Genomic distribution and Inter-Sample variation of Non-CpG methylation across human cell types

PLoS Genetics

Volumn 7, Issue 12, 2011, Pages

  Ziller, Michael J ^a,b,c   Müller, Fabian ^a,b,c,d   Liao, Jing ^a,b,c   Zhang, Yingying ^a,b,c   Gu, Hongcang ^a   Bock, Christoph ^a,b,c,d   Boyle, Patrick ^a   Epstein, Charles B ^a   Bernstein, Bradley E ^a,e,f   Lengauer, Thomas ^d   Gnirke, Andreas ^a   Meissner, Alexander ^a,b,c  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b Harvard University   (United States)

^c HARVARD STEM CELL INSTITUTE   (United States)

^d MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

^e HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^f MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CPA DINUCLEOTIDE; CPC DINUCLEOTIDE; CPT DINUCLEOTIDE; DINUCLEOTIDE; DNA METHYLTRANSFERASE 3A; DNA METHYLTRANSFERASE 3B; UNCLASSIFIED DRUG; CYTOSINE; DNA (CYTOSINE 5) METHYLTRANSFERASE; SMALL INTERFERING RNA;

ARTICLE; CELL DIFFERENTIATION; CELL TYPE; CONTROLLED STUDY; DNA METHYLATION; DNA STRUCTURE; GENE EXPRESSION; HUMAN; HUMAN CELL; HUMAN GENOME; PLURIPOTENT STEM CELL; PROTEIN EXPRESSION; SEQUENCE ANALYSIS; ANIMAL; CELL LINE; CPG ISLAND; EMBRYONIC STEM CELL; GENE SILENCING; GENETIC EPIGENESIS; GENETICS; METABOLISM; MOUSE;

IPS; VERTEBRATA;

ANIMALS; CELL DIFFERENTIATION; CELL LINE; CPG ISLANDS; CYTOSINE; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; DNA METHYLATION; EMBRYONIC STEM CELLS; EPIGENESIS, GENETIC; GENE EXPRESSION; GENE KNOCKDOWN TECHNIQUES; GENOME, HUMAN; HUMANS; INDUCED PLURIPOTENT STEM CELLS; MICE; PLURIPOTENT STEM CELLS; RNA, SMALL INTERFERING;

EID: 84855281409     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002389     Document Type: Article

References (35)

1. Goll MG, Bestor TH, (2005) Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74: 481-514.
2. Ramsahoye BH, Biniszkiewicz D, Lyko F, Clark V, Bird AP, et al. (2000) Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci U S A 97: 5237-5242.
3. Haines TR, Rodenhiser DI, Ainsworth PJ, (2001) Allele-specific non-CpG methylation of the Nf1 gene during early mouse development. Dev Biol 240: 585-598.
4. Law JA, Jacobsen SE, (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11: 204-220.
5. Chan SW, Henderson IR, Jacobsen SE, (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6: 351-360.
6. Jeltsch A, (2006) Molecular enzymology of mammalian DNA methyltransferases. Curr Top Microbiol Immunol 301: 203-225.
7. Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, et al. (2005) Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res 33: 5868-5877.
8. Dodge JE, Ramsahoye BH, Wo ZG, Okano M, Li E, (2002) De novo methylation of MMLV provirus in embryonic stem cells: CpG versus non-CpG methylation. Gene 289: 41-48.
9. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322.
10. Laurent L, Wong E, Li G, Huynh T, Tsirigos A, et al. (2010) Dynamic changes in the human methylome during differentiation. Genome Res 20: 320-331.
11. Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, et al. (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature.
12. Bock C, Kiskinis E, Verstappen G, Gu H, Boulting G, et al. (2011) Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines. Cell 144: 439-452.
13. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.
14. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, et al. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 28: 1097-1105.
15. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, et al. (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454: 766-770.
16. Bird A, (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16: 6-21.
17. Boulting GL, Kiskinis E, Croft GF, Amoroso MW, Oakley DH, et al. (2011) A functionally characterized test set of human induced pluripotent stem cells. Nat Biotechnol.
18. Sandoval J, Heyn HA, Moran S, Serra-Musach J, Pujana MA, et al. (2011) Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics 6: 692-702.
19. Bock C, Tomazou EM, Brinkman AB, Muller F, Simmer F, et al. (2010) Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 28: 1106-1114.
20. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560.
21. Dhayalan A, Rajavelu A, Rathert P, Tamas R, Jurkowska RZ, et al. (2010) The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation. J Biol Chem 285: 26114-26120.
22. Wienholz BL, Kareta MS, Moarefi AH, Gordon CA, Ginno PA, et al. (2010) DNMT3L modulates significant and distinct flanking sequence preference for DNA methylation by DNMT3A and DNMT3B in vivo. PLoS Genet 6: e1001106 doi:10.1371/journal.pgen.1001106.
23. Chen PY, Feng S, Joo JW, Jacobsen SE, Pellegrini M, (2011) A comparative analysis of DNA methylation across human embryonic stem cell lines. Genome Biol 12: R62.
24. Jackson M, Krassowska A, Gilbert N, Chevassut T, Forrester L, et al. (2004) Severe global DNA hypomethylation blocks differentiation and induces histone hyperacetylation in embryonic stem cells. Mol Cell Biol 24: 8862-8871.
25. Tomizawa S, Kobayashi H, Watanabe T, Andrews S, Hata K, et al. (2011) Dynamic stage-specific changes in imprinted differentially methylated regions during early mammalian development and prevalence of non-CpG methylation in oocytes. Development 138: 811-820.
26. Jones PA, Liang GN, (2009) OPINION Rethinking how DNA methylation patterns are maintained. Nature Reviews Genetics 10: 805-811.
27. Chen AE, Egli D, Niakan K, Deng J, Akutsu H, et al. (2009) Optimal timing of inner cell mass isolation increases the efficiency of human embryonic stem cell derivation and allows generation of sibling cell lines. Cell Stem Cell 4: 103-106.
28. Cowan CA, Klimanskaya I, McMahon J, Atienza J, Witmyer J, et al. (2004) Derivation of embryonic stem-cell lines from human blastocysts. N Engl J Med 350: 1353-1356.
29. Smith ZD, Gu H, Bock C, Gnirke A, Meissner A, (2009) High-throughput bisulfite sequencing in mammalian genomes. Methods 48: 226-232.
30. Gu H, Bock C, Mikkelsen TS, Jager N, Smith ZD, et al. (2010) Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7: 133-136.
31. Li H, Ruan J, Durbin R, (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
32. Crooks GE, Hon G, Chandonia JM, Brenner SE, (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190.
33. Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, et al. (2009) Ensembl 2009. Nucleic Acids Res 37: D690-697.
34. Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr AR, James KD, et al. (2010) Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet 6: e1001134 doi:10.1371/journal.pgen.1001134.
35. Hastie T, Tibshirani R, Friedman JH, (2009) The elements of statistical learning: data mining, inference, and prediction New York, NY Springer pp. xxii 745.