Abstract
Epigenetic modifications and their regulations govern the identity of every cell type in an organism. Cell differentiation involves a switch in gene expression profile that is accompanied by heritable changes of epigenetic signatures in the differentiated cell type. Differentiation is generally not reversible, thereby conferring cell fate decisions once an altered epigenetic pattern is set. Nevertheless, attempts have been made to reverse a differentiation cell fate to a pluripotent state by various experimental approaches, such as somatic cell nuclear transfer, cell fusion and ectopic expression of defined transcription factors. The fundamental basis of all these strategies is to mediate epigenetic reprogramming, which allows a permanent and completed conversion of cell fate. A comprehensive understanding of the dynamic of epigenetic changes during cell differentiation would provide a more precise and efficient way of reprogramming cell fate. Here we summarize the epigenetic aspects of different reprogramming strategies and discuss the possible mechanisms underlying these epigenetic reprogramming events.
Keywords
- epigenetic
- reprogramming
- somatic cell nuclear transfer
- cell fusion
- transcription factors
- pluripotency
- differentiation
- cell fate
1. Introduction
Development is a complex process that involves a series of cell differentiation pathways starting from totipotent embryonic cells. According to Waddington’s concept of epigenetic landscape, a cell has to interact with surrounding stimuli and respond by giving a phenotype which defines its identity during development [1]. Each cell experiences different inter/intra-cellular signals and hence has its epigenetic signature of cell identity, which in turn directs its own specific gene expression pattern without alteration of DNA sequences (with the exception of the immunoglobulin genes in B and T cells). It is now clear that the diversity of cell type specific gene expression pattern is mediated by means of epigenetic mechanisms, such as DNA methylation, covalent histone modifications and chromatin remodeling. Once a cell’s identity is set, it is difficult to convert it to other unrelated lineages, thus leading to stable and irreversible differentiated cell states. Nevertheless, there are a few exceptions of cell fate conversion during embryo development and adult tissue/organ regeneration, e.g. vascular endothelium to smooth muscle cells [2], which involve changing a cell’s epigenetic signature into another unrelated kind.
Apart from a few exceptions of natural cell fate conversion events, different strategies have been developed aiming to reprogram differentiated somatic cell fate to a pluripotent state (Figure 1). A historical strategy of reprogramming is by somatic cell nuclear transfer (SCNT) experiments. SCNT involves transplantation of a cell nucleus into an enucleated egg/oocyte in order to generate a “cloned” animal with an equivalent genetic composition as the donor individual. It is possible to derive embryonic stem (ES) cells from nuclear transplanted (NT) embryos (ntES cells), which shows indistinguishable pluripotent gene expression profiles when compared to the normal ES cells derived from fertilized embryos. Another strategy of reprogramming is achieved by fusion of a differentiated cell with a pluripotent cell in order to generate a pluripotent-like tetraploid hybrid cell [3, 4, 5]. It has been proposed that cellular components, such as transcription factors, in the pluripotent cell are able to reprogram the differentiated cell nucleus. This idea aligns with the use of cell extracts from pluripotent cell types to revert differentiated cells into a pluripotent-like state [6, 7]. Presumably the cytoplasmic “reprogramming factors” from the pluripotent cells can be isolated and concentrated to achieve a higher reprogramming efficacy. A third strategy involves ectopic expression of defined transcription factors in somatic differentiated cells to generate induced pluripotent stem (iPS) cells. Delivery of the ectopic transcription factors can be achieved by viral approaches, such as the use of retrovirus, lentivirus, adeno-associated virus or Sendai virus, or by using episomal vesicles, or by direct mRNA or protein transfection. This technique has been successfully applied to reprogram a vast number of differentiated somatic cell types. Importantly, iPS cells can also be generated by using combinations of microRNAs (miRNAs) or small chemical molecules without the needs of ectopic expression of reprogramming factors [8]. The three reprogramming strategies show different reprogramming kinetics and efficiencies, which can be associated with the distinct epigenetic mechanisms in the erasure of somatic cell epigenetic signature and re-establishment of the pluripotent one. In this review, we focus on the dynamic changes of epigenetics mediated by different reprogramming strategies and how the modulation of epigenetic status improves the reprogramming efficiency.
2. Epigenetic reprogramming by SCNT
SCNT was first done by Briggs and Kings in 1952, who transplanted a blastula nucleus into an enucleated egg of the amphibian
Although the rate of successful SCNT is very low, the reprogramming ability of factors in the egg/oocyte is highly efficient as the transplanted nuclei take less than 1 day to initiate cell division and trigger the “normal” developmental program. The donor cell epigenetic status has to be reprogrammed in order to support the embryonic program of development. In fact, genome-wide demethylation was observed in the cloned blastocysts [29]. It has been shown that the
Interestingly, it has been shown that the epigenetic state of a differentiated cell is directly correlated with its reprogrammability [40]. SCNT with ES cell nuclei demonstrated a much higher efficiency of generation of NT blastocysts than using other somatic cell types [41]. This could be associated with a more relaxed chromatin configuration in ES cells that may render their epigenome more susceptible for reprogramming [42]. Alternatively, it has been demonstrated that the cloning efficiency can be significantly improved by pre-treating the more differentiated and condensed chromatin state of somatic nuclei with epigenetic modifying agents, e.g. 5-aza-deoxycytidine and trichostatin A (TSA), that facilitate chromatin relaxation [43, 44, 45]. Interestingly, the effect of TSA treatment in improving SCNT is associated with the reactivation of a subset of genes that are repressed by H3K9me3 in the somatic cells [46], presumably through introducing histone hyper-acetylation at their promoters. Altogether, SCNT provides a quick route of epigenetic reprogramming for a differentiated cell to a pluripotent state. Identification of the responsible reprogramming factors in the egg and oocyte cytoplasm will be one of the key future directions to improve the efficiency of SCNT and therapeutic cloning.
