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<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:ali="http://www.niso.org/schemas/ali/1.0/" article-type="research-article" dtd-version="1.2" xml:lang="en"><front><journal-meta><journal-id journal-id-type="publisher-id">Current Stem Cell Research &amp; Therapy</journal-id><journal-title-group><journal-title xml:lang="en">Current Stem Cell Research &amp; Therapy</journal-title><trans-title-group xml:lang="ru"><trans-title>Current Stem Cell Research &amp; Therapy</trans-title></trans-title-group></journal-title-group><issn publication-format="print">1574-888X</issn><issn publication-format="electronic">2212-3946</issn><publisher><publisher-name xml:lang="en">Bentham Science</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">645766</article-id><article-id pub-id-type="doi">10.2174/1574888X18666230417084518</article-id><article-categories><subj-group subj-group-type="toc-heading"><subject>Medicine</subject></subj-group><subj-group subj-group-type="article-type"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title xml:lang="en">Transcriptional Factors Mediated Reprogramming to Pluripotency</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Fatima</surname><given-names>Nazira</given-names></name><email>info@benthamscience.net</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><name><surname>Saif Ur Rahman</surname><given-names>Muhammad</given-names></name><email>info@benthamscience.net</email><xref ref-type="aff" rid="aff2"/></contrib><contrib contrib-type="author"><name><surname>Qasim</surname><given-names>Muhammad</given-names></name><email>info@benthamscience.net</email><xref ref-type="aff" rid="aff3"/></contrib><contrib contrib-type="author"><name><surname>Ali Ashfaq</surname><given-names>Usman</given-names></name><email>info@benthamscience.net</email><xref ref-type="aff" rid="aff3"/></contrib><contrib contrib-type="author"><name><surname>Ahmed</surname><given-names>Uzair</given-names></name><email>info@benthamscience.net</email><xref ref-type="aff" rid="aff4"/></contrib><contrib contrib-type="author"><name><surname>Masoud</surname><given-names>Muhammad</given-names></name><email>info@benthamscience.net</email><xref ref-type="aff" rid="aff3"/></contrib></contrib-group><aff id="aff1"><institution>Laboratory Animal Center,, Xian Jiaotong University Health Science Center,</institution></aff><aff id="aff2"><institution>Institute of Advanced Studies,, Shenzhen University</institution></aff><aff id="aff3"><institution>Department of Bioinformatics and Biotechnology,, Government College University, Faisalabad</institution></aff><aff id="aff4"><institution>EMBL Partnership Institute for Genome Editing Technologies,, Vilnius University</institution></aff><pub-date date-type="pub" iso-8601-date="2024-03-01" publication-format="electronic"><day>01</day><month>03</month><year>2024</year></pub-date><volume>19</volume><issue>3</issue><issue-title xml:lang="ru"/><fpage>367</fpage><lpage>388</lpage><history><date date-type="received" iso-8601-date="2025-01-11"><day>11</day><month>01</month><year>2025</year></date></history><permissions><copyright-statement xml:lang="en">Copyright ©; 2024, Bentham Science Publishers</copyright-statement><copyright-year>2024</copyright-year><copyright-holder xml:lang="en">Bentham Science Publishers</copyright-holder><ali:free_to_read xmlns:ali="http://www.niso.org/schemas/ali/1.0/"/></permissions><self-uri xlink:href="https://journals.eco-vector.com/1574-888X/article/view/645766">https://journals.eco-vector.com/1574-888X/article/view/645766</self-uri><abstract xml:lang="en"><p id="idm46466589252336">A unique kind of pluripotent cell, i.e., Induced pluripotent stem cells (iPSCs), now being targeted for iPSC synthesis, are produced by reprogramming animal and human differentiated cells (with no change in genetic makeup for the sake of high efficacy iPSCs formation). The conversion of specific cells to iPSCs has revolutionized stem cell research by making pluripotent cells more controllable for regenerative therapy. For the past 15 years, somatic cell reprogramming to pluripotency with force expression of specified factors has been a fascinating field of biomedical study. For that technological primary viewpoint reprogramming method, a cocktail of four transcription factors (TF) has required: Kruppel-like factor 4 (KLF4), four-octamer binding protein 34 (OCT3/4), MYC and SOX2 (together referred to as OSKM) and host cells. IPS cells have great potential for future tissue replacement treatments because of their ability to self-renew and specialize in all adult cell types, although factor-mediated reprogramming mechanisms are still poorly understood medically. This technique has dramatically improved performance and efficiency, making it more useful in drug discovery, disease remodeling, and regenerative medicine. Moreover, in these four TF cocktails, more than 30 reprogramming combinations were proposed, but for reprogramming effectiveness, only a few numbers have been demonstrated for the somatic cells of humans and mice. Stoichiometry, a combination of reprogramming agents and chromatin remodeling compounds, impacts kinetics, quality, and efficiency in stem cell research.</p></abstract><kwd-group xml:lang="en"><kwd>Stem cells</kwd><kwd>regenerative medicine</kwd><kwd>induced pluripotent stem cells (iPSCs)</kwd><kwd>reprogramming</kwd><kwd>transcription factor</kwd><kwd>kruppel-like factor 4 (KLF4).</kwd></kwd-group></article-meta></front><body></body><back><ref-list><ref id="B1"><label>1.</label><mixed-citation>Briggs R, King TJ. Transplantation of living nuclei from blastula cells into enucleated frogs eggs. Proc Natl Acad Sci 1952; 38(5): 455-63. doi: 10.1073/pnas.38.5.455 PMID: 16589125</mixed-citation></ref><ref id="B2"><label>2.</label><mixed-citation>Gurdon JB. The developmental capacity of nuclei taken from intestinal epithelium cells of feeding tadpoles. Development 1962; 10(4): 622-40. doi: 10.1242/dev.10.4.622 PMID: 13951335</mixed-citation></ref><ref id="B3"><label>3.</label><mixed-citation>Hochedlinger K, Jaenisch R. Nuclear reprogramming and pluripotency. Nature 2006; 441(7097): 1061-7. doi: 10.1038/nature04955 PMID: 16810240</mixed-citation></ref><ref id="B4"><label>4.