Abstract
Induced pluripotency is a powerful tool to derive patient-specific stem cells. In addition, it provides a unique assay to study the interplay between transcription factors and chromatin structure. Here, we review the latest insights into chromatin dynamics that are inherent to induced pluripotency. Moreover, we compare and contrast these events with other physiological and pathological processes that involve changes in chromatin and cell state, including germ cell maturation and tumorigenesis. We propose that an integrated view of these seemingly diverse processes could provide mechanistic insights into cell fate transitions in general and might lead to new approaches in regenerative medicine and cancer treatment.
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References
Stadtfeld, M. & Hochedlinger, K. Induced pluripotency: history, mechanisms, and applications. Genes Dev. 24, 2239–2263 (2010).
Yamanaka, S. & Blau, H. M. Nuclear reprogramming to a pluripotent state by three approaches. Nature 465, 704–712 (2010).
Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006).
Brambrink, T. et al. Sequential expression of pluripotency markers during direct reprogramming of mouse somatic cells. Cell Stem Cell 2, 151–159 (2008).
Stadtfeld, M., Maherali, N., Breault, D. & Hochedlinger, K. Defining molecular cornerstones during fibroblast to iPS cell reprogramming in mouse. Cell Stem Cell 2, 230–240 (2008).
Maherali, N. et al. Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell 1, 55–70 (2007).
Orkin, S. H. & Hochedlinger, K. Chromatin connections to pluripotency and cellular reprogramming. Cell 145, 835–850 (2011).
Nakagawa, M. et al. Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts. Nature Biotechnol. 26, 101–106 (2008).
Wernig, M., Meissner, A., Cassady, J. & Jaenisch, R. c-Myc is dispensable for direct reprogramming of mouse fibroblasts. Cell Stem Cell 2, 10–12 (2008).
Polo, J. M. et al. A molecular roadmap of reprogramming somatic cells into iPS cells. Cell 151, 1617–1632 (2012).
Sridharan, R. et al. Role of the murine reprogramming factors in the induction of pluripotency. Cell 136, 364–377 (2009).
Lin, C. Y. et al. Transcriptional amplification in tumor cells with elevated c-Myc. Cell 151, 56–67 (2012).
Rahl, P. B. et al. c-Myc regulates transcriptional pause release. Cell 141, 432–445 (2010).
Mansour, A. A. et al. The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming. Nature 488, 409–413 (2012).
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). This study performed the first single cell transcriptional analysis of nascent iPSCs and identified an early stochastic and a late deterministic phase.
Shu, J. et al. Induction of pluripotency in mouse somatic cells with lineage specifiers. Cell 153, 963–975 (2013). This report demonstrated that iPSCs can be derived through ectopic expression of lineage specifiers rather than conventional pluripotency factors.
Loh, K. M. & Lim, B. A precarious balance: pluripotency factors as lineage specifiers. Cell Stem Cell 8, 363–369 (2011).
Hanna, J. et al. Direct reprogramming of terminally differentiated mature B lymphocytes to pluripotency. Cell 133, 250–264 (2008).
Hikichi, T. et al. Transcription factors interfering with dedifferentiation induce cell type-specific transcriptional profiles. Proc. Natl Acad. Sci. USA 110, 6412–6417 (2013).
Gifford, C. A. et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell 153, 1149–1163 (2013).
Xie, W. et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134–1148 (2013). References 20 and 21 established comprehensive chromatin and DNA methylation maps of pluripotent and diverse lineage-restricted cells.
Zhu, J. et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152, 642–654 (2013).
Koche, R. P. et al. Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell 8, 96–105 (2011).
Soufi, A., Donahue, G. & Zaret, K. Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell 151, 994–1004 (2012). This publication determined how somatic chromatin structure influences access by reprogramming factors and identified important barriers to iPSC formation.
Polo, J. M. & Hochedlinger, K. When fibroblasts MET iPSCs. Cell Stem Cell 7, 5–6 (2010).
Taberlay, P. C. et al. Polycomb-repressed genes have permissive enhancers that initiate reprogramming. Cell 147, 1283–1294 (2011).