3. Epigenetic reprogramming by cell fusion
Cell fusion is a natural event that is crucial for fertilization and in various organs such as placenta, skeletal muscles and bones [47]. It has been proposed that the fusion of bone marrow-derived stem cells and tissue cells, e.g. hepatocytes, is one of the mechanisms of tissue repair [48, 49]. Cell fusion experiments using pluripotent cells, e.g. an ES or embryonic germ (EG) cell, were shown to be able to reprogram a differentiated cell type [3, 4, 5]. Both ES and EG cells possess reprogramming ability and are able to reactivate pluripotent genes and silence differentiation genes in the somatic cell nucleus within a tetraploid hybrid cell after cell fusion. It is indeed the case that the new transcription profile of a hybrid cell is partly contributed by the reprogrammed somatic nucleus to a pluripotent-like state. Moreover, injection of hybrid cells into normal diploid blastocysts demonstrated their contribution to all three germ layers in the chimeras [4, 50], indicating the pluripotent nature of hybrid cells. Similar to the SCNT, different somatic cell types show different kinetics of reprogramming by the cell fusion approach, which could be associated with the somatic chromatin accessibility status [51, 52].
Cell fusion with a pluripotent cell can trigger extensive epigenetic reprogramming in the differentiated cell nucleus. It has been shown that reactivation of
Reprogramming to pluripotency by cell fusion approach requires lengthy selection of the successfully reprogrammed hybrid cells. The reprogramming efficiency of cell fusion is usually less than 0.001%, depending on the somatic cell types [50, 58]. The low reprogramming efficiency in hybrid cells can be largely enhanced by manipulation of key pluripotency-associated genes like
4. Epigenetic reprogramming by defined transcription factors
In a groundbreaking discovery, Yamanaka
By using the defined transcription factor approach to reprogram cell fate, about 0.1–3% of the somatic starting cell population can be converted into iPS cells in around 2–3 weeks. The reprogramming efficiency is believed to be correlated with the differentiation state of the starting somatic cells. It has been shown that hematopoietic stem and progenitor cells can be reprogrammed to iPS cells 300 times more efficient than the terminally differentiated B and T cells [68]. Interestingly, partially de-differentiating mature B cells by either knockdown of
A number of epigenetic remodeling factors are involved in the reprogramming events. Both polycomb (PcG) and trithorax (TrxG) group proteins were found to be crucial in the derivation of iPS cell colonies. Upon knockdown of
Previous studies demonstrated that the partially reprogrammed iPS cells contained significantly fewer genes marked by the bivalent chromatin signature (co-existence of both H3K4 and H3K27 methylation) and an enrichment of DNA hyper-methylated loci when compared to the wild-type ES cells and the fully reprogrammed iPS cells [70]. Therefore, it is proposed that completion of the epigenetic reprogramming process is pre-requisite for the acquisition of pluripotency. This is supported by the observation that treatment of partially reprogrammed iPS cells with the DNA methyltransferase inhibitor 5-aza-cytidine was able to promote their transition into the fully reprogrammed pluripotent state [70]. Besides, inhibition of H3K27 methyltransferase Ezh2 by small molecule, GSK-126, reduced reprogramming efficiency [84], whereas inhibition of DOT1L by small molecule, EPZ004777, showed enhancement of reprogramming [83]. Various histone deacetylase inhibitors (HDACi) were also shown to improve reprogramming [96, 97, 98, 99, 100]. In combination with HDACi valproic acid, human iPS cells can be generated only with Oct4 and Sox2 with a comparable reprogramming efficiency by the four Yamanaka factors [101]. Interestingly, it was found that vitamin C can increase reprogramming efficiency by promoting the transition of pre-iPS cells to fully reprogrammed cells [102], potentially through acting as a cofactor of Kdm2b to induce H3K36me2/3 demethylation [78], activation of H3K9 demethylases (Kdm3a, 3b, 4c and 4d) to remove H3K9me3 [89], and promoting Tet-mediated DNA demethylation [103]. With the aid of small chemical molecules, the iPS cell reprogramming efficiency and duration could be further improved.
5. “Epigenetic memory” in reprogrammed cells
“Epigenetic memory” refers to the persistent expression of parental genes in the daughter cells through the inheritance of distinctive epigenetic marks. Consequently, the epigenetic profile of a parent cell is faithfully passed on to its daughter cells such that the gene expression pattern is memorized and maintained throughout cell generations. In the situation of reprogramming cell fate, the persistent somatic cell epigenetic signature and the expression of lineage genes in the reprogrammed cells is thus regarded as an example of epigenetic memory.
