Quantitative analysis of DNA methylation at all human imprinted regions reveals preservation of epigenetic stability in adult somatic tissue

Epigenetics and Chromatin

Volumn 4, Issue 1, 2011, Pages

  Woodfine, Kathryn ^a   Huddleston, Joanna E ^a   Murrell, Adele ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; TRANSCRIPTION FACTOR CTCF;

ADULT; ARTICLE; CPG ISLAND; DNA METHYLATION; EPIGENETICS; FEMALE; GENETIC STABILITY; GENOME IMPRINTING; GERM LINE; HUMAN; HUMAN CELL; HUMAN TISSUE; MALE; PRIORITY JOURNAL; PYROSEQUENCING; QUANTITATIVE ANALYSIS;

EID: 79251579948     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/1756-8935-4-1     Document Type: Article

References (49)

1. Genetics and epigenetics: stability and plasticity during cellular differentiation. F Mohn D Schubeler, Trends Genet 2009 25 3 129 136 10.1016/j.tig.2008.12.005 19185382
2. Cytosine methylation and human cancer. PM Warnecke TH Bestor, Curr Opin Oncol 2000 12 (Pubitemid 32046841)
3. Epigenomics: genome-wide study of methylation phenomena. KL Novik I Nimmrich B Genc S Maier C Piepenbrock A Olek S Beck, Curr Issues Mol Biol 2002 4 4 111 128 12432963 (Pubitemid 35314717)
4. Genomic imprinting: parental influence on the genome. W Reik J Walter, Nat Rev Genet 2001 2 1 21 32 10.1038/35047554 11253064 (Pubitemid 33674766)
5. Mechanisms regulating imprinted genes in clusters. CA Edwards AC Ferguson-Smith, Curr Opin Cell Biol 2007 19 3 281 289 10.1016/j.ceb.2007.04.013 17467259 (Pubitemid 46899514)
6. Genomic imprinting in mammals: emerging themes and established theories. AJ Wood RJ Oakey, PLoS Genet 2006 2 11 147 10.1371/journal.pgen.0020147 17121465
7. Geneimprint. http://www.geneimprint.com
8. Genomic imprinting and cancer: from primordial germ cells to somatic cells. A Murrell, ScientificWorldJournal 2006 6 1888 1910 10.1100/tsw.2006.318 17205195
9. Multiple imprinted and stemness genes provide a link between normal and tumor progenitor cells of the developing human kidney. B Dekel S Metsuyanim KM Schmidt-Ott E Fridman J Jacob-Hirsch A Simon J Pinthus Y Mor J Barasch N Amariglio,, et al. Cancer Res 2006 66 12 6040 6049 10.1158/0008-5472.CAN-05-4528 16778176
10. Epigenetic alteration at the DLK1-GTL2 imprinted domain in human neoplasia: analysis of neuroblastoma, phaeochromocytoma and Wilms' tumour. D Astuti F Latif K Wagner D Gentle WN Cooper D Catchpoole R Grundy AC Ferguson-Smith ER Maher, Br J Cancer 2005 92 8 1574 1580 10.1038/sj.bjc.6602478 15798773 (Pubitemid 40705027)
11. Imprinted DLK1 is a putative tumor suppressor gene and inactivated by epimutation at the region upstream of GTL2 in human renal cell carcinoma. T Kawakami T Chano K Minami H Okabe Y Okada K Okamoto, Hum Mol Genet 2006 15 6 821 830 10.1093/hmg/ddl001 16439445 (Pubitemid 43338225)
12. The H19 locus acts in vivo as a tumor suppressor. T Yoshimizu A Miroglio MA Ripoche A Gabory M Vernucci A Riccio S Colnot C Godard B Terris H Jammes,, et al. Proc Natl Acad Sci USA 2008 105 34 12417 12422 10.1073/pnas.0801540105 18719115
13. The human retinoblastoma gene is imprinted. D Kanber T Berulava O Ammerpohl D Mitter J Richter R Siebert B Horsthemke D Lohmann K Buiting, PLoS Genet 2009 5 12 1000790 10.1371/journal.pgen.1000790 20041224
14. Loss of IGF2 imprinting: a potential marker of colorectal cancer risk. H Cui M Cruz-Correa FM Giardiello DF Hutcheon DR Kafonek S Brandenburg Y Wu X He NR Powe AP Feinberg, Science 2003 299 5613 1753 1755 10.1126/science.1080902 12637750 (Pubitemid 36337205)
