Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
10.1038/nature09798
Crossref journal-article
Springer Science and Business Media LLC
Nature (297)
Authors 17
  1. Ryan Lister (first)
  2. Mattia Pelizzola (additional)
  3. Yasuyuki S. Kida (additional)
  4. R. David Hawkins (additional)
  5. Joseph R. Nery (additional)
  6. Gary Hon (additional)
  7. Jessica Antosiewicz-Bourget (additional)
  8. Ronan O’Malley (additional)
  9. Rosa Castanon (additional)
  10. Sarit Klugman (additional)
  11. Michael Downes (additional)
  12. Ruth Yu (additional)
  13. Ron Stewart (additional)
  14. Bing Ren (additional)
  15. James A. Thomson (additional)
  16. Ronald M. Evans (additional)
  17. Joseph R. Ecker (additional)
References 37 Referenced 1,304
  1. Soldner, F. et al. Parkinson’s disease patient-derived induced pluripotent stem cells free of viral reprogramming factors. Cell 136, 964–977 (2009) (10.1016/j.cell.2009.02.013) / Cell by F Soldner (2009)
  2. Yamanaka, S. A fresh look at iPS cells. Cell 137, 13–17 (2009) (10.1016/j.cell.2009.03.034) / Cell by S Yamanaka (2009)
  3. Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006) (10.1016/j.cell.2006.07.024) / Cell by K Takahashi (2006)
  4. Takahashi, K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861–872 (2007) (10.1016/j.cell.2007.11.019) / Cell by K Takahashi (2007)
  5. Yu, J. et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 318, 1917–1920 (2007) (10.1126/science.1151526) / Science by J Yu (2007)
  6. Park, I. et al. Reprogramming of human somatic cells to pluripotency with defined factors. Nature 451, 141–146 (2008) (10.1038/nature06534) / Nature by I Park (2008)
  7. Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797–801 (2009) (10.1126/science.1172482) / Science by J Yu (2009)
  8. Zhao, X. Y. et al. iPS cells produce viable mice through tetraploid complementation. Nature 461, 86–90 (2009) (10.1038/nature08267) / Nature by XY Zhao (2009)
  9. Boland, M. J. et al. Adult mice generated from induced pluripotent stem cells. Nature 461, 91–94 (2009) (10.1038/nature08310) / Nature by MJ Boland (2009)
  10. Guenther, M. G. et al. Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. Cell Stem Cell 7, 249–257 (2010) (10.1016/j.stem.2010.06.015) / Cell Stem Cell by MG Guenther (2010)
  11. Deng, J. et al. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nature Biotechnol. 27, 353–360 (2009) (10.1038/nbt.1530) / Nature Biotechnol. by J Deng (2009)
  12. Doi, A. et al. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nature Genet. 41, 1350–1353 (2009) (10.1038/ng.471) / Nature Genet. by A Doi (2009)
  13. Kim, K. et al. Epigenetic memory in induced pluripotent stem cells. Nature 467, 285–290 (2010) (10.1038/nature09342) / Nature by K Kim (2010)
  14. Polo, J. M. et al. Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. Nature Biotechnol. 28, 848–855 (2010) (10.1038/nbt.1667) / Nature Biotechnol. by JM Polo (2010)
  15. Stadtfeld, M. et al. Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature 465, 175–181 (2010) (10.1038/nature09017) / Nature by M Stadtfeld (2010)
  16. Miura, K. et al. Variation in the safety of induced pluripotent stem cell lines. Nature Biotechnol. 27, 743–745 (2009) (10.1038/nbt.1554) / Nature Biotechnol. by K Miura (2009)
  17. Hu, B. Y. et al. Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency. Proc. Natl Acad. Sci. USA 107, 4335–4340 (2010) (10.1073/pnas.0910012107) / Proc. Natl Acad. Sci. USA by BY Hu (2010)
  18. Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009) (10.1038/nature08514) / Nature by R Lister (2009)
  19. Sugii, S. et al. Human and mouse adipose-derived cells support feeder-independent induction of pluripotent stem cells. Proc. Natl Acad. Sci. USA 108, 3558–3563 (2010) (10.1073/pnas.0910172106) / Proc. Natl Acad. Sci. USA by S Sugii (2010)
  20. Daley, G. et al. Broader implications of defining standards for the pluripotency of iPSCs. Cell Stem Cell 4, 200–201 (2009) (10.1016/j.stem.2009.02.009) / Cell Stem Cell by G Daley (2009)
