The human placenta methylome

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 15, 2013, Pages 6037-6042

  Schroeder, Diane I ^a,b   Blair, John D ^c   Lott, Paul ^a   Yu, Hung On Ken ^a   Hong, Danna ^a   Crary, Florence ^a,b   Ashwood, Paul ^a,b   Walker, Cheryl ^a,b   Korf, Ian ^a   Robinson, Wendy P ^c   LaSalle, Janine M ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Epigenomics; Hypomethylation

Indexed keywords

BISULFITE; POLYCOMB GROUP PROTEIN;

ARTICLE; CELL FUNCTION; CELL LINE; CPG ISLAND; DEVELOPMENTAL GENE; DNA METHYLATION; GENETIC ANALYSIS; GENOME; GESTATIONAL AGE; HUMAN; HUMAN TISSUE; PLACENTA; PRIORITY JOURNAL; PROMOTER REGION; RNA SEQUENCE; TISSUE SPECIFICITY;

BIOLOGICAL MARKERS; CHILD; CHILD, PRESCHOOL; CHROMATIN; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; GENOME, HUMAN; HUMANS; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLACENTA; PREGNANCY; SEQUENCE ANALYSIS, RNA; SULFITES;

EID: 84876063296     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1215145110     Document Type: Article

References (43)

1. Ehrlich M, et al. (1982) Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res 10(8):2709-2721.
2. Gama-Sosa MA, et al. (1983) Tissue-specific differences in DNA methylation in various mammals. Biochim Biophys Acta 740(2):212-219.
3. Lister R, et al. (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471(7336):68-73.
4. Shearstone JR, et al. (2011) Global DNA demethylation during mouse erythropoiesis in vivo. Science 334(6057):799-802.
5. Lister R, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271):315-322.
6. Schroeder DI, Lott P, Korf I, LaSalle JM (2011) Large-scale methylation domains mark a functional subset of neuronally expressed genes. Genome Res 21(10):1583-1591.
7. Hansen KD, et al. (2011) Increased methylation variation in epigenetic domains across cancer types. Nat Genet 43(8):768-775.
8. Berman BP, et al. (2012) Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet 44(1):40-46.
9. Shann Y-J, et al. (2008) Genome-wide mapping and characterization of hypomethylated sites in human tissues and breast cancer cell lines. Genome Res 18(5):791-801.
10. Hon GC, et al. (2012) Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res 22(2):246-258.
11. Fuke C, et al. (2004) Age related changes in 5-methylcytosine content in human peripheral leukocytes and placentas: An HPLC-based study. Ann Hum Genet 68(Pt 3):196-204.
12. Cotton AM, et al. (2009) Inactive X chromosome-specific reduction in placental DNA methylation. Hum Mol Genet 18(19):3544-3552.
13. Grigoriu A, et al. (2011) Cell specific patterns of methylation in the human placenta. Epigenetics 6(3):368-379.
14. Novakovic B, Saffery R (2010) DNA methylation profiling highlights the unique nature of the human placental epigenome. Epigenomics 2(5):627-638.
15. Chu T, et al. (2011) Structural and regulatory characterization of the placental epigenome at its maternal interface. PLoS ONE 6(2):e14723.
16. Aran D, Toperoff G, Rosenberg M, Hellman A (2011) Replication timing-related and gene body-specific methylation of active human genes. Hum Mol Genet 20(4):670-680.
17. Yuen RK, Peñaherrera MS, von Dadelszen P, McFadden DE, Robinson WP (2010) DNA methylation profiling of human placentas reveals promoter hypomethylation of multiple genes in early-onset preeclampsia. Eur J Hum Genet 18(9):1006-1012.
18. Banister CE, et al. (2011) Infant growth restriction is associated with distinct patterns of DNA methylation in human placentas. Epigenetics 6(7):920-927.
19. Chavan-Gautam P, et al. (2011) Gestation-dependent changes in human placental global DNA methylation levels. Mol Reprod Dev 78(3):150.
20. Kulkarni A, Chavan-Gautam P, Mehendale S, Yadav H, Joshi S (2011) Global DNA methylation patterns in placenta and its association with maternal hypertension in pre-eclampsia. DNA Cell Biol 30(2):79-84.
21. Lambertini L, et al. (2011) Differential methylation of imprinted genes in growthrestricted placentas. Reprod Sci 18(11):1111-1117.
22. Novakovic B, Saffery R (2012) The ever growing complexity of placental epigenetics - role in adverse pregnancy outcomes and fetal programming. Placenta 33(12):959-970.
23. Lynch MD, et al. (2012) An interspecies analysis reveals a key role for unmethylated CpG dinucleotides in vertebrate Polycomb complex recruitment. EM BO J 31(2):317-329.
24. Mendenhall EM, et al. (2010) GC-rich sequence elements recruit PRC2 in mammalian ES cells. PLoS Genet 6(12):e1001244.
25. Ku M, et al. (2008) Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet 4(10):e1000242.
26. Tanay A, O' Donnell AH, Damelin M, Bestor TH (2007) Hyperconserved CpG domains underlie Polycomb-binding sites. Proc Natl Acad Sci USA 104(13):5521-5526.
27. Branciamore S, Chen Z-X, Riggs AD, Rodin SN (2010) CpG island clusters and proepigenetic selection for CpGs in protein-coding exons of HOX and other transcription factors. Proc Natl Acad Sci USA 107(35):15485-15490.
28. Orlando DA, Guenther MG, Frampton GM, Young RA (2012) CpG island structure and trithorax/polycomb chromatin domains in human cells. Genomics 100(5):320-326.
29. Li J, et al. (2012) Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome. PLoS Genet 8(5):e1002692.
30. Price EM, et al. (2013) Additional annotation enhances potential for biologicallyrelevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array. Epigenetics Chromatin 6(1):4.
31. Pavicic W, Joensuu EI, Nieminen T, Peltomäki P (2012) LINE-1 hypomethylation in familial and sporadic cancer. J Mol Med (Berl) 90(7):827-835.
32. Price EM, et al. (2012) Different measures of "genome-wide" DNA methylation exhibit unique properties in placental and somatic tissues. Epigenetics 7(6):652-663.
33. Huang W, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37(1):1-13.
34. Irizarry RA, et al. (2009) The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41(2):178-186.
35. Ji H, et al. (2010) Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature 467(7313):338-342.
36. Jones PA, Baylin SB (2007) The epigenomics of cancer. Cell 128(4):683-692.
37. Ehrlich M (2009) DNA hypomethylation in cancer cells. Epigenomics 1(2):239-259.
38. Martins-Taylor K, Schroeder DI, Lasalle JM, Lalande M, Xu R-H (2012) Role of DNMT3B in the regulation of early neural and neural crest specifiers. Epigenetics 7(1):71-82.
39. Enstrom AM, et al. (2009) Altered gene expression and function of peripheral blood natural killer cells in children with autism. Brain Behav Immun 23(1):124-133.
40. Chen P-Y, Cokus SJ, Pellegrini M (2010) BS Seeker: Precise mapping for bisulfite sequencing. BMC Bioinformatics 11:203.
41. Maksimovic J, Gordon L, Oshlack A (2012) SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome Biol 13(6):R44.
42. Du P, et al. (2010) Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics 11:587.
43. Trapnell C, et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7(3):562-578.