Extensive epigenetic reprogramming in human somatic tissues between fetus and adult

Epigenetics and Chromatin

Volumn 4, Issue 1, 2011, Pages

  Yuen, Ryan Kc ^a,b   Neumann, Sarah Ma ^b,c   Fok, Alexandra K ^b,c   Pẽaherrera, Maria S ^a,b   McFadden, Deborah E ^a   Robinson, Wendy P ^a,b   Kobor, Michael S ^a,b,c  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c Centre for Molecular Medicine and Therapeutics   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HISTONE;

ADULT; ARTICLE; BRAIN TISSUE; CLINICAL ARTICLE; CONTROLLED STUDY; DNA METHYLATION; EMBRYONIC STEM CELL; EPIGENETICS; FEMALE; FETUS; HISTONE MODIFICATION; HUMAN; HUMAN TISSUE; KIDNEY PARENCHYMA; LUNG PARENCHYMA; MALE; MUSCLE TISSUE; PLASTICITY; PRIORITY JOURNAL; SKIN; TRISOMY 18; TRISOMY 21;

EID: 79955564613     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/1756-8935-4-7     Document Type: Article

References (52)

1. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. R Illingworth A Kerr D Desousa H Jorgensen P Ellis J Stalker D Jackson C Clee R Plumb J Rogers,, et al. PLoS Biol 2008 6 22 10.1371/journal.pbio.0060022 18232738
2. Inactive X chromosome-specific reduction in placental DNA methylation. AM Cotton L Avila MS Penaherrera JG Affleck WP Robinson CJ Brown, Hum Mol Genet 2009 18 3544 3552 10.1093/hmg/ddp299 19586922
3. A genome-wide screen for normally methylated human CpG islands that can identify novel imprinted genes. LZ Strichman-Almashanu RS Lee PO Onyango E Perlman F Flam MB Frieman AP Feinberg, Genome Res 2002 12 543 554 11932239 (Pubitemid 34308634)
4. Decline in genomic DNA methylation through aging in a cohort of elderly subjects. V Bollati J Schwartz R Wright A Litonjua L Tarantini H Suh D Sparrow P Vokonas A Baccarelli, Mech Ageing Dev 2009 130 234 239 10.1016/j.mad.2008.12. 003 19150625
5. The relationship of DNA methylation with age, gender and genotype in twins and healthy controls. MP Boks EM Derks DJ Weisenberger E Strengman E Janson IE Sommer RS Kahn RA Ophoff, PLoS One 2009 4 6767 10.1371/journal.pone. 0006767 19774229
6. Transient cyclical methylation of promoter DNA. S Kangaspeska B Stride R Metivier M Polycarpou-Schwarz D Ibberson RP Carmouche V Benes F Gannon G Reid, Nature 2008 452 112 115 10.1038/nature06640 18322535 (Pubitemid 351355094)
7. Cyclical DNA methylation of a transcriptionally active promoter. R Metivier R Gallais C Tiffoche C Le Peron RZ Jurkowska RP Carmouche D Ibberson P Barath F Demay G Reid,, et al. Nature 2008 452 45 50 10.1038/nature06544 18322525 (Pubitemid 351355084)
8. LINE-1 DNA methylation is inversely correlated with cord plasma homocysteine in man: a preliminary study. AA Fryer TM Nafee KM Ismail WD Carroll RD Emes WE Farrell, Epigenetics 2009 4 394 398 10.4161/epi.4.6.9766 19755846
9. Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abuse. PO McGowan A Sasaki AC D'Alessio S Dymov B Labonte M Szyf G Turecki MJ Meaney, Nat Neurosci 2009 12 342 348 10.1038/nn.2270 19234457
10. Changes in DNA methylation patterns in subjects exposed to low-dose benzene. V Bollati A Baccarelli L Hou M Bonzini S Fustinoni D Cavallo HM Byun J Jiang B Marinelli AC Pesatori,, et al. Cancer Res 2007 67 876 880 10.1158/0008-5472.CAN-06-2995 17283117
11. Rapid DNA methylation changes after exposure to traffic particles. A Baccarelli RO Wright V Bollati L Tarantini AA Litonjua HH Suh A Zanobetti D Sparrow PS Vokonas J Schwartz, Am J Respir Crit Care Med 2009 179 572 578 10.1164/rccm.200807-1097OC 19136372
12. DNA methylation and human disease. KD Robertson, Nat Rev Genet 2005 6 597 610 16136652 (Pubitemid 41044297)
13. Genomic imprinting: parental influence on the genome. W Reik J Walter, Nat Rev Genet 2001 2 21 32 11253064 (Pubitemid 33674766)
14. Stability and flexibility of epigenetic gene regulation in mammalian development. W Reik, Nature 2007 447 425 432 10.1038/nature05918 17522676 (Pubitemid 46816749)
15. DNA methylation programming and reprogramming in primate embryonic stem cells. NM Cohen V Dighe G Landan S Reynisdottir A Palsson S Mitalipov A Tanay, Genome Res 2009 19 2193 2201 10.1101/gr.096685.109 19887575
16. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. AL Brunner DS Johnson SW Kim A Valouev TE Reddy NF Neff E Anton C Medina L Nguyen E Chiao,, et al. Genome Res 2009 19 1044 1056 10.1101/gr.088773.108 19273619
17. Developmental programming of CpG island methylation profiles in the human genome. R Straussman D Nejman D Roberts I Steinfeld B Blum N Benvenisty I Simon Z Yakhini H Cedar, Nat Struct Mol Biol 2009 16 564 571 10.1038/nsmb.1594 19377480
18. DNA methylation profiling of human chromosomes 6, 20 and 22. F Eckhardt J Lewin R Cortese VK Rakyan J Attwood M Burger J Burton TV Cox R Davies TA Down,, et al. Nat Genet 2006 38 1378 1385 10.1038/ng1909 17072317 (Pubitemid 44837559)
19. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. VK Rakyan TA Down S Maslau T Andrew TP Yang H Beyan P Whittaker OT McCann S Finer AM Valdes,, et al. Genome Res 2010 20 434 439 10.1101/gr.103101.109 20219945
20. Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. L Shen Y Kondo Y Guo J Zhang L Zhang S Ahmed J Shu X Chen RA Waterland JP Issa, PLoS Genet 2007 3 2023 2036 17967063
21. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. M Weber I Hellmann MB Stadler L Ramos S Paabo M Rebhan D Schubeler, Nat Genet 2007 39 457 466 10.1038/ng1990 17334365 (Pubitemid 46514772)
22. Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. BC Christensen EA Houseman CJ Marsit S Zheng MR Wrensch JL Wiemels HH Nelson MR Karagas JF Padbury R Bueno,, et al. PLoS Genet 2009 5 1000602 10.1371/journal.pgen.1000602 19680444
23. Epigenetics in cancer. M Esteller, N Engl J Med 2008 358 1148 1159 10.1056/NEJMra072067 18337604
24. Gene silencing in cancer in association with promoter hypermethylation. JG Herman SB Baylin, N Engl J Med 2003 349 2042 2054 10.1056/NEJMra023075 14627790 (Pubitemid 37448928)
25. Transcriptome analysis of human autosomal trisomy. DR FitzPatrick J Ramsay NI McGill M Shade AD Carothers ND Hastie, Hum Mol Genet 2002 11 3249 3256 10.1093/hmg/11.26.3249 12471051 (Pubitemid 36054653)
26. Global disruption of the cerebellar transcriptome in a Down syndrome mouse model. NG Saran MT Pletcher JE Natale Y Cheng RH Reeves, Hum Mol Genet 2003 12 2013 2019 10.1093/hmg/ddg217 12913072 (Pubitemid 37038810)
27. The cerebellar transcriptome during postnatal development of the Ts1Cje mouse, a segmental trisomy model for Down syndrome. L Dauphinot R Lyle I Rivals MT Dang RX Moldrich G Golfier L Ettwiller K Toyama J Rossier L Personnaz,, et al. Hum Mol Genet 2005 14 373 384 15590701 (Pubitemid 40220654)
28. Linking DNA methylation and histone modification: patterns and paradigms. H Cedar Y Bergman, Nat Rev Genet 2009 10 295 304 19308066
29. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. BE Bernstein TS Mikkelsen X Xie M Kamal DJ Huebert J Cuff B Fry A Meissner M Wernig K Plath,, et al. Cell 2006 125 315 326 10.1016/j.cell.2006.02. 041 16630819
30. Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns. HM Byun KD Siegmund F Pan DJ Weisenberger G Kanel PW Laird AS Yang, Hum Mol Genet 2009 18 4808 4817 10.1093/hmg/ddp445 19776032
31. Cancer genes hypermethylated in human embryonic stem cells. V Calvanese A Horrillo A Hmadcha B Suarez-Alvarez AF Fernandez E Lara S Casado P Menendez C Bueno J Garcia-Castro,, et al. PLoS One 2008 3 3294 10.1371/journal.pone.0003294 18820729
32. Human placental-specific epipolymorphism and its association with adverse pregnancy outcomes. RK Yuen L Avila MS Penaherrera P von Dadelszen L Lefebvre MS Kobor WP Robinson, PLoS One 2009 4 7389 10.1371/journal.pone.0007389 19838307
33. DNA methylation profiling of human placentas reveals promoter hypomethylation of multiple genes in early-onset preeclampsia. RK Yuen MS Penaherrera P von Dadelszen DE McFadden WP Robinson, Eur J Hum Genet 2010 18 1006 1012 10.1038/ejhg.2010.63 20442742
34. HOX homeobox genes exhibit spatial and temporal changes in expression during human skin development. EJ Stelnicki LG Komuves AO Kwong D Holmes P Klein S Rozenfeld HJ Lawrence NS Adzick M Harrison C Largman, J Invest Dermatol 1998 110 110 115 9457903 (Pubitemid 28105842)