</label><mixed-citation>Warren L, C. Lin. mRNA-based genetic reprogramming. Molecular Therapy 2019; 27: pp. (4)729-34. doi: 10.1016/j.ymthe.2018.12.009</mixed-citation></ref><ref id="B5"><label>5.</label><mixed-citation>Feng B, Ng JH, Heng JCD, Ng HH. Molecules that promote or enhance reprogramming of somatic cells to induced pluripotent stem cells. Cell Stem Cell 2009; 4(4): 301-12. doi: 10.1016/j.stem.2009.03.005 PMID: 19341620</mixed-citation></ref><ref id="B6"><label>6.</label><mixed-citation>Kim JS, Choi HW, Choi S, Do JT. Reprogrammed pluripotent stem cells from somatic cells. Int J Stem Cells 2011; 4(1): 1-8. doi: 10.15283/ijsc.2011.4.1.1 PMID: 24298328</mixed-citation></ref><ref id="B7"><label>7.</label><mixed-citation>Edwards JL, Schrick FN, McCracken MD, et al. Cloning adult farm animals: A review of the possibilities and problems associated with somatic cell nuclear transfer. Am J Reprod Immunol 2003; 50(2): 113-23. doi: 10.1034/j.1600-0897.2003.00064.x PMID: 12846674</mixed-citation></ref><ref id="B8"><label>8.</label><mixed-citation>Vierbuchen T, Wernig M. Direct lineage conversions: Unnatural but useful? Nat Biotechnol 2011; 29(10): 892-907. doi: 10.1038/nbt.1946 PMID: 21997635</mixed-citation></ref><ref id="B9"><label>9.</label><mixed-citation>Blau HM, Chiu CP, Webster C. Cytoplasmic activation of human nuclear genes in stable heterocaryons. Cell 1983; 32(4): 1171-80. doi: 10.1016/0092-8674(83)90300-8 PMID: 6839359</mixed-citation></ref><ref id="B10"><label>10.</label><mixed-citation>Pfannkuche K, Hannes T, Khalil M, et al. Induced pluripotent stem cells: A new approach for physiological research. Cell Physiol Biochem 2010; 26(2): 105-24. doi: 10.1159/000320514 PMID: 20798495</mixed-citation></ref><ref id="B11"><label>11.</label><mixed-citation>Takahashi K, Yamanaka S. A decade of transcription factor-mediated reprogramming to pluripotency. Nat Rev Mol Cell Biol 2016; 17(3): 183-93. doi: 10.1038/nrm.2016.8 PMID: 26883003</mixed-citation></ref><ref id="B12"><label>12.</label><mixed-citation>Zeineddine D, Hammoud AA, Mortada M, Boeuf H. The Oct4 protein: More than a magic stemness marker. Am J Stem Cells 2014; 3(2): 74-82. PMID: 25232507</mixed-citation></ref><ref id="B13"><label>13.</label><mixed-citation>Buganim Y, Markoulaki S, van Wietmarschen N, et al. The developmental potential of iPSCs is greatly influenced by reprogramming factor selection. Cell Stem Cell 2014; 15(3): 295-309. doi: 10.1016/j.stem.2014.07.003 PMID: 25192464</mixed-citation></ref><ref id="B14"><label>14.</label><mixed-citation>Limaye A, Hall B, Kulkarni AB. Manipulation of mouse embryonic stem cells for knockout mouse production. Curr Protoc Cell Biol 2009; 44(1): 19. doi: 10.1002/0471143030.cb1913s44</mixed-citation></ref><ref id="B15"><label>15.</label><mixed-citation>Saunders A, Faiola F, Wang J. Concise review: Pursuing self-renewal and pluripotency with the stem cell factor Nanog. Stem Cells 2013; 31(7): 1227-36. doi: 10.1002/stem.1384 PMID: 23653415</mixed-citation></ref><ref id="B16"><label>16.</label><mixed-citation>Graf U, Casanova EA, Cinelli P. The role of the leukemia inhibitory factor (LIF)pathway in derivation and maintenance of murine pluripotent stem cells. Genes 2011; 2(1): 280-97. doi: 10.3390/genes2010280 PMID: 24710148</mixed-citation></ref><ref id="B17"><label>17.</label><mixed-citation>Niwa H, Burdon T, Chambers I, Smith A. Self-renewal of pluripotent embryonic stem cells is mediated via activation of STAT3. Genes Dev 1998; 12(13): 2048-60. doi: 10.1101/gad.12.13.2048 PMID: 9649508</mixed-citation></ref><ref id="B18"><label>18.</label><mixed-citation>Yoshida GJ. Emerging roles of Myc in stem cell biology and novel tumor therapies. J Exp Clin Cancer Res 2018; 37(1): 1-20. PMID: 29301578</mixed-citation></ref><ref id="B19"><label>19.</label><mixed-citation>Burdon T, Stracey C, Chambers I, Nichols J, Smith A. Suppression of SHP-2 and ERK signalling promotes self-renewal of mouse embryonic stem cells. Dev Biol 1999; 210(1): 30-43. doi: 10.1006/dbio.1999.9265 PMID: 10364425</mixed-citation></ref><ref id="B20"><label>20.</label><mixed-citation>Cheng AM, Saxton TM, Sakai R, et al. Mammalian Grb2 regulates multiple steps in embryonic development and malignant transformation. Cell 1998; 95(6): 793-803. doi: 10.1016/S0092-8674(00)81702-X PMID: 9865697</mixed-citation></ref><ref id="B21"><label>21.</label><mixed-citation>Yeo JC, Ng HH. The transcriptional regulation of pluripotency. Cell Res 2013; 23(1): 20-32. doi: 10.1038/cr.2012.172 PMID: 23229513</mixed-citation></ref><ref id="B22"><label>22.</label><mixed-citation>Palmqvist L, Glover CH, Hsu L, et al. Correlation of murine embryonic stem cell gene expression profiles with functional measures of pluripotency. Stem Cells 2005; 23(5): 663-80. doi: 10.1634/stemcells.2004-0157 PMID: 15849174</mixed-citation></ref><ref id="B23"><label>23.</label><mixed-citation>Kitamura T, Koshino Y, Shibata F, et al. Retrovirus-mediated gene transfer and expression cloning: powerful tools in functional genomics. Exp Hematol 2003; 31(11): 1007-14. doi: 10.1016/S0301-472X(03)00260-1 PMID: 14585362</mixed-citation></ref><ref id="B24"><label>24.</label><mixed-citation>Han JW, Yoon Y. Induced pluripotent stem cells: emerging techniques for nuclear reprogramming. Antioxid Redox Signal 2011; 15(7): 1799-820. doi: 10.1089/ars.2010.3814 PMID: 21194386</mixed-citation></ref><ref id="B25"><label>25.</label><mixed-citation>Frisén J, Lendahl U, Perimann T. Mature cells can be reprogrammed to become pluripotent. The 2012 Nobel Prize in Physiology or MedicineAdvanced Information. 2012. Available from: http://Nobelprizeorg</mixed-citation></ref><ref id="B26"><label>26.</label><mixed-citation>Wilmut I, Sullivan G, Chambers I. The evolving biology of cell reprogramming. Philos Trans R SocB 2011; 366(1575): 2183-97. doi: 10.1098/rstb.2011.0051</mixed-citation></ref><ref id="B27"><label>27.</label><mixed-citation>Ferreira R, Ohneda K, Yamamoto M, Philipsen S. GATA1 function, a paradigm for transcription factors in hematopoiesis. Mol Cell Biol 2005; 25(4): 1215-27. doi: 10.1128/MCB.25.4.1215-1227.2005 PMID: 15684376</mixed-citation></ref><ref id="B28"><label>28.