Single-Cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

Genome Research

Volumn 23, Issue 12, 2013, Pages 2126-2135

  Guo, Hongshan ^a   Zhu, Ping ^a   Wu, Xinglong ^a   Li, Xianlong ^a   Wen, Lu ^a   Tang, Fuchou ^a  

^a PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; SPACER DNA;

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DEMETHYLATION; DNA METHYLATION; DNA SEQUENCE; EMBRYO; EMBRYO DEVELOPMENT; EMBRYONIC STEM CELL; FEMALE; FERTILIZATION; GENOME ANALYSIS; HAPLOIDY; MALE; MOUSE; NONHUMAN; PRIORITY JOURNAL; SINGLE CELL ANALYSIS; SPERM; ZYGOTE;

ANIMALS; CELL NUCLEUS; CELLS, CULTURED; CPG ISLANDS; DNA METHYLATION; EMBRYO, MAMMALIAN; EMBRYONIC DEVELOPMENT; EMBRYONIC STEM CELLS; EPIGENESIS, GENETIC; FEMALE; FERTILIZATION; GENOME; HAPLOIDY; MALE; MICE; MICE, INBRED C57BL; MOLECULAR SEQUENCE ANNOTATION; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SINGLE-CELL ANALYSIS; SPERMATOZOA; ZYGOTE;

EID: 84890526238     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.161679.113     Document Type: Article

References (46)