  21. Xu, R. H. et al. BMP4 initiates human embryonic stem cell differentiation to trophoblast. Nature Biotechnol. 20, 1261–1264 (2002) (10.1038/nbt761) / Nature Biotechnol. by RH Xu (2002)
  22. Cedar, H. & Bergman, Y. Linking DNA methylation and histone modification: patterns and paradigms. Nature Rev. Genet. 10, 295–304 (2009) (10.1038/nrg2540) / Nature Rev. Genet. by H Cedar (2009)
  23. Chodavarapu, R. K. et al. Relationship between nucleosome positioning and DNA methylation. Nature 466, 388–392 (2010) (10.1038/nature09147) / Nature by RK Chodavarapu (2010)
  24. Laurent, L. et al. Dynamic changes in the human methylome during differentiation. Genome Res. 20, 320–331 (2010) (10.1101/gr.101907.109) / Genome Res. by L Laurent (2010)
  25. Hawkins, R. D. et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479–491 (2010) (10.1016/j.stem.2010.03.018) / Cell Stem Cell by RD Hawkins (2010)
  26. Erhardt, A. et al. TMEM132D, a new candidate for anxiety phenotypes: evidence from human and mouse studies. Mol. Psychiatry advance online publication. 10.1038/mp.2010.4 (6 April 2010) (10.1038/mp.2010.41)
  27. Yilmaz, G., Alexander, J. S., Erkuran Yilmaz, C. & Granger, D. N. Induction of neuro-protective/regenerative genes in stem cells infiltrating post-ischemic brain tissue. Exp. Transl. Stroke Med. 2, 11 (2010) (10.1186/2040-7378-2-11) / Exp. Transl. Stroke Med. by G Yilmaz (2010)
  28. Li, M. Z. et al. Molecular mapping of developing dorsal horn-enriched genes by microarray and dorsal/ventral subtractive screening. Dev. Biol. 292, 555–564 (2006) (10.1016/j.ydbio.2006.01.033) / Dev. Biol. by MZ Li (2006)
  29. Chin, M. H. et al. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 5, 111–123 (2009) (10.1016/j.stem.2009.06.008) / Cell Stem Cell by MH Chin (2009)
  30. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009) (10.1186/gb-2009-10-3-r25) / Genome Biol. by B Langmead (2009)
  31. Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009) (10.1093/bioinformatics/btp120) / Bioinformatics by C Trapnell (2009)
  32. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnol. 28, 511–515 (2010) (10.1038/nbt.1621) / Nature Biotechnol. by C Trapnell (2010)
  33. Ludwig, T. et al. Feeder-independent culture of human embryonic stem cells. Nature Methods 3, 637–646 (2006) (10.1038/nmeth902) / Nature Methods by T Ludwig (2006)
  34. Ludwig, T. et al. Derivation of human embryonic stem cells in defined conditions. Nature Biotechnol. 24, 185–187 (2006) (10.1038/nbt1177) / Nature Biotechnol. by T Ludwig (2006)
  35. O’Malley, R. C., Alonso, J. M., Kim, C. J., Leisse, T. J. & Ecker, J. R. An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome. Nature Protocols 2, 2910–2917 (2007) (10.1038/nprot.2007.425) / Nature Protocols by RC O’Malley (2007)
  36. Chen, P., Cokus, S. J. & Pellegrini, M. B. S. Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics 11, 203 (2010) (10.1186/1471-2105-11-203) / BMC Bioinformatics by P Chen (2010)
  37. Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008) (10.1016/j.cell.2008.03.029) / Cell by R Lister (2008)
Dates
Type When
Created 14 years, 7 months ago (Feb. 2, 2011, 7:02 a.m.)
Deposited 2 years, 3 months ago (May 18, 2023, 1:50 p.m.)
Indexed 6 days, 14 hours ago (Aug. 31, 2025, 6:12 a.m.)
Issued 14 years, 7 months ago (Feb. 2, 2011)
Published 14 years, 7 months ago (Feb. 2, 2011)
Published Online 14 years, 7 months ago (Feb. 2, 2011)
Published Print 14 years, 6 months ago (March 3, 2011)
Funders 0

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@article{Lister_2011, title={Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells}, volume={471}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/nature09798}, DOI={10.1038/nature09798}, number={7336}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Lister, Ryan and Pelizzola, Mattia and Kida, Yasuyuki S. and Hawkins, R. David and Nery, Joseph R. and Hon, Gary and Antosiewicz-Bourget, Jessica and O’Malley, Ronan and Castanon, Rosa and Klugman, Sarit and Downes, Michael and Yu, Ruth and Stewart, Ron and Ren, Bing and Thomson, James A. and Evans, Ronald M. and Ecker, Joseph R.}, year={2011}, month=feb, pages={68–73} }