</label><mixed-citation>Di Tullio A, Manh TPV, Schubert A, Castellano G, Månsson R, Graf T. CCAAT/enhancer binding protein α (C/EBPα)-induced transdifferentiation of pre-B cells into macrophages involves no overt retrodifferentiation. Proc Natl Acad Sci 2011; 108(41): 17016-21. doi: 10.1073/pnas.1112169108 PMID: 21969581</mixed-citation></ref><ref id="B29"><label>29.</label><mixed-citation>Shafa M, Krawetz R, Rancourt DE. Returning to the stem state: Epigenetics of recapitulating pre-differentiation chromatin structure. BioEssays 2010; 32(9): 791-9. doi: 10.1002/bies.201000033 PMID: 20652894</mixed-citation></ref><ref id="B30"><label>30.</label><mixed-citation>Robinton DA, Daley GQ. The promise of induced pluripotent stem cells in research and therapy. Nature 2012; 481(7381): 295-305. doi: 10.1038/nature10761 PMID: 22258608</mixed-citation></ref><ref id="B31"><label>31.</label><mixed-citation>García-León JA, Kumar M, Boon R, et al. SOX10 single transcription factor-based fast and efficient generation of oligodendrocytes from human pluripotent stem cells. Stem Cell Reports 2018; 10(2): 655-72. doi: 10.1016/j.stemcr.2017.12.014 PMID: 29337119</mixed-citation></ref><ref id="B32"><label>32.</label><mixed-citation>Tsai SY, Bouwman BA, Ang YS, et al. Single transcription factor reprogramming of hair follicle dermal papilla cells to induced pluripotent stem cells. Stem Cells 2011; 29(6): 964-71. doi: 10.1002/stem.649 PMID: 21563278</mixed-citation></ref><ref id="B33"><label>33.</label><mixed-citation>Fujino S, Miyoshi N. Oct4 gene expression in primary colorectal cancer promotes liver metastasis. Stem Cells Int 2019; 2019: 7896524. doi: 10.1155/2019/7896524</mixed-citation></ref><ref id="B34"><label>34.</label><mixed-citation>Kim BE, Choi SW, Shin JH, et al. Single-factor SOX2 mediates direct neural reprogramming of human mesenchymal stem cells via transfection of in vitro transcribed mRNA. Cell Transplant 2018; 27(7): 1154-67. doi: 10.1177/0963689718771885 PMID: 29909688</mixed-citation></ref><ref id="B35"><label>35.</label><mixed-citation>Dhaliwal NK, Abatti LE, Mitchell JA. KLF4 protein stability regulated by interaction with pluripotency transcription factors overrides transcriptional control. Genes Dev 2019; 33(15-16): 1069-82. doi: 10.1101/gad.324319.119 PMID: 31221664</mixed-citation></ref><ref id="B36"><label>36.</label><mixed-citation>González F, Huangfu D. Mechanisms underlying the formation of induced pluripotent stem cells. Wiley Interdiscip Rev Dev Biol 2016; 5(1): 39-65. doi: 10.1002/wdev.206 PMID: 26383234</mixed-citation></ref><ref id="B37"><label>37.</label><mixed-citation>Winkler T, Cantilena A, Métais JY, et al. No evidence for clonal selection due to lentiviral integration sites in human induced pluripotent stem cells. Stem Cells 2010; 28(4): 687-94. doi: 10.1002/stem.322 PMID: 20166152</mixed-citation></ref><ref id="B38"><label>38.</label><mixed-citation>Okita K, Yamakawa T, Matsumura Y, et al. An efficient nonviral method to generate integration-free human-induced pluripotent stem cells from cord blood and peripheral blood cells. Stem Cells 2013; 31(3): 458-66. doi: 10.1002/stem.1293 PMID: 23193063</mixed-citation></ref><ref id="B39"><label>39.</label><mixed-citation>Zhou Q, Liu M, Xia X, et al. A mouse tissue transcription factor atlas. Nat Commun 2017; 8(1): 15089. doi: 10.1038/ncomms15089 PMID: 28429721</mixed-citation></ref><ref id="B40"><label>40.</label><mixed-citation>Kribelbauer JF, Rastogi C, Bussemaker HJ, Mann RS. Low-affinity binding sites and the transcription factor specificity paradox in eukaryotes. Annu Rev Cell Dev Biol 2019; 35(1): 357-79. doi: 10.1146/annurev-cellbio-100617-062719 PMID: 31283382</mixed-citation></ref><ref id="B41"><label>41.</label><mixed-citation>Wang X, Cairns MJ, Yan J. Super-enhancers in transcriptional regulation and genome organization. Nucleic Acids Res 2019; 47(22): gkz1038. doi: 10.1093/nar/gkz1038 PMID: 31724731</mixed-citation></ref><ref id="B42"><label>42.</label><mixed-citation>Tang F, Yang Z, Tan Y, Li Y. Super-enhancer function and its application in cancer targeted therapy. NPJ Precis Oncol 2020; 4(1): 2. doi: 10.1038/s41698-020-0108-z PMID: 32128448</mixed-citation></ref><ref id="B43"><label>43.</label><mixed-citation>Lee K, Wong W, Feng B. Decoding the pluripotency network: The emergence of new transcription factors. Biomedicines 2013; 1(1): 49-78. doi: 10.3390/biomedicines1010049 PMID: 28548056</mixed-citation></ref><ref id="B44"><label>44.</label><mixed-citation>Bhinge AA. A functional genomics approach to map transcriptional and post-transcriptional gene regulatory network 2009.</mixed-citation></ref><ref id="B45"><label>45.</label><mixed-citation>Class I. USPC AN Patent application title: SUPER-ENHANCERS AND METHODS OF USE THEREOF Inventors: Denes Hnisz (Cambridge, MA, US) Brian Abraham (Cambridge, MA, US) Tong Ihn Lee (Somerville, MA, US) Richard A Young (Weston, MA, US). Richard A. Young: Weston, MA, US 2014.</mixed-citation></ref><ref id="B46"><label>46.</label><mixed-citation>Schoenfelder S, Fraser P. Long-range enhancerpromoter contacts in gene expression control. Nat Rev Genet 2019; 20(8): 437-55. doi: 10.1038/s41576-019-0128-0 PMID: 31086298</mixed-citation></ref><ref id="B47"><label>47.</label><mixed-citation>Spitz F, Furlong EEM. Transcription factors: From enhancer binding to developmental control. Nat Rev Genet 2012; 13(9): 613-26. doi: 10.1038/nrg3207 PMID: 22868264</mixed-citation></ref><ref id="B48"><label>48.</label><mixed-citation>Heinz S, Romanoski CE, Benner C, Glass CK. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol 2015; 16(3): 144-54. doi: 10.1038/nrm3949 PMID: 25650801</mixed-citation></ref><ref id="B49"><label>49.</label><mixed-citation>Bi X, Xu Y, Li T, Li X, Li W, Shao W. RNA targets ribogenesis factor WDR43 to chromatin for transcription and pluripotency control. Molecular cell 2019; 75(1): 102-16.e9. doi: 10.1016/j.molcel.2019.05.007</mixed-citation></ref><ref id="B50"><label>50.</label><mixed-citation>Kamachi Y, Kondoh H. Sox proteins: Regulators of cell fate specification and differentiation. Development 2013; 140(20): 4129-44. doi: 10.1242/dev.091793 PMID: 24086078</mixed-citation></ref><ref id="B51"><label>51.</label><mixed-citation>Fagnocchi L, Zippo A. Multiple roles of MYC in integrating regulatory networks of pluripotent stem cells. Front Cell Dev Biol 2017; 5: 7. doi: 10.3389/fcell.2017.00007 PMID: 28217689</mixed-citation></ref><ref id="B52"><label>52.