Even though it has been shown that prolonged
The epigenetic memory in NT embryos that maintains the donor expression gene states can be explained by the inheritance of DNA methylation patterns. Heritability of DNA methylation is mediated by the activity of the maintenance DNA methyltransferase Dnmt1 which preferentially targets hemi-methylated DNA. Thus, Dnmt1 restores the parental methylation status on the newly synthesized daughter DNA strand, thereby maintaining a silent gene state after cell division [108]. Methylated donor genes, such as pluripotency genes, remain inactivated after SCNT, apparently owing to the persistent donor-specific methylation pattern in the cloned embryos, possibility mediated by the residual somatic form of Dnmt in the donor nucleus. DNA methylation therefore provides a plausible mechanism for the propagation of a silent memory state in SCNT [109]. On the other hand, an active gene memory of the donor differentiation state is also observed in NT embryos. For example, both the donor endoderm and neurectoderm markers,
Early studies of iPS cells demonstrated that the Nanog-iPS cells displayed not only a highly similar transcriptome to wild-type ES cells, but also an ES cell histone modification profile. Genome-wide comparison of histone modifications (H3K4 and H3K27 tri-methylation) between ES cells, MEFs and MEF-derived iPS cells demonstrated that more than 94% of the ES- or MEF-signature genes in iPS cells have identical histone methylation marks as in ES cells. Only 0.7% of these signature genes retain the histone methylation status of the original MEFs [63]. However, other gene expression profile studies of iPS cells showed that a significant number of differentiation genes have a similar expression pattern to that in the somatic cell of origin, but not in ES cells [114, 115, 116, 117]. This transcriptional memory in iPS cells was found to be correlated with biased differentiation towards the original cell lineage, and with less competence in differentiation to other unrelated somatic lineages [115, 118, 119, 120, 121]. Importantly, the persistent expression of somatic genes in iPS cells was associated with the somatic DNA methylation pattern [117, 122, 123, 124], highlighting the crucial role of epigenetic regulation in the retention of memory. This is in fact similar to the observation that an incomplete removal of donor cell DNA methylation pattern was observed in some aberrantly developed NT embryos [125]. Strikingly, the addition of epigenetic modifying agents, such as DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5-aza-dC), can enhance the iPS cell reprogramming efficiency [70] and improve the differentiation competency to other unrelated somatic lineages [120]. Interestingly, it has been demonstrated that continuous passaging of iPS cells abrogates somatic DNA methylation patterns [115], which suggests a passive replication-dependent mechanism in loss of the parental memory in iPS cells. Nevertheless, a study showed that the epigenetic memory in some iPS cell lines cannot be removed even after extended passages [124]. Apart from DNA methylation, microRNA expression pattern was also shown to have a role in the retention of somatic memory in iPS cells derived from hematopoietic progenitors [126]. However, it should be emphasized that other profiling studies of iPS cells failed to find the gene expression and epigenetic differences when compared to ES cells [127, 128]. It thus proposes that the “somatic memory” in iPS cells could be an artifact of incomplete reprogramming resulting in variation between iPS cell lines [129]. It is also possible that there are individual iPS cell lines expressing gene signatures owing to culture conditions and laboratory practices [130], similar to the scenario that some ES cell lines exhibit preferential differentiation towards specific lineages [131, 132, 133]. In summary, the epigenetic memory in iPS cells remains a contentious issue.
6. Conclusions and perspectives
Although the term “epigenetic landscape” was first introduced by Waddington in 1942 [1], our understanding of how the epigenome of a cell type is maintained and altered during differentiation is still far from complete. The reversal of the differentiated state of a cell has important implications for our understanding of normal development and for regenerative medicine. Epigenetic reprogramming provides heritable changes of cell identity, and thus is a key event for the complete and permanent conversion of cell fate (Figure 2). Although reprogramming of cell fate can be achieved by different strategies, the rate (reprogramming time) and efficiency (number of reprogrammed cells) are far from comparable to the natural event during fertilization/de-differentiation. Achieving a complete epigenetic reversion to generate reprogrammed cells or iPS cells with a comparable potency state of early embryos would imply that these cells can respond correctly to differentiation-promoting signals, and more importantly, decrease the tumorigenic potential owing to pre-disposing epimutations. Notably, the status of epigenetic memory in iPS cells can be regarded as a state of incomplete reprogramming. The biased differentiation owing to the persistent somatic epigenetic memory in iPS cells might be useful in efficient differentiation to the desired cell type of origin, which usually results in a heterogeneous cell population by using un-optimized differentiation protocols. On the contrary, it has been shown that
Acknowledgments
This work was supported by the Research Grants Council of the Hong Kong Special Administrative Region (SAR), China (Grant no. HKU775510M and HKU774712M).
References
- 1.
Waddington CH. The epigenotype. Endeavour. 1942; 1 :18-20 - 2.
Frid MG, Kale VA, Stenmark KR. Mature vascular endothelium can give rise to smooth muscle cells via endothelial-mesenchymal transdifferentiation: In vitro analysis. Circulation Research. 2002; 90 :1189-1196 - 3.
Tada M, Tada T, Lefebvre L, Barton SC, Surani MA. Embryonic germ cells induce epigenetic reprogramming of somatic nucleus in hybrid cells. The EMBO Journal. 1997; 16 :6510-6520 - 4.
Tada M, Takahama Y, Abe K, Nakatsuji N, Tada T. Nuclear reprogramming of somatic cells by in vitro hybridization with ES cells. Current Biology. 2001; 11 :1553-1558 - 5.
Tada M, Morizane A, Kimura H, Kawasaki H, Ainscough JF, Sasai Y, et al. Pluripotency of reprogrammed somatic genomes in embryonic stem hybrid cells. Developmental Dynamics. 2003; 227 :504-510 - 6.
Hakelien AM, Landsverk HB, Robl JM, Skalhegg BS, Collas P. Reprogramming fibroblasts to express T-cell functions using cell extracts. Nature Biotechnology. 2002; 20 :460-466 - 7.
Taranger CK, Noer A, Sorensen AL, Hakelien AM, Boquest AC, Collas P. Induction of dedifferentiation, genomewide transcriptional programming, and epigenetic reprogramming by extracts of carcinoma and embryonic stem cells. Molecular Biology of the Cell. 2005; 16 :5719-5735 - 8.
Hochedlinger K, Jaenisch R. Induced pluripotency and epigenetic reprogramming. Cold Spring Harbor Perspectives in Biology. 2015; 7 :1-24. DOI: 10.1101/cshperspect.a019448 - 9.
Briggs R, King TJ. Transplantation of living nuclei from blastula cells into enucleated frogs' eggs. Proceedings of the National Academy of Sciences of the United States of America. 1952; 38 :455-463 - 10.
Gurdon JB, Uehlinger V. "Fertile" intestine nuclei. Nature. 1966; 210 :1240-1241 - 11.
Wilmut I, Schnieke AE, McWhir J, Kind AJ, Campbell KH. Viable offspring derived from fetal and adult mammalian cells. Nature. 1997; 385 :810-813 - 12.
Loi P, Iuso D, Czernik M, Ogura A. A new, dynamic era for somatic cell nuclear transfer? Trends in Biotechnology. 2016; 34 :791-797. DOI: 10.1016/j.tibtech.2016.03.008 - 13.
Meissner A, Jaenisch R. Mammalian nuclear transfer. Developmental Dynamics. 2006; 235 :2460-2469 - 14.