Wen, B., Wu, H., Shinkai, Y., Irizarry, R. A. & Feinberg, A. P. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nature Genet. 41, 246–250 (2009).
Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006).
Marks, H. et al. The transcriptional and epigenomic foundations of ground state pluripotency. Cell 149, 590–604 (2012).
Jia, J. et al. Regulation of pluripotency and self- renewal of ESCs through epigenetic-threshold modulation and mRNA pruning. Cell 151, 576–589 (2012).
Onder, T. T. et al. Chromatin-modifying enzymes as modulators of reprogramming. Nature 483, 598–602 (2012).
Fragola, G. et al. Cell reprogramming requires silencing of a core subset of polycomb targets. PLoS Genet. 9, e1003292 (2013).
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).
Zhao, W. et al. Jmjd3 inhibits reprogramming by upregulating expression of INK4a/Arf and targeting PHF20 for ubiquitination. Cell 152, 1037–1050 (2013).
Liang, G., He, J. & Zhang, Y. Kdm2b promotes induced pluripotent stem cell generation by facilitating gene activation early in reprogramming. Nature Cell Biol. 14, 457–466 (2012).
Chen, J. et al. H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nature Genet. 45, 34–42 (2013).
Sridharan, R. et al. Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency. Nature Cell Biol. 15, 872–882 (2013). Reports 36 and 37 identified H3K9 methylation as a major chromatin barrier of cellular reprogramming into iPSCs.
Ang, Y. S. et al. Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell 145, 183–197 (2011).
Esch, D. et al. A unique Oct4 interface is crucial for reprogramming to pluripotency. Nature Cell Biol. 15, 295–301 (2013).
Kohli, R. M. & Zhang, Y. TET enzymes, TDG and the dynamics of DNA demethylation. Nature 502, 472–479 (2013).
Pawlak, M. & Jaenisch, R. De novo DNA methylation by Dnmt3a and Dnmt3b is dispensable for nuclear reprogramming of somatic cells to a pluripotent state. Genes Dev. 25, 1035–1040 (2011).
Mikkelsen, T. S. et al. Dissecting direct reprogramming through integrative genomic analysis. Nature 454, 49–55 (2008).
Doege, C. A. et al. Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2. Nature 488, 652–655 (2012).
Costa, Y. et al. NANOG-dependent function of TET1 and TET2 in establishment of pluripotency. Nature 495, 370–374 (2013).
Silva, J. et al. Nanog is the gateway to the pluripotent ground state. Cell 138, 722–737 (2009).
Gao, Y. et al. Replacement of Oct4 by Tet1 during iPSC induction reveals an important role of DNA methylation and hydroxymethylation in reprogramming. Cell Stem Cell 12, 453–469 (2013).
Lister, R. et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471, 68–73 (2011).
de Laat, W. & Duboule, D. Topology of mammalian developmental enhancers and their regulatory landscapes. Nature 502, 499–506 (2013).
Skene, P. J. & Henikoff, S. Histone variants in pluripotency and disease. Development 140, 2513–2524 (2013).
Gaspar-Maia, A. et al. MacroH2A histone variants act as a barrier upon reprogramming towards pluripotency. Nature Commun. 4, 1565 (2013).
Pasque, V. et al. Histone variant macroH2A marks embryonic differentiation in vivo and acts as an epigenetic barrier to induced pluripotency. J. Cell Sci. 125, 6094–6104 (2012).
Barrero, M. J. et al. Macrohistone variants preserve cell identity by preventing the gain of H3K4me2 during reprogramming to pluripotency. Cell Rep. 3, 1005–1011 (2013).
Singhal, N. et al. Chromatin-remodeling components of the BAF complex facilitate reprogramming. Cell 141, 943–955 (2010).
Gaspar-Maia, A. et al. Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature 460, 863–868 (2009).
Luo, M. et al. NuRD Blocks reprogramming of mouse somatic cells into pluripotent stem cells. Stem Cells 31, 1278–1286 (2013).
Rais, Y et al. Deterministic direct reprogramming of somatic cells to pluipotency. Nature http://dx.doi.org/10.1038/nature12587 (18 September 2013). This study reports that the depletion of the NURD component Mbd3 during iPSC induction is sufficient to render reprogramming a deterministic process.