</label><mixed-citation>Malik V, Glaser LV, Zimmer D, et al. Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2. Nat Commun 2019; 10(1): 3477. doi: 10.1038/s41467-019-11054-7 PMID: 31375664</mixed-citation></ref><ref id="B53"><label>53.</label><mixed-citation>Niwa H. The principles that govern transcription factor network functions in stem cells. Development 2018; 145(6): dev157420. doi: 10.1242/dev.157420</mixed-citation></ref><ref id="B54"><label>54.</label><mixed-citation>Soufi A, Garcia MF, Jaroszewicz A, Osman N, Pellegrini M, Zaret KS. Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming. Cell 2015; 161(3): 555-68. doi: 10.1016/j.cell.2015.03.017 PMID: 25892221</mixed-citation></ref><ref id="B55"><label>55.</label><mixed-citation>Aksoy I, Jauch R, Chen J, et al. Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm. EMBO J 2013; 32(7): 938-53. doi: 10.1038/emboj.2013.31 PMID: 23474895</mixed-citation></ref><ref id="B56"><label>56.</label><mixed-citation>Zhang S, Cui W. Sox2, a key factor in the regulation of pluripotency and neural differentiation. World J Stem Cells 2014; 6(3): 305-11. doi: 10.4252/wjsc.v6.i3.305 PMID: 25126380</mixed-citation></ref><ref id="B57"><label>57.</label><mixed-citation>Costa RH, Kalinichenko VV, Lim L. Transcription factors in mouse lung development and function. Am J Physiol Lung Cell Mol Physiol 2001; 280(5): L823-38. doi: 10.1152/ajplung.2001.280.5.L823 PMID: 11290504</mixed-citation></ref><ref id="B58"><label>58.</label><mixed-citation>Kashyap V, Rezende NC, Scotland KB, et al. Regulation of stem cell pluripotency and differentiation involves a mutual regulatory circuit of the NANOG, OCT4, and SOX2 pluripotency transcription factors with polycomb repressive complexes and stem cell microRNAs. Stem Cells Dev 2009; 18(7): 1093-108. doi: 10.1089/scd.2009.0113 PMID: 19480567</mixed-citation></ref><ref id="B59"><label>59.</label><mixed-citation>Rodda DJ, Chew JL, Lim LH, et al. Transcriptional regulation of nanog by OCT4 and SOX2. J Biol Chem 2005; 280(26): 24731-7. doi: 10.1074/jbc.M502573200 PMID: 15860457</mixed-citation></ref><ref id="B60"><label>60.</label><mixed-citation>Niwa H. The principles that govern transcription factor network functions in stem cells. Development 2018; 145(6): dev157420. doi: 10.1242/dev.157420 PMID: 29540464</mixed-citation></ref><ref id="B61"><label>61.</label><mixed-citation>Davies K. Regulation of Stomatal Development Initiation and Cell Fate Transitions by the bHLH Transcription Factor Speechless. PhD Dissertation Stanford University 2014.</mixed-citation></ref><ref id="B62"><label>62.</label><mixed-citation>Chen JX, et al. Inefficient reprogramming of fibroblasts into cardiomyocytes using Gata4, Mef2c, and Tbx5 Circulation research 2012; 111(1): 50-5.</mixed-citation></ref><ref id="B63"><label>63.</label><mixed-citation>Gökbuget D, Blelloch R. Epigenetic control of transcriptional regulation in pluripotency and early differentiation. Development 2019; 146(19): dev164772. doi: 10.1242/dev.164772 PMID: 31554624</mixed-citation></ref><ref id="B64"><label>64.</label><mixed-citation>Chen AF, Liu AJ, Krishnakumar R, Freimer JW, DeVeale B, Blelloch R. GRHL2-dependent enhancer switching maintains a pluripotent stem cell transcriptional subnetwork after exit from naive pluripotency. Cell Stem Cell 2018; 23(2): 226-38. doi: 10.1016/j.stem.2018.06.005</mixed-citation></ref><ref id="B65"><label>65.</label><mixed-citation>Buganim Y, Faddah DA, Jaenisch R. Mechanisms and models of somatic cell reprogramming. Nat Rev Genet 2013; 14(6): 427-39. doi: 10.1038/nrg3473 PMID: 23681063</mixed-citation></ref><ref id="B66"><label>66.</label><mixed-citation>Sterner DE, Berger SL. Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev 2000; 64(2): 435-59. doi: 10.1128/MMBR.64.2.435-459.2000 PMID: 10839822</mixed-citation></ref><ref id="B67"><label>67.</label><mixed-citation>Schmidt R, Plath K. The roles of the reprogramming factors Oct4, Sox2 and Klf4 in resetting the somatic cell epigenome during induced pluripotent stem cell generation. Genome Biol 2012; 13(10): 251. doi: 10.1186/gb-2012-13-10-251 PMID: 23088445</mixed-citation></ref><ref id="B68"><label>68.</label><mixed-citation>Koche RP, Smith ZD, Adli M, et al. Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell 2011; 8(1): 96-105. doi: 10.1016/j.stem.2010.12.001 PMID: 21211784</mixed-citation></ref><ref id="B69"><label>69.</label><mixed-citation>Sridharan R, Tchieu J, Mason MJ, et al. Role of the murine reprogramming factors in the induction of pluripotency. Cell 2009; 136(2): 364-77. doi: 10.1016/j.cell.2009.01.001 PMID: 19167336</mixed-citation></ref><ref id="B70"><label>70.</label><mixed-citation>Soufi A, Donahue G, Zaret KS. Facilitators and impediments of the pluripotency reprogramming factors initial engagement with the genome. Cell 2012; 151(5): 994-1004. doi: 10.1016/j.cell.2012.09.045 PMID: 23159369</mixed-citation></ref><ref id="B71"><label>71.</label><mixed-citation>Chen J, Liu H, Liu J, et al. H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nat Genet 2013; 45(1): 34-42. doi: 10.1038/ng.2491 PMID: 23202127</mixed-citation></ref><ref id="B72"><label>72.</label><mixed-citation>Liang G, He J, Zhang Y. Kdm2b promotes induced pluripotent stem cell generation by facilitating gene activation early in reprogramming. Nat Cell Biol 2012; 14(5): 457-66. doi: 10.1038/ncb2483 PMID: 22522173</mixed-citation></ref><ref id="B73"><label>73.</label><mixed-citation>Wang T, Chen K, Zeng X, et al. The histone demethylases Jhdm1a/1b enhance somatic cell reprogramming in a vitamin-C-dependent manner. Cell Stem Cell 2011; 9(6): 575-87. doi: 10.1016/j.stem.2011.10.005 PMID: 22100412</mixed-citation></ref><ref id="B74"><label>74.</label><mixed-citation>Onder TT, Kara N, Cherry A, et al. Chromatin-modifying enzymes as modulators of reprogramming. Nature 2012; 483(7391): 598-602. doi: 10.1038/nature10953 PMID: 22388813</mixed-citation></ref><ref id="B75"><label>75.</label><mixed-citation>Zhang B, Day DS, Ho JW, et al. A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity. Genome Res 2013; 23(6): 917-27. doi: 10.1101/gr.149674.112 PMID: 23547170</mixed-citation></ref><ref id="B76"><label>76.