Yang X, Smith SL, Tian XC, Lewin HA, Renard JP, Wakayama T. Nuclear reprogramming of cloned embryos and its implications for therapeutic cloning. Nature Genetics. 2007; 39 :295-302 - 15.
Wilmut I, Bai Y, Taylor J. Somatic cell nuclear transfer: Origins, the present position and future opportunities. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 2015; 370 :20140366. DOI: 10.1098/rstb.2014.0366 - 16.
Boiani M, Eckardt S, Scholer HR, McLaughlin KJ. Oct4 distribution and level in mouse clones: Consequences for pluripotency. Genes & Development. 2002; 16 :1209-1219 - 17.
Bortvin A, Eggan K, Skaletsky H, Akutsu H, Berry DL, Yanagimachi R, et al. Incomplete reactivation of Oct4-related genes in mouse embryos cloned from somatic nuclei. Development. 2003; 130 :1673-1680 - 18.
Ng RK, Gurdon JB. Epigenetic memory of active gene transcription is inherited through somatic cell nuclear transfer. Proceedings of the National Academy of Sciences of the United States of America. 2005; 102 :1957-1962 - 19.
Inoue K, Kohda T, Lee J, Ogonuki N, Mochida K, Noguchi Y, et al. Faithful expression of imprinted genes in cloned mice. Science. 2002; 295 :297 - 20.
Mann MR, Chung YG, Nolen LD, Verona RI, Latham KE, Bartolomei MS. Disruption of imprinted gene methylation and expression in cloned preimplantation stage mouse embryos. Biology of Reproduction. 2003; 69 :902-914 - 21.
Liu JH, Yin S, Xiong B, Hou Y, Chen DY, Sun QY. Aberrant DNA methylation imprints in aborted bovine clones. Molecular Reproduction and Development. 2008; 75 :598-607 - 22.
Eggan K, Akutsu H, Loring J, Jackson-Grusby L, Klemm M, Rideout WM 3rd, et al. Hybrid vigor, fetal overgrowth, and viability of mice derived by nuclear cloning and tetraploid embryo complementation. Proceedings of the National Academy of Sciences of the United States of America. 2001; 98 :6209-6214 - 23.
Rideout WM 3rd, Eggan K, Jaenisch R. Nuclear cloning and epigenetic reprogramming of the genome. Science. 2001; 293 :1093-1098 - 24.
Shen CJ, Lin CC, Shen PC, Cheng WT, Chen HL, Chang TC, et al. Imprinted genes and satellite loci are differentially methylated in bovine somatic cell nuclear transfer clones. Cellular Reprogramming. 2013; 15 :413-424. DOI: 10.1089/cell.2013.0012 - 25.
Murphey P, Yamazaki Y, McMahan CA, Walter CA, Yanagimachi R, McCarrey JR. Epigenetic regulation of genetic integrity is reprogrammed during cloning. Proceedings of the National Academy of Sciences of the United States of America. 2009; 106 :4731-4735. DOI: 10.1073/pnas.0900687106 - 26.
Tamashiro KL, Wakayama T, Akutsu H, Yamazaki Y, Lachey JL, Wortman MD, et al. Cloned mice have an obese phenotype not transmitted to their offspring. Nature Medicine. 2002; 8 :262-267 - 27.
Chan MM, Smith ZD, Egli D, Regev A, Meissner A. Mouse ooplasm confers context-specific reprogramming capacity. Nature Genetics. 2012; 44 :978-980. DOI: 10.1038/ng.2382 - 28.
Dean W, Santos F, Reik W. Epigenetic reprogramming in early mammalian development and following somatic nuclear transfer. Seminars in Cell & Developmental Biology. 2003; 14 :93-100 - 29.
Niemann H, Carnwath JW, Herrmann D, Wieczorek G, Lemme E, Lucas-Hahn A, et al. DNA methylation patterns reflect epigenetic reprogramming in bovine embryos. Cellular Reprogramming. 2010; 12 :33-42. DOI: 10.1089/cell.2009.0063 - 30.
Simonsson S, Gurdon J. DNA demethylation is necessary for the epigenetic reprogramming of somatic cell nuclei. Nature Cell Biology. 2004; 6 :984-990 - 31.
Gu TP, Guo F, Yang H, Wu HP, Xu GF, Liu W, et al. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature. 2011; 477 :606-610. DOI: 10.1038/nature10443 - 32.
Kikyo N, Wade PA, Guschin D, Ge H, Wolffe AP. Active remodeling of somatic nuclei in egg cytoplasm by the nucleosomal ATPase ISWI. Science. 2000; 289 :2360-2362 - 33.
Hansis C, Barreto G, Maltry N, Niehrs C. Nuclear reprogramming of human somatic cells by xenopus egg extract requires BRG1. Current Biology. 2004; 14 :1475-1480 - 34.
Wen D, Banaszynski LA, Rosenwaks Z, Allis CD, Rafii S. H3.3 replacement facilitates epigenetic reprogramming of donor nuclei in somatic cell nuclear transfer embryos. Nucleus. 2014; 5 :369-375. DOI: 10.4161/nucl.36231 - 35.
Pasque V, Gillich A, Garrett N, Gurdon JB. Histone variant macroH2A confers resistance to nuclear reprogramming. The EMBO Journal. 2011; 30 :2373-2387. DOI: 10.1038/emboj.2011.144 - 36.
Antony J, Oback F, Chamley LW, Oback B, Laible G. Transient JMJD2B-mediated reduction of H3K9me3 levels improves reprogramming of embryonic stem cells into cloned embryos. Molecular and Cellular Biology. 2013; 33 :974-983. DOI: 10.1128/MCB.01014-12 - 37.
Matoba S, Liu Y, Lu F, Iwabuchi KA, Shen L, Inoue A, et al. Embryonic development following somatic cell nuclear transfer impeded by persisting histone methylation. Cell. 2014; 159 :884-895. DOI: 10.1016/j.cell.2014.09.055 - 38.