Yildirim, O. et al. Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell 147, 1498–1510 (2011).
Peric-Hupkes, D. et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol. Cell 38, 603–613 (2010).
Phillips-Cremins, J. E. et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 153, 1281–1295 (2013).
Kagey, M. H. et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 467, 430–435 (2010).
Apostolou, E. et al. Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell 12, 699–712 (2013).
Wei, Z. et al. Klf4 organizes long-range chromosomal interactions with the Oct4 locus in reprogramming and pluripotency. Cell Stem Cell 13, 36–47 (2013).
Zhang, H. et al. Intrachromosomal looping is required for activation of endogenous pluripotency genes during reprogramming. Cell Stem Cell 13, 30–35 (2013). References 61–63 identified pluripotency-specific, genome-wide interaction networks around pluripotency loci and implicate mediator and cohesin in their regulation.
Levasseur, D. N., Wang, J., Dorschner, M., Stamatoyannopoulos, J. & Orkin, S. Oct4 dependence of chromatin structure within the extended Nanog locus in ES cells. Genes Dev. 22, 575–580 (2008).
Schoenfelder, S. et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nature Genet. 42, 53–61 (2010).
Whyte, W. A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307–319 (2013).
Silva, J. et al. Promotion of reprogramming to ground state pluripotency by signal inhibition. PLoS Biol. 6, e253 (2008).
Yang, J. et al. Stat3 activation is limiting for reprogramming to ground state pluripotency. Cell Stem Cell 7, 319–328 (2010).
Ichida, J. K. et al. A small-molecule inhibitor of Tgf-β signaling replaces Sox2 in reprogramming by inducing Nanog. Cell Stem Cell 5, 491–503 (2009).
Maherali, N. & Hochedlinger, K. Tgfβ signal inhibition cooperates in the induction of iPSCs and replaces Sox2 and cMyc. Curr. Biol. 19, 1718–1723 (2009).
Ho, L. et al. esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function. Nature Cell Biol. 13, 903–913 (2011).
Leitch, H. G. et al. Naive pluripotency is associated with global DNA hypomethylation. Nature Struct. Mol. Biol. 20, 311–316 (2013).
Yamaji, M. et al. PRDM14 ensures naive pluripotency through dual regulation of signaling and epigenetic pathways in mouse embryonic stem cells. Cell Stem Cell 12, 368–382 (2013). References 71 and 72 characterize the effect of combined Gsk3/Mapk signal inhibition ('2i') on the epigenome of ES cells and provide an intriguing link to Prdm14.
Ho, R., Papp, B., Hoffman, J. A., Merrill, B. J. & Plath, K. Stage-specific regulation of reprogramming to induced pluripotent stem cells by wnt signaling and T cell factor proteins. Cell Rep. 3, 2113–2126 (2013).
Esteban, M. A. et al. Vitamin C enhances the generation of mouse and human induced pluripotent stem cells. Cell Stem Cell 6, 71–79 (2010).
Stadtfeld, M. et al. Ascorbic acid prevents loss of Dlk1–Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells. Nature Genet. 44, 398–405 (2012).
Blaschke, K. et al. Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells. Nature 500, 222–226 (2013).
O'Malley, J. et al. High-resolution analysis with novel cell-surface markers identifies routes to iPS cells. Nature 499, 88–91 (2013).
Hansson, J. et al. Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency. Cell Rep. 2, 1579–1592 (2012).
Tanabe, K., Nakamura, M., Narita, M., Takahashi, K. & Yamanaka, S. Maturation, not initiation, is the major roadblock during reprogramming toward pluripotency from human fibroblasts. Proc. Natl Acad. Sci. USA 110, 12172–12179 (2013).
Golipour, A. et al. A late transition in somatic cell reprogramming requires regulators distinct from the pluripotency network. Cell Stem Cell 11, 769–782 (2012).
Hou, P. et al. Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds. Science 341, 651–654 (2013). This provocative report suggests that induced pluripotency can be achieved with four small compounds and without the use of transcription factors.