</label><mixed-citation>Xie G, Lee JE, McKernan K, et al. (2020) MLL3/MLL4 methyltransferase activities regulate embryonic stem cell differentiation independent of enhancer H3K4me1. bioRxiv 2020; 09</mixed-citation></ref><ref id="B77"><label>77.</label><mixed-citation>Seymour T, Twigger AJ, Kakulas F. Pluripotency genes and their functions in the normal and aberrant breast and brain. Int J Mol Sci 2015; 16(11): 27288-301. doi: 10.3390/ijms161126024 PMID: 26580604</mixed-citation></ref><ref id="B78"><label>78.</label><mixed-citation>Cao K, Collings CK, Morgan MA, et al. An Mll4/COMPASS-Lsd1 epigenetic axis governs enhancer function and pluripotency transition in embryonic stem cells. Sci Adv 2018; 4(1): eaap8747. doi: 10.1126/sciadv.aap8747 PMID: 29404406</mixed-citation></ref><ref id="B79"><label>79.</label><mixed-citation>Sze CC, Shilatifard A. MLL3/MLL4/COMPASS family on epigenetic regulation of enhancer function and cancer. Cold Spring Harb Perspect Med 2016; 6(11): a026427. doi: 10.1101/cshperspect.a026427 PMID: 27638352</mixed-citation></ref><ref id="B80"><label>80.</label><mixed-citation>Yan J, Chen SAA, Local A, et al. Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers. Cell Res 2018; 28(2): 204-20. doi: 10.1038/cr.2018.1 PMID: 29313530</mixed-citation></ref><ref id="B81"><label>81.</label><mixed-citation>Bernatavichute YV. Mechanisms of CMT3 activation and histone methylation in Arabidopsis thaliana. PhD Dissertation Los Angeles: University of California 2009.</mixed-citation></ref><ref id="B82"><label>82.</label><mixed-citation>Vignali M, Hassan AH, Neely KE, Workman JL. ATP-dependent chromatin-remodeling complexes. Mol Cell Biol 2000; 20(6): 1899-910. doi: 10.1128/MCB.20.6.1899-1910.2000 PMID: 10688638</mixed-citation></ref><ref id="B83"><label>83.</label><mixed-citation>Zhang H, Gayen S, Xiong J, et al. MLL1 inhibition reprograms epiblast stem cells to naive pluripotency. Cell Stem Cell 2016; 18(4): 481-94. doi: 10.1016/j.stem.2016.02.004 PMID: 26996599</mixed-citation></ref><ref id="B84"><label>84.</label><mixed-citation>Prakash K, Fournier D. Evidence for the implication of the histone code in building the genome structure. Biosystems 2018; 164: 49-59. doi: 10.1016/j.biosystems.2017.11.005 PMID: 29158132</mixed-citation></ref><ref id="B85"><label>85.</label><mixed-citation>Hayakawa T, Nakayama J-i. Physiological roles of class I HDAC complex and histone demethylase. J Biomed Biotechnol 2011; 2011: 129383. doi: 10.1155/2011/129383</mixed-citation></ref><ref id="B86"><label>86.</label><mixed-citation>Jamaladdin SJ. Investigating the physiological role of HDAC1 and HDAC2 in embryonic stem cells. PhD Dissertation University of Leicester 2016.</mixed-citation></ref><ref id="B87"><label>87.</label><mixed-citation>Parbin S, Kar S, Shilpi A, et al. Histone Deacetylases. J Histochem Cytochem 2014; 62(1): 11-33. doi: 10.1369/0022155413506582 PMID: 24051359</mixed-citation></ref><ref id="B88"><label>88.</label><mixed-citation>Yang XJ, Grégoire S. Class II histone deacetylases: From sequence to function, regulation, and clinical implication. Mol Cell Biol 2005; 25(8): 2873-84. doi: 10.1128/MCB.25.8.2873-2884.2005 PMID: 15798178</mixed-citation></ref><ref id="B89"><label>89.</label><mixed-citation>Baas R. Mechanisms controlling SMAD-dependent transcription and chromatin modification. Utrecht University 2017.</mixed-citation></ref><ref id="B90"><label>90.</label><mixed-citation>Biddlestone J, Batie M, Bandarra D, Munoz I, Rocha S. SINHCAF/FAM60A and SIN3A specifically repress HIF-2α expression. Biochem J 2018; 475(12): 2073-90. doi: 10.1042/BCJ20170945 PMID: 29784889</mixed-citation></ref><ref id="B91"><label>91.</label><mixed-citation>Ohi Y, Qin H, Hong C, et al. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol 2011; 13(5): 541-9. doi: 10.1038/ncb2239 PMID: 21499256</mixed-citation></ref><ref id="B92"><label>92.</label><mixed-citation>Nashun B, Hill PWS, Hajkova P. Reprogramming of cell fate: Epigenetic memory and the erasure of memories past. EMBO J 2015; 34(10): 1296-308. doi: 10.15252/embj.201490649 PMID: 25820261</mixed-citation></ref><ref id="B93"><label>93.</label><mixed-citation>Chang G, Gao S, Hou X, et al. High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells. Cell Res 2014; 24(3): 293-306. doi: 10.1038/cr.2013.173 PMID: 24381111</mixed-citation></ref><ref id="B94"><label>94.</label><mixed-citation>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 2011; 25(10): 1035-40. doi: 10.1101/gad.2039011 PMID: 21576263</mixed-citation></ref><ref id="B95"><label>95.</label><mixed-citation>Kallingappa PK, Turner PM, Eichenlaub MP, Green AL, Oback FC, Chibnall AM. Quiescence loosens epigenetic constraints in bovine somatic cells and improves their reprogramming into totipotency. Biol Reprod 2016; 95(1): 16. doi: 10.1095/biolreprod.115.137109</mixed-citation></ref><ref id="B96"><label>96.</label><mixed-citation>Hermann A, Gowher H, Jeltsch A. Biochemistry and biology of mammalian DNA methyltransferases. Cell Mol Life Sci 2004; 61(19-20): 2571-87. doi: 10.1007/s00018-004-4201-1 PMID: 15526163</mixed-citation></ref><ref id="B97"><label>97.</label><mixed-citation>Guo H, Zhu P, Yan L, et al. The DNA methylation landscape of human early embryos. Nature 2014; 511(7511): 606-10. doi: 10.1038/nature13544 PMID: 25079557</mixed-citation></ref><ref id="B98"><label>98.</label><mixed-citation>Paniza T, Deshpande M, Wang N, et al. Pluripotent stem cells with low differentiation potential contain incompletely reprogrammed DNA replication. J Cell Biol 2020; 219(9): e201909163. doi: 10.1083/jcb.201909163 PMID: 32673399</mixed-citation></ref><ref id="B99"><label>99.</label><mixed-citation>Parry A, Rulands S, Reik W. (2021); Active turnover of DNA methylation during cell fate decisions. Natture Reviews Genetics 22(1): 59-66.</mixed-citation></ref><ref id="B100"><label>100.</label><mixed-citation>Suetake I, Watanebe M, Takeshita K, Takahashi S, Carlton P. The Molecular Basis of DNA Methylation In: Kameda A, Tsukada Yi, Eds DNA and Histone Methylation as Cancer Targets. Cham: Humana Press 2017; pp. 19-51. doi: 10.1007/978-3-319-59786-7_2</mixed-citation></ref><ref id="B101"><label>101.