Liu X, Wang Y, Gao Y, Su J, Zhang J, Xing X, et al. H3K9 demethylase KDM4E is an epigenetic regulator for bovine embryonic development and a defective factor for nuclear reprogramming. Development. 2018; 145 :dev158261. DOI: 10.1242/dev.158261 - 39.
Chung YG, Matoba S, Liu Y, Eum JH, Lu F, Jiang W, et al. Histone demethylase expression enhances human somatic cell nuclear transfer efficiency and promotes derivation of pluripotent stem cells. Cell Stem Cell. 2015; 17 :758-766. DOI: 10.1016/j.stem.2015.10.001 - 40.
Oback B, Wells DN. Donor cell differentiation, reprogramming, and cloning efficiency: Elusive or illusive correlation? Molecular Reproduction and Development. 2007; 74 :646-654. DOI: 10.1002/mrd.20654 - 41.
Hochedlinger K, Jaenisch R. Nuclear reprogramming and pluripotency. Nature. 2006; 441 :1061-1067 - 42.
Meshorer E, Misteli T. Chromatin in pluripotent embryonic stem cells and differentiation. Nature Reviews. Molecular Cell Biology. 2006; 7 :540-546 - 43.
Enright BP, Kubota C, Yang X, Tian XC. Epigenetic characteristics and development of embryos cloned from donor cells treated by trichostatin A or 5-aza-2'-deoxycytidine. Biology of Reproduction. 2003; 69 :896-901 - 44.
Enright BP, Sung LY, Chang CC, Yang X, Tian XC. Methylation and acetylation characteristics of cloned bovine embryos from donor cells treated with 5-aza-2'-deoxycytidine. Biology of Reproduction. 2005; 72 :944-948 - 45.
Kishigami S, Bui HT, Wakayama S, Tokunaga K, Van Thuan N, Hikichi T, et al. Successful mouse cloning of an outbred strain by trichostatin A treatment after somatic nuclear transfer. The Journal of Reproduction and Development. 2007; 53 :165-170 - 46.
Inoue K, Oikawa M, Kamimura S, Ogonuki N, Nakamura T, Nakano T, et al. Trichostatin A specifically improves the aberrant expression of transcription factor genes in embryos produced by somatic cell nuclear transfer. Scientific Reports. 2015; 5 :10127. DOI: 10.1038/srep10127 - 47.
Larsson LI, Bjerregaard B, Talts JF. Cell fusions in mammals. Histochemistry and Cell Biology. 2008; 129 :551-561 - 48.
Wang X, Willenbring H, Akkari Y, Torimaru Y, Foster M, Al-Dhalimy M, et al. Cell fusion is the principal source of bone-marrow-derived hepatocytes. Nature. 2003; 422 :897-901 - 49.
Vassilopoulos G, Wang PR, Russell DW. Transplanted bone marrow regenerates liver by cell fusion. Nature. 2003; 422 :901-904 - 50.
Cowan CA, Atienza J, Melton DA, Eggan K. Nuclear reprogramming of somatic cells after fusion with human embryonic stem cells. Science. 2005; 309 :1369-1373 - 51.
Malinowski AR, Fisher AG. Reprogramming of somatic cells towards pluripotency by cell fusion. Methods in Molecular Biology. 2016; 1480 :289-299. DOI: 10.1007/978-1-4939-6380-5_25 - 52.
Soza-Ried J, Fisher AG. Reprogramming somatic cells towards pluripotency by cellular fusion. Current Opinion in Genetics & Development. 2012; 22 :459-465. DOI: 10.1016/j.gde.2012.07.005 - 53.
Pereira CF, Terranova R, Ryan NK, Santos J, Morris KJ, Cui W, et al. Heterokaryon-based reprogramming of human B lymphocytes for pluripotency requires Oct4 but not Sox2. PLoS Genetics. 2008; 4 :e1000170. DOI: 10.1371/journal.pgen.1000170 - 54.
Bhutani N, Brady JJ, Damian M, Sacco A, Corbel SY, Blau HM. Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature. 2010; 463 :1042-1047. DOI: 10.1038/nature08752 - 55.
Piccolo FM, Bagci H, Brown KE, Landeira D, Soza-Ried J, Feytout A, et al. Different roles for Tet1 and Tet2 proteins in reprogramming-mediated erasure of imprints induced by EGC fusion. Molecular Cell. 2013; 49 :1023-1033. DOI: 10.1016/j.molcel.2013.01.032 - 56.
Kimura H, Tada M, Nakatsuji N, Tada T. Histone code modifications on pluripotential nuclei of reprogrammed somatic cells. Molecular and Cellular Biology. 2004; 24 :5710-5720 - 57.
Pereira CF, Piccolo FM, Tsubouchi T, Sauer S, Ryan NK, Bruno L, et al. ESCs require PRC2 to direct the successful reprogramming of differentiated cells toward pluripotency. Cell Stem Cell. 2010; 6 :547-556. DOI: 10.1016/j.stem.2010.04.013 - 58.
Silva J, Chambers I, Pollard S, Smith A. Nanog promotes transfer of pluripotency after cell fusion. Nature. 2006; 441 :997-1001 - 59.
Theunissen TW, van Oosten AL, Castelo-Branco G, Hall J, Smith A, Silva JC. Nanog overcomes reprogramming barriers and induces pluripotency in minimal conditions. Current Biology. 2011; 21 :65-71. DOI: 10.1016/j.cub.2010.11.074 - 60.
Wong CC, Gaspar-Maia A, Ramalho-Santos M, Reijo Pera RA. High-efficiency stem cell fusion-mediated assay reveals Sall4 as an enhancer of reprogramming. PLoS One. 2008; 3 :e1955 - 61.
Lluis F, Pedone E, Pepe S, Cosma MP. Periodic activation of Wnt/beta-catenin signaling enhances somatic cell reprogramming mediated by cell fusion. Cell Stem Cell. 2008; 3 :493-507 - 62.
Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006; 126 :663-676 - 63.
Wernig M, Meissner A, Foreman R, Brambrink T, Ku M, Hochedlinger K, et al. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature. 2007; 448 :318-324 - 64.
Okita K, Ichisaka T, Yamanaka S. Generation of germline-competent induced pluripotent stem cells. Nature. 2007; 448 :313-317 - 65.
Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, et al. Induced pluripotent stem cell lines derived from human somatic cells. Science. 2007; 318 :1917-1920 - 66.
Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell. 2007; 131 :861-872 - 67.
Park IH, Zhao R, West JA, Yabuuchi A, Huo H, Ince TA, et al. Reprogramming of human somatic cells to pluripotency with defined factors. Nature. 2008; 451 :141-146 - 68.
Eminli S, Foudi A, Stadtfeld M, Maherali N, Ahfeldt T, Mostoslavsky G, et al. Differentiation stage determines potential of hematopoietic cells for reprogramming into induced pluripotent stem cells. Nature Genetics. 2009; 41 :968-976. DOI: 10.1038/ng.428 - 69.
Hanna J, Markoulaki S, Schorderet P, Carey BW, Beard C, Wernig M, et al. Direct reprogramming of terminally differentiated mature B lymphocytes to pluripotency. Cell. 2008; 133 :250-264 - 70.
Mikkelsen TS, Hanna J, Zhang X, Ku M, Wernig M, Schorderet P, et al. Dissecting direct reprogramming through integrative genomic analysis. Nature. 2008; 454 :49-55 - 71.
Koche RP, Smith ZD, Adli M, Gu H, Ku M, Gnirke A, et al. Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell. 2011; 8 :96-105. DOI: 10.1016/j.stem.2010.12.001 - 72.
Hussein SM, Puri MC, Tonge PD, Benevento M, Corso AJ, Clancy JL, et al. Genome-wide characterization of the routes to pluripotency. Nature. 2014; 516 :198-206. DOI: 10.1038/nature14046 - 73.
Stadtfeld M, Maherali N, Breault DT, Hochedlinger K. Defining molecular cornerstones during fibroblast to iPS cell reprogramming in mouse. Cell Stem Cell. 2008; 2 :230-240. DOI: 10.1016/j.stem.2008.02.001 - 74.
Sridharan R, Tchieu J, Mason MJ, Yachechko R, Kuoy E, Horvath S, et al. Role of the murine reprogramming factors in the induction of pluripotency. Cell. 2009; 136 :364-377. DOI: 10.1016/j.cell.2009.01.001 - 75.
Samavarchi-Tehrani P, Golipour A, David L, Sung HK, Beyer TA, Datti A, et al. Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell Stem Cell. 2010; 7 :64-77. DOI: 10.1016/j.stem.2010.04.015 - 76.
Li R, Liang J, Ni S, Zhou T, Qing X, Li H, et al. A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. Cell Stem Cell. 2010; 7 :51-63. DOI: 10.1016/j.stem.2010.04.014 - 77.
Nguyen AT, Zhang Y. The diverse functions of Dot1 and H3K79 methylation. Genes & Development. 2011; 25 :1345-1358. DOI: 10.1101/gad.2057811 - 78.
Wang T, Chen K, Zeng X, Yang J, Wu Y, Shi X, et al. The histone demethylases Jhdm1a/1b enhance somatic cell reprogramming in a vitamin-C-dependent manner. Cell Stem Cell. 2011; 9 :575-587. DOI: 10.1016/j.stem.2011.10.005 - 79.
Polo JM, Anderssen E, Walsh RM, Schwarz BA, Nefzger CM, Lim SM, et al. A molecular roadmap of reprogramming somatic cells into iPS cells. Cell. 2012; 151 :1617-1632. DOI: 10.1016/j.cell.2012.11.039 - 80.
Pasque V, Tchieu J, Karnik R, Uyeda M, Sadhu Dimashkie A, Case D, et al. X chromosome reactivation dynamics reveal stages of reprogramming to pluripotency. Cell. 2014; 159 :1681-1697. DOI: 10.1016/j.cell.2014.11.040 - 81.
Kim JS, Choi HW, Arauzo-Bravo MJ, Scholer HR, Do JT. Reactivation of the inactive X chromosome and post-transcriptional reprogramming of Xist in iPSCs. Journal of Cell Science. 2015; 128 :81-87. DOI: 10.1242/jcs.154294 - 82.
Ang YS, Tsai SY, Lee DF, Monk J, Su J, Ratnakumar K, et al. Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell. 2011; 145 :183-197. DOI: 10.1016/j.cell.2011.03.003 - 83.
Onder TT, Kara N, Cherry A, Sinha AU, Zhu N, Bernt KM, et al. Chromatin-modifying enzymes as modulators of reprogramming. Nature. 2012; 483 :598-602. DOI: 10.1038/nature10953 - 84.
Rao RA, Dhele N, Cheemadan S, Ketkar A, Jayandharan GR, Palakodeti D, et al. Ezh2 mediated H3K27me3 activity facilitates somatic transition during human pluripotent reprogramming. Scientific Reports. 2015; 5 :8229. DOI: 10.1038/srep08229 - 85.
Mansour AA, Gafni O, Weinberger L, Zviran A, Ayyash M, Rais Y, et al. The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming. Nature. 2012; 488 :409-413. DOI: 10.1038/nature11272 - 86.
Pasque V, Radzisheuskaya A, Gillich A, Halley-Stott RP, Panamarova M, Zernicka-Goetz M, et al. Histone variant macroH2A marks embryonic differentiation in vivo and acts as an epigenetic barrier to induced pluripotency. Journal of Cell Science. 2012; 125 :6094-6104. DOI: 10.1242/jcs.113019 - 87.
Gaspar-Maia A, Qadeer ZA, Hasson D, Ratnakumar K, Leu NA, Leroy G, et al. MacroH2A histone variants act as a barrier upon reprogramming towards pluripotency. Nature Communications. 2013; 4 :1565. DOI: 10.1038/ncomms2582 - 88.