Egli, D. et al. Reprogramming within hours following nuclear transfer into mouse but not human zygotes. Nature Commun. 2, 488 (2011).
Gu, T. P. et al. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 477, 606–610 (2011).
Wu, G. et al. Establishment of totipotency does not depend on Oct4A. Nature Cell Biol. 15, 1089–1097 (2013). The authors of this study discovered that Oct4 is dispensable for reprogramming somatic nuclei by SCNT, which pointed to important mechanistic differences with induced pluripotency.
Maekawa, M. et al. Direct reprogramming of somatic cells is promoted by maternal transcription factor Glis1. Nature 474, 225–229 (2011).
Jullien, J., Astrand, C., Halley-Stott, R. P., Garrett, N. & Gurdon, J. B. Characterization of somatic cell nuclear reprogramming by oocytes in which a linker histone is required for pluripotency gene reactivation. Proc. Natl Acad. Sci. USA 107, 5483–5488 (2010).
Lu, X. et al. Drosophila H1 regulates the genetic activity of heterochromatin by recruitment of Su(var)3–9. Science 340, 78–81 (2013).
Yang, S. M., Kim, B. J., Norwood Toro, L. & Skoultchi, A. I. H1 linker histone promotes epigenetic silencing by regulating both DNA methylation and histone H3 methylation. Proc. Natl Acad. Sci. USA 110, 1708–1713 (2013).
Nashun, B., Akiyama, T., Suzuki, M. G. & Aoki, F. Dramatic replacement of histone variants during genome remodeling in nuclear-transferred embryos. Epigenetics 6, 1489–1497 (2011).
Jullien, J. et al. HIRA dependent H3.3 deposition is required for transcriptional reprogramming following nuclear transfer to Xenopus oocytes. Epigenetics Chromatin 5, 17 (2012).
Pasque, V., Gillich, A., Garrett, N. & Gurdon, J. B. Histone variant macroH2A confers resistance to nuclear reprogramming. EMBO J. 30, 2373–2387 (2011).
Han, D. W. et al. Pluripotential reprogramming of the somatic genome in hybrid cells occurs with the first cell cycle. Stem Cells 26, 445–454 (2008).
Piccolo, F. M. et al. Different roles for Tet1 and Tet2 proteins in reprogramming-mediated erasure of imprints induced by EGC fusion. Mol. Cell 49, 1023–1033 (2013).
Pereira, C. F. et al. Heterokaryon-based reprogramming of human B lymphocytes for pluripotency requires Oct4 but not Sox2. PLoS Genet. 4, e1000170 (2008).
Do, J. T. et al. Enhanced reprogramming of Xist by induced upregulation of Tsix and Dnmt3a. Stem Cells 26, 2821–2831 (2008).
Foshay, K. M. et al. Embryonic stem cells induce pluripotency in somatic cell fusion through biphasic reprogramming. Mol. Cell 46, 159–170 (2012).
Ma, D. K., Chiang, C. H., Ponnusamy, K., Ming, G. L. & Song, H. G9a and Jhdm2a regulate embryonic stem cell fusion-induced reprogramming of adult neural stem cells. Stem Cells 26, 2131–2141 (2008).
Pereira, C. F. et al. ESCs require PRC2 to direct the successful reprogramming of differentiated cells toward pluripotency. Cell Stem Cell 6, 547–556 (2010).
Hajkova, P. et al. Chromatin dynamics during epigenetic reprogramming in the mouse germ line. Nature 452, 877–881 (2008).
Magnúsdóttir, E., Gillich, A., Grabole, N. & Surani, M. A. Combinatorial control of cell fate and reprogramming in the mammalian germline. Curr. Opin. Genet. Dev. 22, 466–474 (2012).
Chuva de Sousa Lopes, S. M. et al. X chromosome activity in mouse XX primordial germ cells. PLoS Genet. 4, e30 (2008).
Sachs, M. et al. Bivalent chromatin marks developmental regulatory genes in the mouse embryonic germline in vivo. Cell Rep. 3, 1777–1784 (2013).
Durcova-Hills, G., Tang, F., Doody, G., Tooze, R. & Surani, M. A. Reprogramming primordial germ cells into pluripotent stem cells. PLoS ONE 3, e3531 (2008).
