An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator

Nature Communications

Volumn 5, Issue , 2014, Pages

  Lee, Dong Sung ^a   Shin, Jong Yeon ^a,b   Tonge, Peter D ^c   Puri, Mira C ^c,d   Lee, Seungbok ^a   Park, Hansoo ^a   Lee, Won Chul ^a,b   Hussein, Samer M I ^c   Bleazard, Thomas ^e   Yun, Ji Young ^a,b   Kim, Jihye ^a,b   Li, Mira ^c   Cloonan, Nicole ^f,g   Wood, David ^f   Clancy, Jennifer L ^h   Mosbergen, Rowland ^f   Yi, Jae Hyuk ^a   Yang, Kap Seok ^b   Kim, Hyungtae ^b   Rhee, Hwanseok ^b   Wells, Christine A ^f,i   Preiss, Thomas ^h,j   Grimmond, Sean M ^f,i   Rogers, Ian M ^c,d   Nagy, Andras ^c,d   Seo, Jeong Sun ^a,b   more..

^a Seoul National University   (South Korea)

^b Macrogen Inc   (South Korea)

^c MOUNT SINAI HOSPITAL   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

^e UNIVERSITY OF MANCHESTER   (United Kingdom)

^f UNIVERSITY OF QUEENSLAND   (Australia)

^g QIMR BERGHOFER MEDICAL RESEARCH INSTITUTE   (Australia)

^h Biology and Environment   (Australia)

ⁱ UNIVERSITY OF GLASGOW   (United Kingdom)

^j VICTOR CHANG CARDIAC RESEARCH INSTITUTE   (Australia)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BONE MORPHOGENETIC PROTEIN 4; HISTONE; HISTONE H3; KRUPPEL LIKE FACTOR 4; OCTAMER TRANSCRIPTION FACTOR 4; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR NANOG; TRANSCRIPTION FACTOR SOX2;

CELL ORGANELLE; DNA; GENETICS; GENOMICS; METHYLATION; PROTEIN;

ANIMAL CELL; ARTICLE; CHROMATIN IMMUNOPRECIPITATION; CPG ISLAND; DNA METHYLATION; EMBRYONIC STEM CELL; EPIGENETICS; GENE EXPRESSION; HISTONE MODIFICATION; MOUSE; NONHUMAN; PLURIPOTENT STEM CELL; PROMOTER REGION; RNA SEQUENCE; SOMATIC CELL;

MURINAE;

EID: 84923368892     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms6619     Document Type: Article

References (37)

1. Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663-676 (2006).
2. Maherali, N. et al. Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell 1, 55-70 (2007).
3. Takahashi, K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861-872 (2007).
4. Yu, J. et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 318, 1917-1920 (2007).
5. Park, I. H. et al. Reprogramming of human somatic cells to pluripotency with defined factors. Nature 451, 141-146 (2008).
6. Kang, L., Wang, J., Zhang, Y., Kou, Z. & Gao, S. iPS cells can support full-term development of tetraploid blastocyst-complemented embryos. Cell Stem Cell 5, 135-138 (2009).
7. Zhao, X. Y. et al. iPS cells produce viable mice through tetraploid complementation. Nature 461, 86-90 (2009).
8. Onder, T. T. et al. Chromatin-modifying enzymes as modulators of reprogramming. Nature 483, 598-602 (2012).
9. Singhal, N. et al. Chromatin-remodeling components of the BAF complex facilitate reprogramming. Cell 141, 943-955 (2010).
10. Woltjen, K. et al. piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells. Nature 458, 766-770 (2009).
11. Samavarchi-Tehrani, P. et al. Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell Stem Cell 7, 64-77 (2010).
12. Mikkelsen, T. S. et al. Dissecting direct reprogramming through integrative genomic analysis. Nature 454, 49-55 (2008).
13. Polo, J. M. et al. A molecular roadmap of reprogramming somatic cells into iPS cells. Cell 151, 1617-1632 (2012).
14. Buganim, Y. et al. Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase. Cell 150, 1209-1222 (2012).
15. Chen, J. et al. Vitamin C modulates TET1 function during somatic cell reprogramming. Nat. Genet. 45, 1504-1509 (2013).
16. Wang, T. et al. The histone demethylases Jhdm1a/1b enhance somatic cell reprogramming in a vitamin-C-dependent manner. Cell Stem Cell 9, 575-587 (2011).
17. Plath, K. & Lowry, W. E. Progress in understanding reprogramming to the induced pluripotent state. Nat. Rev. Genet. 12, 253-265 (2011).
18. Lister, R. et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471, 68-73 (2011).
19. Papp, B. & Plath, K. Epigenetics of reprogramming to induced pluripotency. Cell 152, 1324-1343 (2013).
20. Surani, M. A., Hayashi, K. & Hajkova, P. Genetic and epigenetic regulators of pluripotency. Cell 128, 747-762 (2007).
21. Tonge, P. D. et al. Divergent reprogramming routes lead to alternative stem cell states. Nature doi: 10.1038/nature14047 (2014).
22. Hussein, S. M. I. et al. Genome-wide characterization of the routes to pluripotency. Nature doi: 10.1038/nature14046 (2014).
23. Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106-1117 (2008).
24. Ku, M. et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 4, e1000242 (2008).
25. Wu, H. et al. Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 473, 389-393 (2011).
26. Visel, A., Minovitsky, S., Dubchak, I. & Pennacchio, L. A. VISTA Enhancer Browser-a database of tissue-specific human enhancers. Nucleic Acids Res. 35, D88-D92 (2007).
27. Feng, B. et al. Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb. Nat. Cell Biol. 11, 197-203 (2009).
28. Fischedick, G. et al. Zfp296 is a novel, pluripotent-specific reprogramming factor. PloS ONE 7, e34645 (2012).
29. Stormo, G. D. DNA binding sites: representation and discovery. Bioinformatics 16, 16-23 (2000).
30. Ho Sui, S. J. et al. oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes. Nucleic Acids Res. 33, 3154-3164 (2005).
31. Nagy, A. & Gertsenstein, M. Manipulating the Mouse Embryo: A Laboratory Manual (Cold Spring Harbor Press, 2003).
32. O'Geen, H., Echipare, L. & Farnham, P. J. in Epigenetics Protocols 791, 265-286 (Humana Press, 2011).
33. Gaspar-Maia, A. et al. Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature 460, 863-868 (2009).
34. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
35. Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for bisulfite-Seq applications. Bioinformatics 27, 1571-1572, 2011).
36. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
37. Wells, C. A. et al. Stemformatics: visualisation and sharing of stem cell gene expression. Stem Cell Res. 10, 387-395 (2013).