Chromosome Research

, Volume 13, Issue 8, pp 809–818

Allele-specific methylation of a functional CTCF binding site upstream of MEG3 in the human imprinted domain of 14q32

  • Alberto L. Rosa
  • Yuan-Qing Wu
  • Bernard Kwabi-Addo
  • Karen J. Coveler
  • V. Reid Sutton
  • Lisa G. Shaffer
Article

Abstract

The gene MEG3 is located in the imprinted human chromosomal region on 14q32. Imprinting of a structurally homologous region IGF2/H19 on 11p15 is mediated through cytosine methylation-controlled binding of the protein CTCF to target sites upstream of H19. We identified five new CTCF binding sites around the promoter of MEG3. Using an electrophoretic mobility shift assay, we showed that these sites bind CTCF in vitro. Using one of these sites, chromatin immunoprecipitation (ChIP) analysis confirmed CTCF binding in-vivo, and differential allele-specific methylation was demonstrated in seven individuals with either maternal or paternal uniparental disomy 14 (UPD14). The site was unmethylated on the maternally inherited chromosomes 14 and methylated on the paternally inherited chromosomes 14, suggesting parent-specific methylation of sequences upstream of MEG3. We speculate that this CTCF-binding region may provide a mechanism for the transcriptional regulation of MEG3 and DLK1.