35. Cadherin-17 is required to maintain pronephric duct integrity during zebrafish development. J Horsfield A Ramachandran K Reuter E LaVallie L Collins-Racie K Crosier P Crosier, Mech Dev 2002 115 15 26 10.1016/S0925- 4773(02)00094-1 12049763 (Pubitemid 34615663)
36. The receptor tyrosine kinase MuSK is required for neuromuscular junction formation in vivo. TM DeChiara DC Bowen DM Valenzuela MV Simmons WT Poueymirou S Thomas E Kinetz DL Compton E Rojas JS Park,, et al. Cell 1996 85 501 512 10.1016/S0092-8674(00)81251-9 8653786 (Pubitemid 26157189)
37. Significance analysis of microarrays applied to the ionizing radiation response. VG Tusher R Tibshirani G Chu, Proc Natl Acad Sci USA 2001 98 5116 5121 10.1073/pnas.091062498 11309499 (Pubitemid 32397092)
38. High-throughput DNA methylation profiling using universal bead arrays. M Bibikova Z Lin L Zhou E Chudin EW Garcia B Wu D Doucet NJ Thomas Y Wang E Vollmer,, et al. Genome Res 2006 16 383 393 10.1101/gr.4410706 16449502 (Pubitemid 43327509)
39. 15q11-13 GABAA receptor genes are normally biallelically expressed in brain yet are subject to epigenetic dysregulation in autism-spectrum disorders. A Hogart RP Nagarajan KA Patzel DH Yasui JM Lasalle, Hum Mol Genet 2007 16 691 703 17339270 (Pubitemid 46585668)
40. Detailed analysis of the methylation patterns of the KvDMR1 imprinting control region of human chromosome 11. L Beatty R Weksberg PD Sadowski, Genomics 2006 87 46 56 10.1016/j.ygeno.2005.05.015 16321503 (Pubitemid 43005101)
41. DNA methylation analysis of the mammalian PEG3 imprinted domain. JM Huang J Kim, Gene 2009 442 18 25 10.1016/j.gene.2009.04.016 19397955
42. Innate immunity of the newborn: basic mechanisms and clinical correlates. O Levy, Nat Rev Immunol 2007 7 379 390 10.1038/nri2075 17457344 (Pubitemid 46674489)
43. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. W Huang da BT Sherman RA Lempicki, Nat Protoc 2009 4 44 57 19131956
44. DAVID: Database for Annotation, Visualization, and Integrated Discovery. G Dennis Jr BT Sherman DA Hosack J Yang W Gao HC Lane RA Lempicki, Genome Biol 2003 4 3 10.1186/gb-2003-4-5-p3 12734009
45. Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. G Pan S Tian J Nie C Yang V Ruotti H Wei GA Jonsdottir R Stewart JA Thomson, Cell Stem Cell 2007 1 299 312 10.1016/j.stem.2007.08.003 18371364 (Pubitemid 47355329)
46. Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. XD Zhao X Han JL Chew J Liu KP Chiu A Choo YL Orlov WK Sung A Shahab VA Kuznetsov,, et al. Cell Stem Cell 2007 1 286 298 10.1016/j.stem.2007.08.004 18371363 (Pubitemid 47370914)
47. Control of developmental regulators by Polycomb in human embryonic stem cells. TI Lee RG Jenner LA Boyer MG Guenther SS Levine RM Kumar B Chevalier SE Johnstone MF Cole K Isono,, et al. Cell 2006 125 301 313 10.1016/j.cell.2006.02. 043 16630818 (Pubitemid 44313811)
48. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). VK Rakyan TA Down NP Thorne P Flicek E Kulesha S Graf EM Tomazou L Backdahl N Johnson M Herberth,, et al. Genome Res 2008 18 1518 1529 10.1101/gr.077479.108 18577705
49. Altered DNA methylation in leukocytes with trisomy 21. K Kerkel N Schupf K Hatta D Pang M Salas A Kratz M Minden V Murty WB Zigman RP Mayeux,, et al. PLoS Genet 2010 6 1001212 10.1371/journal.pgen.1001212 21124956
50. Impact of aging on DNA methylation. B Richardson, Ageing Res Rev 2003 2 245 261 10.1016/S1568-1637(03)00010-2 12726774 (Pubitemid 38340315)
51. Intra-individual change over time in DNA methylation with familial clustering. HT Bjornsson MI Sigurdsson MD Fallin RA Irizarry T Aspelund H Cui W Yu MA Rongione TJ Ekstrom TB Harris,, et al. Jama 2008 299 2877 2883 10.1001/jama.299.24.2877 18577732 (Pubitemid 351930887)
52. Developmental control of allelic methylation in the imprinted mouse Igf2 and H19 genes. R Feil J Walter ND Allen W Reik, Development 1994 120 2933 2943 7607083 (Pubitemid 24312061)