Liang G, He J, Zhang Y. Kdm2b promotes induced pluripotent stem cell generation by facilitating gene activation early in reprogramming. Nature Cell Biology. 2012; 14 :457-466. DOI: 10.1038/ncb2483 - 89.
Chen J, Liu H, Liu J, Qi J, Wei B, Yang J, et al. H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nature Genetics. 2013; 45 :34-42. DOI: 10.1038/ng.2491 - 90.
Soufi A, Donahue G, Zaret KS. Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell. 2012; 151 :994-1004. DOI: 10.1016/j.cell.2012.09.045 - 91.
Sridharan R, Gonzales-Cope M, Chronis C, Bonora G, McKee R, Huang C, et al. Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1gamma in reprogramming to pluripotency. Nature Cell Biology. 2013; 15 :872-882. DOI: 10.1038/ncb2768 - 92.
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 & Development. 2011; 25 :1035-1040. DOI: 10.1101/gad.2039011 - 93.
Gao Y, Chen J, Li K, Wu T, Huang B, Liu W, et al. Replacement of Oct4 by Tet1 during iPSC induction reveals an important role of DNA methylation and hydroxymethylation in reprogramming. Cell Stem Cell. 2013; 12 :453-469. DOI: 10.1016/j.stem.2013.02.005 - 94.
Doege CA, Inoue K, Yamashita T, Rhee DB, Travis S, Fujita R, et al. Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2. Nature. 2012; 488 :652-655. DOI: 10.1038/nature11333 - 95.
Hu X, Zhang L, Mao SQ, Li Z, Chen J, Zhang RR, et al. Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming. Cell Stem Cell. 2014; 14 :512-522. DOI: 10.1016/j.stem.2014.01.001 - 96.
Huangfu D, Maehr R, Guo W, Eijkelenboom A, Snitow M, Chen AE, et al. Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nature Biotechnology. 2008; 26 :795-797. DOI: 10.1038/nbt1418 - 97.
Liang G, Taranova O, Xia K, Zhang Y. Butyrate promotes induced pluripotent stem cell generation. The Journal of Biological Chemistry. 2010; 285 :25516-25521. DOI: 10.1074/jbc.M110.142059 - 98.
Mali P, Chou BK, Yen J, Ye Z, Zou J, Dowey S, et al. Butyrate greatly enhances derivation of human induced pluripotent stem cells by promoting epigenetic remodeling and the expression of pluripotency-associated genes. Stem Cells. 2010; 28 :713-720. DOI: 10.1002/stem.402 - 99.
Zhang Z, Gao Y, Gordon A, Wang ZZ, Qian Z, Wu WS. Efficient generation of fully reprogrammed human iPS cells via polycistronic retroviral vector and a new cocktail of chemical compounds. PLoS One. 2011; 6 :e26592. DOI: 10.1371/journal.pone.0026592 - 100.
Zhang Z, Wu WS. Sodium butyrate promotes generation of human induced pluripotent stem cells through induction of the miR302/367 cluster. Stem Cells and Development. 2013; 22 :2268-2277. DOI: 10.1089/scd.2012.0650 - 101.
Huangfu D, Osafune K, Maehr R, Guo W, Eijkelenboom A, Chen S, et al. Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2. Nature Biotechnology. 2008; 26 :1269-1275 - 102.
Esteban MA, Wang T, Qin B, Yang J, Qin D, Cai J, et al. Vitamin C enhances the generation of mouse and human induced pluripotent stem cells. Cell Stem Cell. 2010; 6 :71-79. DOI: 10.1016/j.stem.2009.12.001 - 103.
Minor EA, Court BL, Young JI, Wang G. Ascorbate induces ten-eleven translocation (Tet) methylcytosine dioxygenase-mediated generation of 5-hydroxymethylcytosine. The Journal of Biological Chemistry. 2013; 288 :13669-13674. DOI: 10.1074/jbc.C113.464800 - 104.
Wrenzycki C, Herrmann D, Keskintepe L, Martins A Jr, Sirisathien S, Brackett B, et al. Effects of culture system and protein supplementation on mRNA expression in pre-implantation bovine embryos. Human Reproduction. 2001; 16 :893-901 - 105.
Farin PW, Piedrahita JA, Farin CE. Errors in development of fetuses and placentas from in vitro-produced bovine embryos. Theriogenology. 2006; 65 :178-191. DOI: 10.1016/j.theriogenology.2005.09.022 - 106.
Kang YK, Koo DB, Park JS, Choi YH, Chung AS, Lee KK, et al. Aberrant methylation of donor genome in cloned bovine embryos. Nature Genetics. 2001; 28 :173-177 - 107.
Dean W, Santos F, Stojkovic M, Zakhartchenko V, Walter J, Wolf E, et al. Conservation of methylation reprogramming in mammalian development: Aberrant reprogramming in cloned embryos. Proceedings of the National Academy of Sciences of the United States of America. 2001; 98 :13734-13738 - 108.
Pradhan S, Esteve PO. Mammalian DNA (cytosine-5) methyltransferases and their expression. Clinical Immunology. 2003; 109 :6-16 - 109.
Ng RK, Gurdon JB. Maintenance of epigenetic memory in cloned embryos. Cell Cycle. 2005; 4 :760-763 - 110.
Ng RK, Gurdon JB. Epigenetic memory of an active gene state depends on histone H3.3 incorporation into chromatin in the absence of transcription. Nature Cell Biology. 2008; 10 :102-109 - 111.
McKittrick E, Gafken PR, Ahmad K, Henikoff S. Histone H3.3 is enriched in covalent modifications associated with active chromatin. Proceedings of the National Academy of Sciences of the United States of America. 2004; 101 :1525-1530 - 112.
Hake SB, Garcia BA, Duncan EM, Kauer M, Dellaire G, Shabanowitz J, et al. Expression patterns and post-translational modifications associated with mammalian histone H3 variants. The Journal of Biological Chemistry. 2006; 281 :559-568 - 113.