Key words

epigenetics imprinting methylation protein binding sites UPD 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Antonarakis SE, Blouin JL, Maher J, Avramopoulos D, Thomas G, Talbot CC, Jr (1993) Maternal uniparental disomy for human chromosome 14, due to loss of a chromosome 14 from somatic cells with t(13;14) trisomy 14. Am J Hum Genet 52: 1145–1152.PubMedGoogle Scholar
  2. Bell AC, Felsenfeld G (2000) Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405: 482–485.PubMedGoogle Scholar
  3. Bell AC, West AG, Felsenfeld G (1999) The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell 98: 387–396.CrossRefPubMedGoogle Scholar
  4. Berend SA, Bejjani BA, McCaskill C, Shaffer LG (2002) Identification of uniparental disomy in phenotypically abnormal carriers of isochromosomes or Robertsonian translocations. Am J Med Genet 111: 362–365.CrossRefPubMedGoogle Scholar
  5. Bird AP (1995) Gene number, noise reduction and biological complexity. Trends Genet 11: 94–100.PubMedGoogle Scholar
  6. Charlier C, Segers K, Karim L et al. (2001a) The callipyge mutation enhances the expression of coregulated imprinted genes in cis without affecting their imprinting status. Nat Genet 27: 367–369.CrossRefPubMedGoogle Scholar
  7. Charlier C, Segers K, Wagenaar D et al. (2001b) Human–ovine comparative sequencing of a 250-kb imprinted domain encompassing the callipyge (clpg) locus and identification of six imprinted transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8. Genome Res 11: 850–862.CrossRefPubMedGoogle Scholar
  8. Chung JH, Whiteley M, Felsenfeld G (1993) A 5′ element of the chicken beta-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila. Cell 74: 505–514.CrossRefPubMedGoogle Scholar
  9. Chung JH, Bell AC, Felsenfeld G (1997) Characterization of the chicken beta-globin insulator. Proc Natl Acad Sci USA 94: 575–580.CrossRefPubMedGoogle Scholar
  10. Coveler KJ, Yang SP, Sutton R et al. (2002) A case of segmental paternal isodisomy of chromosome 14. Hum Genet 110: 251–256.CrossRefPubMedGoogle Scholar
  11. Croteau S, Charron MC, Latham KE, Naumova AK (2003) Alternative splicing and imprinting control of the Meg3/Gtl2-Dlk1 locus in mouse embryos. Mamm Genome 14: 231–241.CrossRefPubMedGoogle Scholar
  12. Engel E (1980) A new genetic concept: uniparental disomy and its potential effect, isodisomy. Am J Med Genet 6: 137–143.CrossRefPubMedGoogle Scholar
  13. Filippova GN, Thienes CP, Penn BH et al. (2001) CTCF-binding sites flank CTG/CAG repeats and form a methylation-sensitive insulator at the DM1 locus. Nat Genet 28: 335–343.CrossRefPubMedGoogle Scholar
  14. Georgiades P, Chierakul C, Ferguson-Smith AC (1998) Parental origin effects in human trisomy for chromosome 14q: implications for genomic imprinting. J Med Genet 35: 821–824.PubMedCrossRefGoogle Scholar
  15. Hark AT, Schoenherr CJ, Katz DJ, Ingram RS, Levorse JM, Tilghman SM (2000) CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature 405: 486–489.PubMedGoogle Scholar
  16. Kanduri C, Holmgren C, Pilartz M et al. (2000a) The 5′ flank of mouse H19 in an unusual chromatin conformation unidirectionally blocks enhancer-promoter communication. Curr Biol 10: 449–457.PubMedGoogle Scholar
  17. Kanduri C, Pant V, Loukinov D et al. (2000b) Functional association of CTCF with the insulator upstream of the H19 gene is parent of origin-specific and methylation-sensitive. Curr Biol 10: 853–856.PubMedGoogle Scholar
  18. Kobayashi S, Wagatsuma H, Ono R et al. (2000) Mouse Peg9/Dlk1 and human PEG9/DLK1 are paternally expressed imprinted genes closely located to the maternally expressed imprinted genes: mouse Meg3/Gtl2 and human MEG3. Genes Cells 5: 1029–1037.PubMedGoogle Scholar
  19. Lewis A, Murrell A (2004) Genomic imprinting: CTCF protects the boundaries. Curr Biol 14: R284–R286.CrossRefPubMedGoogle Scholar
  20. McGowan KD, Weiser JJ, Horwitz J et al. (2002) The importance of investigating for uniparental disomy in prenatally identified balanced acrocentric rearrangements. Prenat Diagn 22: 141–143.CrossRefPubMedGoogle Scholar
  21. Miyoshi N, Wagatsuma H, Wakana S et al. (2000) Identification of an imprinted gene, Meg3/Gtl2 and its human homologue MEG3, first mapped on mouse distal chromosome 12 and human chromosome 14q. Genes Cells 5: 211–220.CrossRefPubMedGoogle Scholar
  22. Morison IM, Reeve AE (1998) A catalogue of imprinted genes and parent-of-origin effects in humans and animals. Hum Mol Genet 7: 1599–1609.CrossRefPubMedGoogle Scholar
  23. Ohlsson R, Renkawitz R, Lobanenkov V (2001) CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends Genet 17: 520–527.PubMedGoogle Scholar
  24. Paulsen M, Takada S, Youngson NA et al. (2001) Comparative sequence analysis of the imprinted Dlk1-Gtl2 locus in three mammalian species reveals highly conserved genomic elements and refines comparison with the Igf2-H19 region. Genome Res 11: 2085–2094.CrossRefPubMedGoogle Scholar