1. Bao S, Tang F, Li X, Hayashi K, Gillich A, Lao K, Surani MA. 2009. Epigenetic reversion of post-implantation epiblast to pluripotent embryonic stem cells. Nature 461: 1292-1295
2. Bird A. 2002. DNA methylation patterns and epigenetic memory. Genes Dev 16: 6-21
3. Bock C. 2012. Analysing and interpreting DNA methylation data. Nat Rev Genet 13: 705-719
4. Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, ReikW, Balasubramanian S. 2012. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336: 934-937
5. Chan MM, Smith ZD, Egli D, Regev A, Meissner A. 2012. Mouse ooplasm confers context-specific reprogramming capacity. Nat Genet 44: 978-980
6. Deaton AM, Bird A. 2011. CpG islands and the regulation of transcription. Genes Dev 25: 1010-1022
7. Farthing CR, Ficz G, Ng RK, Chan CF, Andrews S, Dean W, Hemberger M, ReikW. 2008. Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes. PLoS Genet 4: e1000116
8. Ferreira J, Carmo-Fonseca M. 1997. Genome replication in early mouse embryos follows a defined temporal and spatial order. J Cell Sci 110: 889-897
9. Gomez D, Shankman LS, Nguyen AT, Owens GK. 2013. Detection of histone modifications at specific gene loci in single cells in histological sections. Nat Methods 10: 171-177
10. Gu H, Bock C, Mikkelsen TS, Jäger N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A. 2010. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7: 133-136
11. Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A. 2011a. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc 6: 468-481
12. Gu TP, Guo F, Yang H,Wu HP, Xu GF, LiuW, Xie ZG, Shi L, He X, Jin SG, et al. 2011b. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 477: 606-610
13. Hackett JA, Reddington JP, Nestor CE, Dunican DS, Branco MR, Reichmann J, Reik W, Surani MA, Adams IR, Meehan RR. 2012. Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline. Development 139: 3623-3632
14. Hackett JA, Sengupta R, Zylicz JJ, Murakami K, Lee C, Down TA, Surani MA. 2013. Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine. Science 339: 448-452
15. Inoue A, Matoba S, Zhang Y. 2012. Transcriptional activation of transposable elements in mouse zygotes is independent of Tet3- mediated 5-methylcytosine oxidation. Cell Res 22: 1640-1649
16. Iqbal K, Jin SG, Pfeifer GP, Szabó PE. 2011. Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc Natl Acad Sci 108: 3642-3647
17. Jaenisch R, Bird A. 2003. Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals. Nat Genet 33 (Suppl):245-254
18. Kalisky T, Quake SR. 2011. Single-cell genomics. Nat Methods 8: 311-314
19. Krueger F, Andrews SR. 2011. Bismark: A flexible aligner and methylation caller for bisulfite-seq applications. Bioinformatics 27: 1571-1572
20. Kurimoto K, Yabuta Y, Ohinata Y, Ono Y, Uno KD, Yamada RG, Ueda HR, SaitouM. 2006. An improved single-cell cDNA amplificationmethod for efficient high-density oligonucleotide microarray analysis. Nucleic Acids Res 34: e42
21. Li E. 2002. Chromatin modification and epigenetic reprogramming in mammalian development. Nat Rev Genet 3: 662-673
22. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al. 2009. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322
23. Marusyk A, Almendro V, Polyak K. 2012. Intra-tumour heterogeneity: A looking glass for cancer? Nat Rev Cancer 12: 323-334
24. Mayer W, Niveleau A, Walter J, Fundele R, Haaf T. 2000. Demethylation of the zygotic paternal genome. Nature 403: 501-502
25. Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R. 2005. Reduced representation bisulfite sequencing for comparative highresolution DNA methylation analysis. Nucleic Acids Res 33: 5868-5877
26. Mikkelsen TS, KuM, Jaffe DB, Issac B, Lieberman E,GiannoukosG, Alvarez P, Brockman W, Kim TK, Koche RP, et al. 2007. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560
27. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, et al. 2011. Tumour evolution inferred by single-cell sequencing. Nature 472: 90-94
28. Okada Y, Yamagata K, Hong K, Wakayama T, Zhang Y. 2010. A role for the elongator complex in zygotic paternal genome demethylation. Nature 463: 554-558
29. Okano M, Bell DW, Haber DA, Li E. 1999. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99: 247-257
30. Oswald J, Engemann S, Lane N, Mayer W, Olek A, Fundele R, Dean W, Reik W, Walter J. 2000. Active demethylation of the paternal genome in the mouse zygote. Curr Biol 10: 475-478
31. Reik W. 2007. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447: 425-432
32. Rodriguez-Paredes M, Esteller M. 2011. Cancer epigenetics reaches mainstream oncology. Nat Med 17: 330-339
33. Santos F, Hendrich B, Reik W, Dean W. 2002. Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev Biol 241: 172-182
34. Smallwood SA, Kelsey G. 2012. Genome-wide analysis of DNA methylation in low cell numbers by reduced representation bisulfite sequencing. Methods Mol Biol 925: 187-197
35. Smallwood SA, Tomizawa S, Krueger F, Ruf N, Carli N, Segonds-Pichon A, Sato S, Hata K, Andrews SR, Kelsey G. 2011. Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nat Genet 43: 811-814
36. Smith ZD, Gu H, Bock C, Gnirke A, Meissner A. 2009. High-throughput bisulfite sequencing in mammalian genomes. Methods 48: 226-232
37. Smith ZD, Chan MM, Mikkelsen TS, Gu H, Gnirke A, Regev A, Meissner A. 2012. A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature 484: 339-344
38. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N,Wang X, Bodeau J, Tuch BB, Siddiqui A, et al. 2009. mRNA-seq whole-transcriptome analysis of a single cell. Nat Methods 6: 377-382
39. Tang F, Barbacioru C, Nordman E, Bao S, Lee C,Wang X, Tuch BB, Heard E, Lao K, Surani MA. 2011a. Deterministic and stochastic allele specific gene expression in single mouse blastomeres. PLoS ONE 6: e21208
40. Tang F, Lao K, Surani MA. 2011b. Development and applications of singlecell transcriptome analysis. Nat Methods 8: S6-S11
41. Toyooka Y, Shimosato D, Murakami K, Takahashi K, Niwa H. 2008. Identification and characterization of subpopulations in undifferentiated ES cell culture. Development 135: 909-918
42. Wossidlo M, Nakamura T, Lepikhov K, Marques CJ, Zakhartchenko V, Boiani M, Arand J, Nakano T, ReikW,Walter J. 2011. 5-Hydroxymethylcytosine in themammalian zygote is linked with epigenetic reprogramming. Nat Commun 2: 241
43. Wu H, Zhang Y. 2011. Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. Genes Dev 25: 2436-2452
44. Xu YN, Cui XS, Tae JC, Jin YX, Kim NH. 2011. DNA synthesis and epigenetic modification during mouse oocyte fertilization by human or hamster sperm injection. J Assist Reprod Genet 28: 325-333
45. Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B, et al. 2012. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 149: 1368-1380
46. Zong C, Lu S, Chapman AR, Xie XS. 2012. Genome-wide detection of singlenucleotide and copy-number variations of a single human cell. Science 338: 1622-1626