</label><mixed-citation>von Meyenn F, Iurlaro M, Habibi E, et al. Impairment of DNA methylation maintenance is the main cause of global demethylation in naive embryonic stem cells. Mol Cell 2016; 62(6): 848-61. doi: 10.1016/j.molcel.2016.04.025 PMID: 27237052</mixed-citation></ref><ref id="B102"><label>102.</label><mixed-citation>Zhang J, Gao Q, Li P, et al. S phase-dependent interaction with DNMT1 dictates the role of UHRF1 but not UHRF2 in DNA methylation maintenance. Cell Res 2011; 21(12): 1723-39. doi: 10.1038/cr.2011.176 PMID: 22064703</mixed-citation></ref><ref id="B103"><label>103.</label><mixed-citation>Kalkan T, Olova N, Roode M, et al. Tracking the embryonic stem cell transition from ground state pluripotency.Development 2017; 144(7): dev.142711. doi: 10.1242/dev.142711 PMID: 28174249</mixed-citation></ref><ref id="B104"><label>104.</label><mixed-citation>Singer ZS, Yong J, Tischler J, et al. Dynamic heterogeneity and DNA methylation in embryonic stem cells. Mol Cell 2014; 55(2): 319-31. doi: 10.1016/j.molcel.2014.06.029 PMID: 25038413</mixed-citation></ref><ref id="B105"><label>105.</label><mixed-citation>Rasmussen KD, Helin K. Role of TET enzymes in DNA methylation, development, and cancer. Genes Dev 2016; 30(7): 733-50. doi: 10.1101/gad.276568.115 PMID: 27036965</mixed-citation></ref><ref id="B106"><label>106.</label><mixed-citation>Dawlaty MM, Breiling A, Le T, et al. Loss of Tet enzymes compromises proper differentiation of embryonic stem cells. Dev Cell 2014; 29(1): 102-11. doi: 10.1016/j.devcel.2014.03.003 PMID: 24735881</mixed-citation></ref><ref id="B107"><label>107.</label><mixed-citation>Pantier R, Tatar T, Colby D, Chambers I. Endogenous epitope-tagging of Tet1, Tet2 and Tet3 identifies TET2 as a naïve pluripotency marker. Life Sci Alliance 2019; 2(5): e201900516. doi: 10.26508/lsa.201900516 PMID: 31582397</mixed-citation></ref><ref id="B108"><label>108.</label><mixed-citation>Fidalgo M, Huang X, Guallar D, et al. Zfp281 coordinates opposing functions of Tet1 and Tet2 in pluripotent states. Cell Stem Cell 2016; 19(3): 355-69. doi: 10.1016/j.stem.2016.05.025 PMID: 27345836</mixed-citation></ref><ref id="B109"><label>109.</label><mixed-citation>Kim K, Zhao R, Doi A, et al. Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nat Biotechnol 2011; 29(12): 1117-9. doi: 10.1038/nbt.2052 PMID: 22119740</mixed-citation></ref><ref id="B110"><label>110.</label><mixed-citation>Liu MY. Deciphering the tetrad of epigenetic cytosine modifications 2016.</mixed-citation></ref><ref id="B111"><label>111.</label><mixed-citation>Dahl C, Grønbæk K, Guldberg P. Advances in DNA methylation: 5-hydroxymethylcytosine revisited. Clin Chim Acta 2011; 412(11-12): 831-6. doi: 10.1016/j.cca.2011.02.013 PMID: 21324307</mixed-citation></ref><ref id="B112"><label>112.</label><mixed-citation>Olariu V, Lövkvist C, Sneppen K. Nanog, Oct4 and Tet1 interplay in establishing pluripotency. Sci Rep 2016; 6(1): 25438. doi: 10.1038/srep25438 PMID: 27146218</mixed-citation></ref><ref id="B113"><label>113.</label><mixed-citation>Hu X, Zhang L, Mao SQ, et al. Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming. Cell Stem Cell 2014; 14(4): 512-22. doi: 10.1016/j.stem.2014.01.001 PMID: 24529596</mixed-citation></ref><ref id="B114"><label>114.</label><mixed-citation>Huang Y, Rao A. Connections between TET proteins and aberrant DNA modification in cancer. Trends Genet 2014; 30(10): 464-74. doi: 10.1016/j.tig.2014.07.005 PMID: 25132561</mixed-citation></ref><ref id="B115"><label>115.</label><mixed-citation>De Carvalho DD, You JS, Jones PA. DNA methylation and cellular reprogramming. Trends Cell Biol 2010; 20(10): 609-17. doi: 10.1016/j.tcb.2010.08.003 PMID: 20810283</mixed-citation></ref><ref id="B116"><label>116.</label><mixed-citation>Han C, Deng R, Mao T, et al. Overexpression of Tet3 in donor cells enhances goat somatic cell nuclear transfer efficiency. FEBS J 2018; 285(14): 2708-23. doi: 10.1111/febs.14515 PMID: 29791079</mixed-citation></ref><ref id="B117"><label>117.</label><mixed-citation>Ringrose L. Epigenetics and Systems Biology. Academic Press 2017.</mixed-citation></ref><ref id="B118"><label>118.</label><mixed-citation>Kim KP, Wu Y, Yoon J, et al. Reprogramming competence of OCT factors is determined by transactivation domains. Sci Adv 2020; 6(36): eaaz7364. doi: 10.1126/sciadv.aaz7364 PMID: 32917606</mixed-citation></ref><ref id="B119"><label>119.</label><mixed-citation>Spehalski E, Kovalchuk AL, Collins JT, et al. Oncogenic Myc translocations are independent of chromosomal location and orientation of the immunoglobulin heavy chain locus. Proc Natl Acad Sci 2012; 109(34): 13728-32. doi: 10.1073/pnas.1202882109 PMID: 22869734</mixed-citation></ref><ref id="B120"><label>120.</label><mixed-citation>Wuputra K, Ku CC, Wu DC, Lin YC, Saito S, Yokoyama KK. Prevention of tumor risk associated with the reprogramming of human pluripotent stem cells. J Exp Clin Cancer Res 2020; 39(1): 100. doi: 10.1186/s13046-020-01584-0 PMID: 32493501</mixed-citation></ref><ref id="B121"><label>121.</label><mixed-citation>Wang T, Shi S, Sha H. MicroRNAs in regulation of pluripotency and somatic cell reprogramming. RNA Biol 2013; 10(8): 1255-61. doi: 10.4161/rna.25828 PMID: 23921205</mixed-citation></ref><ref id="B122"><label>122.</label><mixed-citation>Choi YJ, Lin CP, Risso D, et al. Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells.Science 2017; 355(6325): eaag1927. doi: 10.1126/science.aag1927 PMID: 28082412</mixed-citation></ref><ref id="B123"><label>123.</label><mixed-citation>Festuccia N, Gonzalez I, Navarro P. The epigenetic paradox of pluripotent ES cells. J Mol Biol 2017; 429(10): 1476-503. doi: 10.1016/j.jmb.2016.12.009 PMID: 27988225</mixed-citation></ref><ref id="B124"><label>124.</label><mixed-citation>Ding H, Blair A, Yang Y, Stuart JM. Biological process activity transformation of single cell gene expression for cross-species alignment. Nat Commun 2019; 10(1): 4899. doi: 10.1038/s41467-019-12924-w PMID: 31653878</mixed-citation></ref><ref id="B125"><label>125.</label><mixed-citation>Kim H, Lee G, Ganat Y, et al. miR-371-3 expression predicts neural differentiation propensity in human pluripotent stem cells. Cell Stem Cell 2011; 8(6): 695-706. doi: 10.1016/j.stem.2011.04.002 PMID: 21624813</mixed-citation></ref><ref id="B126"><label>126.