  25. Pentao L, Lewis RA, Ledbetter DH, Patel PI, Lupski JR (1992) Maternal uniparental isodisomy of chromosome 14: association with autosomal recessive rod monochromacy. Am J Hum Genet 50: 690–699.PubMedGoogle Scholar
  26. Prawitt D, Enklaar T, Gartner-Rupprecht B et al. (2005) Microdeletion of target sites for insulator protein CTCF in a chromosome 11p15 imprinting center in Beckwith–Wiedemann syndrome and Wilms' tumor. Proc Natl Acad Sci USA 102: 4085–4090.CrossRefPubMedGoogle Scholar
  27. Robin NH, Harari-Shacham A, Schwartz S, Wolff DJ (1997) Duplication 14(q24.3q31) in a father and daughter: delineation of a possible imprinted region. Am J Med Genet 71: 361–365.PubMedGoogle Scholar
  28. Sasaki H, Ishihara K, Kato R (2000) Mechanisms of Igf2/H19 imprinting: DNA methylation, chromatin and long-distance gene regulation. J Biochem (Tokyo) 127: 711–715.Google Scholar
  29. Schiff R, Reddy P, Ahotupa M et al. (2000) Oxidative stress and AP-1 activity in tamoxifen-resistant breast tumors in-vivo. J Natl Cancer Inst 92: 1926–1934.CrossRefPubMedGoogle Scholar
  30. Schmidt JV, Matteson PG, Jones BK, Guan XJ, Tilghman SM (2000) The Dlk1 and Gtl2 genes are linked and reciprocally imprinted. Genes Dev 14: 1997–2002.PubMedGoogle Scholar
  31. Schuster-Gossler K, Bilinski P, Sado T, Ferguson-Smith A, Gossler A (1998) The mouse Gtl2 gene is differentially expressed during embryonic development, encodes multiple alternatively spliced transcripts, and may act as an RNA. Dev Dyn 212: 214–228.CrossRefPubMedGoogle Scholar
  32. Sparago A, Cerrato F, Vernucci M, Ferrero GB, Silengo MC, Riccio A (2004) Microdeletions in the human H19 DMR result in loss of IGF2 imprinting and Beckwith–Wiedemann syndrome. Nat Genet 36: 958–960.CrossRefPubMedGoogle Scholar
  33. Sutton VR, Shaffer LG (2000) Search for imprinted regions on chromosome 14: comparison of maternal and paternal UPD cases with cases of chromosome 14 deletion. Am J Med Genet 93: 381–387.CrossRefPubMedGoogle Scholar
  34. Sutton VR, Coveler KJ, Lalani SR, Kashork CD, Shaffer LG (2002) Subtelomeric FISH uncovers trisomy 14q32: lessons for imprinted regions, cryptic rearrangements and variant acrocentric short arms. Am J Med Genet 112: 23–27.CrossRefPubMedGoogle Scholar
  35. Szabo PE, Tang SH, Silva FJ, Tsark WM, Mann JR (2004) Role of CTCF binding sites in the Igf2/H19 imprinting control region. Mol Cell Biol 24: 4791–4800.PubMedGoogle Scholar
  36. Takada S, Tevendale M, Baker J et al. (2000) Delta-like and gtl2 are reciprocally expressed, differentially methylated linked imprinted genes on mouse chromosome 12. Curr Biol 10: 1135–1138.CrossRefPubMedGoogle Scholar
  37. Towner D, Yang SP, Shaffer LG (2001a) Prenatal ultrasound findings in a fetus with paternal uniparental disomy 14q12-qter. Ultrasound Obstet Gynecol 18: 268–271.CrossRefPubMedGoogle Scholar
  38. Towner DR, Shaffer LG, Yang SP, Walgenbach DD (2001b) Confined placental mosaicism for trisomy 14 and maternal uniparental disomy in association with elevated second trimester maternal serum human chorionic gonadotrophin and third trimester fetal growth restriction. Prenat Diagn 21: 395–398.CrossRefPubMedGoogle Scholar
  39. Walter CA, Shaffer LG, Kaye CI et al. (1996) Short-limb dwarfism and hypertrophic cardiomyopathy in a patient with paternal isodisomy 14: 45,XY,idic(14)(p11). Am J Med Genet 65: 259–265.CrossRefPubMedGoogle Scholar
  40. Wolffe AP (2000) Transcriptional control: imprinting insulation. Curr Biol 10: R463–R465.CrossRefPubMedGoogle Scholar
  41. Wylie AA, Murphy SK, Orton TC, Jirtle RL (2000) Novel imprinted DLK1/GTL2 domain on human chromosome 14 contains motifs that mimic those implicated in IGF2/H19 regulation. Genome Res 10: 1711–1718.CrossRefPubMedGoogle Scholar
  42. Yu W, Ginjala V, Pant V et al. (2004) Poly(ADP-ribosyl)ation regulates CTCF-dependent chromatin insulation. Nat Genet 36: 1105–1110.PubMedGoogle Scholar
  43. Zhang X, Zhou Y, Mehta KR et al. (2003) A pituitary-derived MEG3 isoform functions as a growth suppressor in tumor cells. J Clin Endocrinol Metab 88: 5119–5126.CrossRefPubMedGoogle Scholar
  44. Zimarino V, Wu C (1987) Induction of sequence-specific binding of Drosophila heat shock activator protein without protein synthesis. Nature 327: 727–730.CrossRefPubMedGoogle Scholar

Copyright information

© Springer 2005

Authors and Affiliations

  • Alberto L. Rosa
    • 1
  • Yuan-Qing Wu
    • 2
  • Bernard Kwabi-Addo
    • 2
  • Karen J. Coveler
    • 2
  • V. Reid Sutton
    • 2
  • Lisa G. Shaffer
    • 1
  1. 1.Health Research and Education CenterWashington State UniversitySpokaneUSA
  2. 2.Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUSA

Personalised recommendations