Krentz, A. D. et al. The DM domain protein DMRT1 is a dose-sensitive regulator of fetal germ cell proliferation and pluripotency. Proc. Natl Acad. Sci. USA 106, 22323–22328 (2009).
Hackett, J. A. et al. Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine. Science 339, 448–452 (2013).
Dawlaty, M. M. et al. Combined deficiency of Tet1 and Tet2 causes epigenetic abnormalities but is compatible with postnatal development. Dev. Cell 24, 310–323 (2013).
Kagiwada, S., Kurimoto, K., Hirota, T., Yamaji, M. & Saitou, M. Replication-coupled passive DNA demethylation for the erasure of genome imprints in mice. EMBO J. 32, 340–353 (2013).
Eminli, S. et al. Differentiation stage determines potential of hematopoietic cells for reprogramming into induced pluripotent stem cells. Nature Genet. 41, 968–976 (2009).
Tan, K. Y., Eminli, S., Hettmer, S., Hochedlinger, K. & Wagers, A. J. Efficient generation of iPS cells from skeletal muscle stem cells. PLoS ONE 6, e26406 (2011).
White, A. C. et al. Defining the origins of Ras/p53-mediated squamous cell carcinoma. Proc. Natl Acad. Sci. USA 108, 7425–7430 (2011).
Barker, N. et al. Crypt stem cells as the cells-of-origin of intestinal cancer. Nature 457, 608–611 (2009).
Folmes, C. D. et al. Somatic oxidative bioenergetics transitions into pluripotency-dependent glycolysis to facilitate nuclear reprogramming. Cell Metab. 14, 264–271 (2011).
Suvà, M. L., Riggi, N. & Bernstein, B. E. Epigenetic reprogramming in cancer. Science 339, 1567–1570 (2013).
He, J., Nguyen, A. T. & Zhang, Y. KDM2b/JHDM1b, an H3K36me2-specific demethylase, is required for initiation and maintenance of acute myeloid leukemia. Blood 117, 3869–3880 (2011).
Tzatsos, A. et al. KDM2B promotes pancreatic cancer via Polycomb-dependent and -independent transcriptional programs. J. Clin. Invest. 123, 727–739 (2013).
Kapoor, A. et al. The histone variant macroH2A suppresses melanoma progression through regulation of CDK8. Nature 468, 1105–1109 (2010).
Gaudet, F. et al. Induction of tumors in mice by genomic hypomethylation. Science 300, 489–492 (2003).
Moran-Crusio, K. et al. Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation. Cancer Cell 20, 11–24 (2011).
Krivtsov, A. V. et al. H3K79 methylation profiles define murine and human MLL–AF4 leukemias. Cancer Cell 14, 355–368 (2008).
Kadoch, C. et al. Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy. Nature Genet. 45, 592–601 (2013).
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).
Hochedlinger, K. et al. Reprogramming of a melanoma genome by nuclear transplantation. Genes Dev. 18, 1875–1885 (2004).
Stricker, S. H. et al. Widespread resetting of DNA methylation in glioblastoma-initiating cells suppresses malignant cellular behavior in a lineage-dependent manner. Genes Dev. 27, 654–669 (2013).
Rapino, F. et al. C/EBPα induces highly efficient macrophage transdifferentiation of B lymphoma and leukemia cell lines and impairs their tumorigenicity. Cell Rep. 3, 1153–1163 (2013).
Acknowledgements
We thank A. Bortvin, D. Egli, V. Pasque, B. Payer, B. Ren, X. Wei, M. Tahiliani and members of the laboratory for helpful suggestions, and B. Lowry, K. Plath and M. Stadtfeld for critical reading of the manuscript. We apologize to those colleagues whose work we could not cite due to space constraints. Support to E.A. was by HHMI and to K.H. by HHMI and NIH (R01HD058013).
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Apostolou, E., Hochedlinger, K. Chromatin dynamics during cellular reprogramming. Nature 502, 462–471 (2013). https://doi.org/10.1038/nature12749
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DOI: https://doi.org/10.1038/nature12749
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