</label><mixed-citation>Mo CF, Wu FC, Tai KY, et al. Loss of non-coding RNA expression from the DLK1-DIO3 imprinted locus correlates with reduced neural differentiation potential in human embryonic stem cell lines. Stem Cell Res Ther 2015; 6(1): 1-17. doi: 10.1186/scrt535 PMID: 25559585</mixed-citation></ref><ref id="B127"><label>127.</label><mixed-citation>Zhu L, Gomez-Duran A, Saretzki G, et al. The mitochondrial protein CHCHD2 primes the differentiation potential of human induced pluripotent stem cells to neuroectodermal lineages. J Cell Biol 2016; 215(2): 187-202. doi: 10.1083/jcb.201601061 PMID: 27810911</mixed-citation></ref><ref id="B128"><label>128.</label><mixed-citation>Jiang W, Zhang D, Bursac N, Zhang Y. WNT3 is a biomarker capable of predicting the definitive endoderm differentiation potential of hESCs. Stem Cell Reports 2013; 1(1): 46-52. doi: 10.1016/j.stemcr.2013.03.003 PMID: 24052941</mixed-citation></ref><ref id="B129"><label>129.</label><mixed-citation>Butcher LM, Ito M, Brimpari M, et al. Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells. Nat Commun 2016; 7(1): 10458. doi: 10.1038/ncomms10458 PMID: 26822956</mixed-citation></ref><ref id="B130"><label>130.</label><mixed-citation>Yanagihara K, Liu Y, Kanie K, et al. Prediction of differentiation tendency toward hepatocytes from gene expression in undifferentiated human pluripotent stem cells. Stem Cells Dev 2016; 25(24): 1884-97. doi: 10.1089/scd.2016.0099 PMID: 27733097</mixed-citation></ref><ref id="B131"><label>131.</label><mixed-citation>Ran D, Shia WJ, Lo MC, et al. RUNX1a enhances hematopoietic lineage commitment from human embryonic stem cells and inducible pluripotent stem cells. Blood 2013; 121(15): 2882-90. doi: 10.1182/blood-2012-08-451641 PMID: 23372166</mixed-citation></ref><ref id="B132"><label>132.</label><mixed-citation>Ramos-Mejia V, Melen GJ, Sanchez L, et al. Nodal/Activin signaling predicts human pluripotent stem cell lines prone to differentiate toward the hematopoietic lineage. Mol Ther 2010; 18(12): 2173-81. doi: 10.1038/mt.2010.179 PMID: 20736931</mixed-citation></ref><ref id="B133"><label>133.</label><mixed-citation>Bock C, Kiskinis E, Verstappen G, et al. Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell 2011; 144(3): 439-52. doi: 10.1016/j.cell.2010.12.032 PMID: 21295703</mixed-citation></ref><ref id="B134"><label>134.</label><mixed-citation>Nishizawa M, Chonabayashi K, Nomura M, et al. Epigenetic variation between human induced pluripotent stem cell lines is an indicator of differentiation capacity. Cell Stem Cell 2016; 19(3): 341-54. doi: 10.1016/j.stem.2016.06.019 PMID: 27476965</mixed-citation></ref><ref id="B135"><label>135.</label><mixed-citation>Park J, Son Y, Lee NG, et al. DSG2 is a functional cell surface marker for identification and isolation of human pluripotent stem cells. Stem Cell Reports 2018; 11(1): 115-27. doi: 10.1016/j.stemcr.2018.05.009 PMID: 29910125</mixed-citation></ref><ref id="B136"><label>136.</label><mixed-citation>Merkle FT, Ghosh S, Kamitaki N, et al. Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations. Nature 2017; 545(7653): 229-33. doi: 10.1038/nature22312 PMID: 28445466</mixed-citation></ref><ref id="B137"><label>137.</label><mixed-citation>Lin T, Lin Y. p53 switches off pluripotency on differentiation. Stem Cell Res Ther 2017; 8(1): 44. doi: 10.1186/s13287-017-0498-1 PMID: 28241890</mixed-citation></ref><ref id="B138"><label>138.</label><mixed-citation>Alvarez-Palomo AB, Requena-Osete J, Delgado-Morales R, et al. A synthetic mRNA cell reprogramming method using CYCLIN D1 promotes DNA repair, generating improved genetically stable human induced pluripotent stem cells. Stem Cells 2021; 39(7): 866-81. doi: 10.1002/stem.3358 PMID: 33621399</mixed-citation></ref><ref id="B139"><label>139.</label><mixed-citation>Petropoulos S, Edsgärd D, Reinius B, et al. Single-cell RNA-seq reveals lineage and X chromosome dynamics in human preimplantation embryos. Cell 2016; 165(4): 1012-26. doi: 10.1016/j.cell.2016.03.023 PMID: 27062923</mixed-citation></ref><ref id="B140"><label>140.</label><mixed-citation>Liu X, Nefzger CM, Rossello FJ, et al. Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming. Nat Methods 2017; 14(11): 1055-62. doi: 10.1038/nmeth.4436 PMID: 28945704</mixed-citation></ref><ref id="B141"><label>141.</label><mixed-citation>Davidson KC, Mason EA, Pera MF. The pluripotent state in mouse and human. Development 2015; 142(18): 3090-9. doi: 10.1242/dev.116061 PMID: 26395138</mixed-citation></ref><ref id="B142"><label>142.</label><mixed-citation>Yan L, Yang M, Guo H, et al. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol 2013; 20(9): 1131-9. doi: 10.1038/nsmb.2660 PMID: 23934149</mixed-citation></ref><ref id="B143"><label>143.</label><mixed-citation>Sahakyan A, Kim R, Chronis C, et al. Human naive pluripotent stem cells model X chromosome dampening and X inactivation. Cell Stem Cell 2017; 20(1): 87-101. doi: 10.1016/j.stem.2016.10.006 PMID: 27989770</mixed-citation></ref><ref id="B144"><label>144.</label><mixed-citation>Xiao L, Shan Y, Ma L, Dunk C, Yu Y, Wei Y. Tuning FOXD3 expression dose-dependently balances human embryonic stem cells between pluripotency and meso-endoderm fates. Biochim Biophys Acta Mol Cell Res 2019; 1866(12): 118531. doi: 10.1016/j.bbamcr.2019.118531 PMID: 31415841</mixed-citation></ref><ref id="B145"><label>145.</label><mixed-citation>Cantone I, Fisher AG. Epigenetic programming and reprogramming during development. Nat Struct Mol Biol 2013; 20(3): 282-9. doi: 10.1038/nsmb.2489 PMID: 23463313</mixed-citation></ref><ref id="B146"><label>146.</label><mixed-citation>Stadhouders R, Filion GJ, Graf T. Transcription factors and 3D genome conformation in cell-fate decisions. Nature 2019; 569(7756): 345-54. doi: 10.1038/s41586-019-1182-7 PMID: 31092938</mixed-citation></ref><ref id="B147"><label>147.</label><mixed-citation>Serrano-Gomez SJ, Maziveyi M, Alahari SK. Regulation of epithelial-mesenchymal transition through epigenetic and post-translational modifications. Mol Cancer 2016; 15(1): 18. doi: 10.1186/s12943-016-0502-x PMID: 26905733</mixed-citation></ref><ref id="B148"><label>148.