al. Functional DNA methylation differences betw een tissues, cell types, and across individuals discovered using theM&Malgorithm.GenomeRes. 2013;23:1522-1540.
39. Curradi M, Izzo A, Badaracco G, Landsberger N. Molecular mechanisms of gene silencing mediated by DNA methylation. Mol Cell Biol. 2002;22:3157-3173.
40. Choi JS, Kim KH, Jeon YK, et al. Promoter hypermethylation of the ADAM23 gene in colorectal cancer cell lines and cancer tissues. Int J Cancer. 2009;124:1258-1262.
41. Kuang SQ, Tong WG, Yang H, et al. Genome-wide identification of aberrantly methylated promoter associated CpG islands in acute lymphocytic leukemia. Leukemia. 2008;22:1529-1538.
42. Bell A, Bell D, Weber RS, El-Naggar AK. CpG island methylation profiling in human salivary gland adenoid cystic carcinoma. Cancer. 2011;117:2898-2909.
43. Grant DJ, Shi H, Teng CT. Tissue and site-specific methylation correlates with expression of the mouse lactoferrin gene. J Mol Endocrinol. 1999;23:45-55.
44. Boa tright JH, Nickerson JM, Borst DE. Site-specific DNA hypomethylation permits expression of the IRBP gene. Brain Res. 2000; 887:211-221.
45. Ben-Hattar J, Jiricny J. Methylation of single CpG dinucleotides within a promoter element of the Herpes simplex virus tk gene reduces its transcription in vivo. Gene. 1988;65:219-227.
46. Wicki R, Franz C, Scholl FA, Heizmann CW, Schafer BW. Repression of the candidate tumor suppressor geneS100A2in breast cancer is mediated by site-specific hypermethylation. Cell Calcium. 1997; 22:243-254.
47. Gonzalgo ML, Hayashida T, Bender CM, et al. The role of DNA methylation in expression of the p19/p16 locus in human bladder cancer cell lines. Cancer Res. 1998;58:1245-1252.
48. Robertson KD,Jones PA The human ARF cell cycle regulatory gene promoter is aCpGisland which can be silenced byDNAmethylation and down-regulated by wild-type p53 Mol Cell Biol. 1998,18,6457-6473
49. Pogribny IP, Pogribna M, Christman JK, James SJ. Single-site methylation within the p53 promoter region reduces gene expression in a reporter gene construct: possible in vivo relevance during tumorigenesis. Cancer Res. 200 0;60:588-594.
50. Yoo CB, Jones PA. Epigenetic therapy of cancer: past, present and future. Nat Rev Drug Discov. 2006;5:37-50.
51. NanX,NgHH,Johnson CA, et al. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature. 1998;393:386-389.
52. Nan X, Meehan RR, Bird A. Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. Nucleic Acids Res. 1993;21:4886-4892.
53. Lynch MD, Smith AJ, De Gobbi M, et al. An interspec ies analysis reveals a key role for unmethylated CpG dinucleotides in vertebrate Polycomb complex recruitment. EMBO J. 2012;31:317-329.
54. Cedar H, Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet. 2009;10:295-304.
55. Bell JT, Tsai PC, Yang TP, et al. Epigenome-wide scans identify differentially methylated regions for age and age-related pheno types in a healthy ageing population. PLoS Genet. 2012;8:e1002629.
56. Liu J, Morgan M, Hutchison K, Calhoun VD. A study of the influence of sex on genome wide methylation. PLoS One. 2010;5: e10028.