15. Somatically acquired hypomethylation of IGF2 in breast and colorectal cancer. Y Ito T Koessler AE Ibrahim S Rai SL Vowler S Abu-Amero AL Silva AT Maia JE Huddleston S Uribe-Lewis,, et al. Hum Mol Genet 2008 17 17 2633 2643 10.1093/hmg/ddn163 18541649
16. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. AC Bell G Felsenfeld, Nature 2000 405 6785 482 485 10.1038/35013100 10839546 (Pubitemid 30367427)
17. The nucleotides responsible for the direct physical contact between the chromatin insulator protein CTCF and the H19 imprinting control region manifest parent of origin-specific long-distance insulation and methylation-free domains. V Pant P Mariano C Kanduri A Mattsson V Lobanenkov R Heuchel R Ohlsson, Genes Dev 2003 17 5 586 590 10.1101/gad.254903 12629040 (Pubitemid 36307542)
18. Transgenic RNAi reveals essential function for CTCF in H19 gene imprinting. AM Fedoriw P Stein P Svoboda RM Schultz MS Bartolomei, Science 2004 303 5655 238 240 10.1126/science.1090934 14716017 (Pubitemid 38057575)
19. CTCF maintains differential methylation at the Igf2/H19 locus. CJ Schoenherr JM Levorse SM Tilghman, Nat Genet 2003 33 1 66 69 10.1038/ng1057 12461525 (Pubitemid 36068684)
20. Distinct methylation changes at the IGF2-H19 locus in congenital growth disorders and cancer. A Murrell Y Ito G Verde J Huddleston K Woodfine MC Silengo F Spreafico D Perotti A De Crescenzo A Sparago,, et al. PLoS One 2008 3 3 1849 10.1371/journal.pone.0001849 18365005
21. CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. S Kurukuti VK Tiwari G Tavoosidana E Pugacheva A Murrell Z Zhao V Lobanenkov W Reik R Ohlsson, Proc Natl Acad Sci USA 2006 103 28 10684 10689 10.1073/pnas.0600326103 16815976 (Pubitemid 44078037)
22. Cohesin Is required for higher-order chromatin conformation at the imprinted IGF2-H19l locus. R Nativio KS Wendt Y Ito JE Huddleston S Uribe-Lewis K Woodfine C Krueger W Reik J-M Peters A Murrell, PLoS Genet 2009 5 11 1000739 10.1371/journal.pgen.1000739 19956766
23. Zac1 regulates an imprinted gene network critically involved in the control of embryonic growth. A Varrault C Gueydan A Delalbre A Bellmann S Houssami C Aknin D Severac L Chotard M Kahli A Le Digarcher,, et al. Dev Cell 2006 11 5 711 722 10.1016/j.devcel.2006.09.003 17084362 (Pubitemid 44752557)
24. A maternal-zygotic effect gene, Zfp57, maintains both maternal and paternal imprints. X Li M Ito F Zhou N Youngson X Zuo P Leder AC Ferguson-Smith, Dev Cell 2008 15 4 547 557 10.1016/j.devcel.2008.08.014 18854139
25. Hypomethylation of multiple imprinted loci in individuals with transient neonatal diabetes is associated with mutations in ZFP57. DJ Mackay JL Callaway SM Marks HE White CL Acerini SE Boonen P Dayanikli HV Firth JA Goodship AP Haemers,, et al. Nat Genet 2008 40 8 949 951 10.1038/ng.187 18622393
26. Origins of extreme sexual dimorphism in genomic imprinting. D Bourc'his TH Bestor, Cytogenet Genome Res 2006 113 1-4 36 40 10.1159/000090813 16575161
27. Epigenetic profiling at mouse imprinted gene clusters reveals novel epigenetic and genetic features at differentially methylated regions. SV Dindot R Person M Strivens R Garcia AL Beaudet, Genome Res 2009 19 8 1374 1383 10.1101/gr.089185.108 19542493
28. Identification and quantification of differentially methylated loci by the pyrosequencing technology. E Dejeux H El abdalaoui IG Gut J Tost, Methods Mol Biol 2009 507 189 205 full-text 18987816
29. Genome-wide analysis of DNA methylation patterns. D Zilberman S Henikoff, Development 2007 134 22 3959 3965 10.1242/dev.001131 17928417 (Pubitemid 350269413)
30. From genome to epigenome. A Murrell VK Rakyan S Beck, Hum Mol Genet 2005 14 Spec No 1 3 R10 10.1093/hmg/ddi110 15809270
31. Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias. SS Nair MW Coolen C Stirzaker JZ Song AL Statham D Strbenac MD Robinson SJ Clark, Epigenetics 2010 6 1
32. Biallelic expression of imprinted genes in the mouse germ line: implications for erasure, establishment, and mechanisms of genomic imprinting. PE Szabo JR Mann, Genes Dev 1995 9 15 1857 1868 10.1101/gad.9.15.1857 7649473
33. Sex-specific parent-of-origin allelic expression in the mouse brain. C Gregg J Zhang JE Butler D Haig C Dulac, Science 329 5992 682 685 10.1126/science.1190831 20616234
34. Epigenetics and imprinting. Cancer Research UK, http://www. cambridgecancer.org.uk/research/loc/cambridge/ccri/murrella/?view= CRI&source=research
35. Mechanisms of imprinting of the Prader-Willi/Angelman region. B Horsthemke J Wagstaff, Am J Med Genet A 2008 146A 16 2041 2052 10.1002/ajmg.a.32364 18627066
36. The neuronatin gene resides in a 'micro-imprinted' domain on human chromosome 20q11.2. HK Evans AA Wylie SK Murphy RL Jirtle, Genomics 2001 77 1-2 99 104 10.1006/geno.2001.6612 11543638 (Pubitemid 32826491)
37. Limited evolutionary conservation of imprinting in the human placenta. D Monk P Arnaud S Apostolidou FA Hills G Kelsey P Stanier R Feil GE Moore, Proc Natl Acad Sci USA 2006 103 17 6623 6628 10.1073/pnas.0511031103 16614068
38. The evolution of the DLK1-DIO3 imprinted domain in mammals. CA Edwards AJ Mungall L Matthews E Ryder DJ Gray AJ Pask G Shaw JA Graves J Rogers I Dunham,, et al. PLoS Biol 2008 6 6 135 10.1371/journal.pbio.0060135 18532878
39. A novel variant of Inpp5f is imprinted in brain, and its expression is correlated with differential methylation of an internal CpG island. JD Choi LA Underkoffler AJ Wood JN Collins PT Williams JA Golden EF Schuster Jr KM Loomes RJ Oakey, Mol Cell Biol 2005 25 13 5514 5522 10.1128/MCB.25.13.5514-5522.2005 15964807 (Pubitemid 40853586)
40. Expression data base. University of Tokyo Laboratory for Systems Biology and Medicine, http://www.lsbm.org/site-e/index.html
41. Imprinting of PEG1/MEST isoform 2 in human placenta. J McMinn M Wei Y Sadovsky HM Thaker B Tycko, Placenta 2006 27 2-3 119 126 10.1016/j.placenta. 2004.12.003 16338457 (Pubitemid 41763453)
42. Unlocking the secrets of the genome. SE Celniker LA Dillon MB Gerstein KC Gunsalus S Henikoff GH Karpen M Kellis EC Lai JD Lieb DM MacAlpine,, et al. Nature 2009 459 7249 927 930 10.1038/459927a 19536255
43. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. TS Mikkelsen M Ku DB Jaffe B Issac E Lieberman G Giannoukos P Alvarez W Brockman TK Kim RP Koche,, et al. Nature 2007 448 7153 553 560 10.1038/nature06008 17603471 (Pubitemid 47206934)
44. SKY Karyotypes and FISH analysis of Epithelial Cancer Cell Lines. http://www.path.cam.ac.uk/∼pawefish/
45. H19 imprinting control region methylation requires an imprinted environment only in the male germ line. C Gebert D Kunkel A Grinberg K Pfeifer, Mol Cell Biol 30 5 1108 1115 10.1128/MCB.00575-09 20038532
46. Universal primer applications for pyrosequencing. DC Guo DM Milewicz, Methods Mol Biol 2007 373 57 62 17185757
47. Pyrosequencing protocol using a universal biotinylated primer for mutation detection and SNP genotyping. JL Royo M Hidalgo A Ruiz, Nat Protoc 2007 2 7 1734 1739 10.1038/nprot.2007.244 17641638
48. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. RA Irizarry C Ladd-Acosta B Wen Z Wu C Montano P Onyango H Cui K Gabo M Rongione M Webster,, et al. Nat Genet 2009 41 2 178 186 10.1038/ng.298 19151715
49. Using galaxy to perform large-scale interactive data analyses. J Taylor I Schenck D Blankenberg A Nekrutenko, Curr Protoc Bioinformatics 2007 Chapter 10 Unit 10 15. 18428782