Ng RK, Gurdon JB. Epigenetic inheritance of cell differentiation status. Cell Cycle. 2008; 7 :1173-1177 - 114.
Chin MH, Mason MJ, Xie W, Volinia S, Singer M, Peterson C, et al. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell. 2009; 5 :111-123. DOI: 10.1016/j.stem.2009.06.008 - 115.
Polo JM, Liu S, Figueroa ME, Kulalert W, Eminli S, Tan KY, et al. Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. Nature Biotechnology. 2010; 28 :848-855. DOI: 10.1038/nbt.1667 - 116.
Marchetto MC, Yeo GW, Kainohana O, Marsala M, Gage FH, Muotri AR. Transcriptional signature and memory retention of human-induced pluripotent stem cells. PLoS One. 2009; 4 :e7076. DOI: 10.1371/journal.pone.0007076 - 117.
Ohi Y, Qin H, Hong C, Blouin L, Polo JM, Guo T, et al. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nature Cell Biology. 2011; 13 :541-549. DOI: 10.1038/ncb2239 - 118.
Bar-Nur O, Russ HA, Efrat S, Benvenisty N. Epigenetic memory and preferential lineage-specific differentiation in induced pluripotent stem cells derived from human pancreatic islet beta cells. Cell Stem Cell. 2011; 9 :17-23. DOI: 10.1016/j.stem.2011.06.007 - 119.
Sanchez-Freire V, Lee AS, Hu S, Abilez OJ, Liang P, Lan F, et al. Effect of human donor cell source on differentiation and function of cardiac induced pluripotent stem cells. Journal of the American College of Cardiology. 2014; 64 :436-448. DOI: 10.1016/j.jacc.2014.04.056 - 120.
Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P, et al. Epigenetic memory in induced pluripotent stem cells. Nature. 2010; 467 :285-290. DOI: 10.1038/nature09342 - 121.
Feng Q, Lu SJ, Klimanskaya I, Gomes I, Kim D, Chung Y, et al. Hemangioblastic derivatives from human induced pluripotent stem cells exhibit limited expansion and early senescence. Stem Cells. 2010; 28 :704-712. DOI: 10.1002/stem.321 - 122.
Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 2011; 471 :68-73. DOI: 10.1038/nature09798 - 123.
Ruiz S, Diep D, Gore A, Panopoulos AD, Montserrat N, Plongthongkum N, et al. Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells. Proceedings of the National Academy of Sciences of the United States of America. 2012; 109 :16196-16201. DOI: 10.1073/pnas.1202352109 - 124.
Kim K, Zhao R, Doi A, Ng K, Unternaehrer J, Cahan P, et al. Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nature Biotechnology. 2011; 29 :1117-1119. DOI: 10.1038/nbt.2052 - 125.
Kawasumi M, Unno Y, Matsuoka T, Nishiwaki M, Anzai M, Amano T, et al. Abnormal DNA methylation of the Oct-4 enhancer region in cloned mouse embryos. Molecular Reproduction and Development. 2009; 76 :342-350. DOI: 10.1002/mrd.20966 - 126.
Vitaloni M, Pulecio J, Bilic J, Kuebler B, Laricchia-Robbio L, Izpisua Belmonte JC. MicroRNAs contribute to induced pluripotent stem cell somatic donor memory. The Journal of Biological Chemistry. 2014; 289 :2084-2098. DOI: 10.1074/jbc.M113.538702 - 127.
Guenther MG, Frampton GM, Soldner F, Hockemeyer D, Mitalipova M, Jaenisch R, et al. Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. Cell Stem Cell. 2010; 7 :249-257. DOI: 10.1016/j.stem.2010.06.015 - 128.
Bock C, Kiskinis E, Verstappen G, Gu H, Boulting G, Smith ZD, et al. Reference maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell. 2011; 144 :439-452. DOI: 10.1016/j.cell.2010.12.032 - 129.
Sullivan GJ, Bai Y, Fletcher J, Wilmut I. Induced pluripotent stem cells: Epigenetic memories and practical implications. Molecular Human Reproduction. 2010; 16 :880-885. DOI: 10.1093/molehr/gaq091 - 130.
Newman AM, Cooper JB. Lab-specific gene expression signatures in pluripotent stem cells. Cell Stem Cell. 2010; 7 :258-262. DOI: 10.1016/j.stem.2010.06.016 - 131.
Allegrucci C, Young LE. Differences between human embryonic stem cell lines. Human Reproduction Update. 2007; 13 :103-120. DOI: 10.1093/humupd/dml041 - 132.
Osafune K, Caron L, Borowiak M, Martinez RJ, Fitz-Gerald CS, Sato Y, et al. Marked differences in differentiation propensity among human embryonic stem cell lines. Nature Biotechnology. 2008; 26 :313-315. DOI: 10.1038/nbt1383 - 133.
Sharova LV, Sharov AA, Piao Y, Shaik N, Sullivan T, Stewart CL, et al. Global gene expression profiling reveals similarities and differences among mouse pluripotent stem cells of different origins and strains. Developmental Biology. 2007; 307 :446-459. DOI: 10.1016/j.ydbio.2007.05.004 - 134.
Stadtfeld M, Apostolou E, Ferrari F, Choi J, Walsh RM, Chen T, et al. Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells. Nature Genetics. 2012; 44 :398-405, S1-2. DOI: 10.1038/ng.1110 - 135.
Hou P, Li Y, Zhang X, Liu C, Guan J, Li H, et al. Pluripotent stem cells induced from mouse somatic cells by small-molecule compounds. Science. 2013; 341 :651-654. DOI: 10.1126/science.1239278 - 136.
Zhao Y, Zhao T, Guan J, Zhang X, Fu Y, Ye J, et al. A XEN-like state bridges somatic cells to pluripotency during chemical reprogramming. Cell. 2015; 163 :1678-1691. DOI: 10.1016/j.cell.2015.11.017