Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells

PLoS Genetics

Volumn 7, Issue 6, 2011, Pages

  Szulwach, Keith E ^a   Li, Xuekun ^a   Li, Yujing ^a   Song, Chun Xiao ^b   Han, Ji Woong ^a   Kim, SangSung ^a   Namburi, Sandeep ^a   Hermetz, Karen ^a   Kim, Julie J ^a   Rudd, M Katharine ^a   Yoon, Young Sup ^a   Ren, Bing ^c,d,e   He, Chuan ^b   Jin, Peng ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c LUDWIG INSTITUTE FOR CANCER RESEARCH   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; GENOMIC DNA; HISTONE; KRUPPEL LIKE FACTOR 4; OCTAMER TRANSCRIPTION FACTOR 4; PROTEIN P300; PROTEIN TAF1; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR NANOG; TRANSCRIPTION FACTOR SOX2; UNCLASSIFIED DRUG; 5 METHYLCYTOSINE; 5-HYDROXYMETHYLCYTOSINE; CYTOSINE; DRUG DERIVATIVE;

ARTICLE; BINDING AFFINITY; BINDING SITE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; EMBRYO; EMBRYONIC STEM CELL; EPIGENETICS; GENETIC ASSOCIATION; GENETIC REGULATION; GENOME ANALYSIS; HETEROCHROMATIN; HISTONE MODIFICATION; HUMAN; HUMAN CELL; IMMUNOPRECIPITATION; METAPHASE CHROMOSOME; PLURIPOTENT STEM CELL; PROMOTER REGION; PROTEIN BINDING; SEQUENCE ANALYSIS; CELL LINE; CHEMISTRY; CHROMOSOME MAP; CYTOLOGY; GENE EXPRESSION REGULATION; GENE LIBRARY; HUMAN GENOME; IMMUNOBLOTTING; METABOLISM; METAPHASE; SEQUENCE ALIGNMENT;

5-METHYLCYTOSINE; BINDING SITES; CELL LINE; CHROMOSOME MAPPING; CYTOSINE; DNA METHYLATION; EMBRYONIC STEM CELLS; EPIGENOMICS; GENE EXPRESSION REGULATION; GENE LIBRARY; GENOME, HUMAN; HETEROCHROMATIN; HISTONES; HUMANS; IMMUNOBLOTTING; METAPHASE; PROMOTER REGIONS, GENETIC; SEQUENCE ALIGNMENT; TRANSCRIPTION FACTORS;

EID: 79959859654     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002154     Document Type: Article

References (28)

1. Jaenisch R, Bird A, (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33 (SUPPL): 245-254.
2. Li E, Bestor TH, Jaenisch R, (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69: 915-926.
3. 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.
4. Ito S, D'Alessio AC, Taranova OV, Hong K, Sowers LC, et al. (2010) Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466: 1129-1133.
5. Iyer LM, Tahiliani M, Rao A, Aravind L, (2009) Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle 8: 1698-1710.
6. Koh KP, Yabuuchi A, Rao S, Huang Y, Cunniff K, et al. (2011) Tet1 and tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell 8: 200-213.
7. Huang Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, et al. (2010) The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS ONE 5: e8888 doi:10.1371/journal.pone.0008888.
8. Jin SG, Kadam S, Pfeifer GP, (2010) Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res 38: e125.
9. Wu H, D'Alessio AC, Ito S, Wang Z, Cui K, et al. (2011) Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes and Development April 2011 679-684: 679-684.
10. Wu H, D'Alessio AC, Ito S, Xia K, Wang Z, et al. (2011) Dual funtions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature.
11. Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, et al. (2011) Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature.
12. Xu Y, Wu F, Tan L, Kong L, Xiong L, et al. (2011) Genome-wide Regulation of 5hmC, 5mC, and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells. Mol Cell.
13. Williams K, Christensen J, Pedersen MT, Johansen JV, Cloos PA, et al. (2011) TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature.
14. Song CX, Szulwach KE, Fu Y, Dai Q, Yi C, et al. (2011) Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol 29: 68-72.
15. Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, et al. (2010) Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6: 479-491.
16. 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.
17. Ferrari R, Pellegrini M, Horwitz GA, Xie W, Berk AJ, et al. (2008) Epigenetic reprogramming by adenovirus e1a. Science 321: 1086-1088.
18. Horwitz GA, Zhang K, McBrian MA, Grunstein M, Kurdistani SK, et al. (2008) Adenovirus small e1a alters global patterns of histone modification. Science 321: 1084-1085.
19. 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.
20. Chia NY, Chan YS, Feng B, Lu X, Orlov YL, et al. (2010) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Nature 468: 316-320.
21. Ma Z, Swigut T, Valouev A, Rada-Iglesias A, Wysocka J, (2011) Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates. Nat Struct Mol Biol 18: 120-127.
22. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, et al. (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324: 930-935.
23. Core LJ, Waterfall JJ, Lis JT, (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322: 1845-1848.
24. Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, et al. (2008) Divergent transcription from active promoters. Science 322: 1849-1851.
25. Bangs CD, Donlon TA, (2005) Metaphase chromosome preparation from cultured peripheral blood cells. Curr Protoc Hum Genet Chapter 4: Unit 4 1.
26. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
27. Hon GC, Hawkins RD, Ren B, (2009) Predictive chromatin signatures in the mammalian genome. Hum Mol Genet 18: R195-201.
28. Hon G, Ren B, Wang W, (2008) ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol 4: e1000201 doi:10.1371/journal.pcbi.1000201.