</label><mixed-citation>Vacík T, Lađinović D, Raka I. KDM2A/B lysine demethylases and their alternative isoforms in development and disease. Nucleus 2018; 9(1): 431-41. doi: 10.1080/19491034.2018.1498707 PMID: 30059280</mixed-citation></ref><ref id="B149"><label>149.</label><mixed-citation>Shinagawa T, Takagi T, Tsukamoto D, et al. Histone variants enriched in oocytes enhance reprogramming to induced pluripotent stem cells. Cell Stem Cell 2014; 14(2): 217-27. doi: 10.1016/j.stem.2013.12.015 PMID: 24506885</mixed-citation></ref><ref id="B150"><label>150.</label><mixed-citation>Christophorou MA, Castelo-Branco G, Halley-Stott RP, et al. Citrullination regulates pluripotency and histone H1 binding to chromatin. Nature 2014; 507(7490): 104-8. doi: 10.1038/nature12942 PMID: 24463520</mixed-citation></ref><ref id="B151"><label>151.</label><mixed-citation>Gao L, Emperle M, Guo Y, et al. Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms. Nat Commun 2020; 11(1): 3355. doi: 10.1038/s41467-020-17109-4 PMID: 32620778</mixed-citation></ref><ref id="B152"><label>152.</label><mixed-citation>Messerschmidt DM, Knowles BB, Solter D. DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. Genes Dev 2014; 28(8): 812-28. doi: 10.1101/gad.234294.113 PMID: 24736841</mixed-citation></ref><ref id="B153"><label>153.</label><mixed-citation>Wang G, Weng R, Lan Y, et al. Synergetic effects of DNA methylation and histone modification during mouse induced pluripotent stem cell generation. Sci Rep 2017; 7(1): 39527. doi: 10.1038/srep39527 PMID: 28155862</mixed-citation></ref><ref id="B154"><label>154.</label><mixed-citation>Mao J, Zhang Q, Deng W, et al. Epigenetic modifiers facilitate induction and pluripotency of porcine iPSCs. Stem Cell Reports 2017; 8(1): 11-20. doi: 10.1016/j.stemcr.2016.11.013 PMID: 28041878</mixed-citation></ref><ref id="B155"><label>155.</label><mixed-citation>Tessarz P, Kouzarides T. Histone core modifications regulating nucleosome structure and dynamics. Nat Rev Mol Cell Biol 2014; 15(11): 703-8. doi: 10.1038/nrm3890 PMID: 25315270</mixed-citation></ref><ref id="B156"><label>156.</label><mixed-citation>Federation AJ, Bradner JE, Meissner A. The use of small molecules in somatic-cell reprogramming. Trends Cell Biol 2014; 24(3): 179-87. doi: 10.1016/j.tcb.2013.09.011 PMID: 24183602</mixed-citation></ref><ref id="B157"><label>157.</label><mixed-citation>Fingerman IM, McDaniel L, Zhang X, et al. NCBI Epigenomics: A new public resource for exploring epigenomic data sets. Nucleic Acids Res 2011; 39((Database)): D908-12. doi: 10.1093/nar/gkq1146 PMID: 21075792</mixed-citation></ref><ref id="B158"><label>158.</label><mixed-citation>Banaszynski LA, Wen D, Dewell S, et al. Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells. Cell 2013; 155(1): 107-20. doi: 10.1016/j.cell.2013.08.061 PMID: 24074864</mixed-citation></ref><ref id="B159"><label>159.</label><mixed-citation>Gaspar-Maia A, Alajem A, Meshorer E, Ramalho-Santos M. Open chromatin in pluripotency and reprogramming. Nat Rev Mol Cell Biol 2011; 12(1): 36-47. doi: 10.1038/nrm3036 PMID: 21179060</mixed-citation></ref><ref id="B160"><label>160.</label><mixed-citation>Egli D, Birkhoff G, Eggan K. Mediators of reprogramming: Transcription factors and transitions through mitosis. Nat Rev Mol Cell Biol 2008; 9(7): 505-16. doi: 10.1038/nrm2439 PMID: 18568039</mixed-citation></ref><ref id="B161"><label>161.</label><mixed-citation>Gaspar-Maia A, Qadeer ZA, Hasson D, et al. MacroH2A histone variants act as a barrier upon reprogramming towards pluripotency. Nat Commun 2013; 4(1): 1565. doi: 10.1038/ncomms2582 PMID: 23463008</mixed-citation></ref><ref id="B162"><label>162.</label><mixed-citation>Bortvin A, Eggan K, Skaletsky H, et al. Incomplete reactivation of Oct4 -related genes in mouse embryos cloned from somatic nuclei. Development 2003; 130(8): 1673-80. doi: 10.1242/dev.00366 PMID: 12620990</mixed-citation></ref><ref id="B163"><label>163.</label><mixed-citation>Vallabhaneni H, Lynch PJ, Chen G, et al. High basal levels of γH2AX in human induced pluripotent stem cells are linked to replication-associated DNA damage and repair. Stem Cells 2018; 36(10): 1501-13. doi: 10.1002/stem.2861 PMID: 29873142</mixed-citation></ref><ref id="B164"><label>164.</label><mixed-citation>Ayuningtyas FD, Kim MH, Kino-oka M. Muscle lineage switching by migratory behaviour-driven epigenetic modifications of human mesenchymal stem cells on a dendrimer-immobilized surface. Acta Biomater 2020; 106: 170-80. doi: 10.1016/j.actbio.2020.02.026 PMID: 32092429</mixed-citation></ref><ref id="B165"><label>165.</label><mixed-citation>Mansour AA, Gafni O, Weinberger L, et al. The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming. Nature 2012; 488(7411): 409-13. doi: 10.1038/nature11272 PMID: 22801502</mixed-citation></ref><ref id="B166"><label>166.</label><mixed-citation>Singhal N, Graumann J, Wu G, et al. Chromatin-remodeling components of the BAF complex facilitate reprogramming. Cell 2010; 141(6): 943-55. doi: 10.1016/j.cell.2010.04.037 PMID: 20550931</mixed-citation></ref><ref id="B167"><label>167.</label><mixed-citation>Doege CA, Inoue K, Yamashita T, et al. Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2. Nature 2012; 488(7413): 652-5. doi: 10.1038/nature11333 PMID: 22902501</mixed-citation></ref><ref id="B168"><label>168.</label><mixed-citation>Costa Y, Ding J, Theunissen TW, et al. NANOG-dependent function of TET1 and TET2 in establishment of pluripotency. Nature 2013; 495(7441): 370-4. doi: 10.1038/nature11925 PMID: 23395962</mixed-citation></ref><ref id="B169"><label>169.</label><mixed-citation>Gao Y, Chen J, Li K, 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(4): 453-69. doi: 10.1016/j.stem.2013.02.005 PMID: 23499384</mixed-citation></ref><ref id="B170"><label>170.</label><mixed-citation>Ang YS, Tsai SY, Lee DF, et al. Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell 2011; 145(2): 183-97. doi: 10.1016/j.cell.2011.03.003 PMID: 21477851</mixed-citation></ref><ref id="B171"><label>171.</label><mixed-citation>Stadtfeld M, Hochedlinger K. Induced pluripotency: History, mechanisms, and applications. Genes Dev 2010; 24(20): 2239-63. doi: 10.1101/gad.1963910 PMID: 20952534</mixed-citation></ref><ref id="B172"><label>172.</label><mixed-citation>Sauer V, Roy-Chowdhury N, Guha C, Roy-Chowdhury J. Induced pluripotent stem cells as a source of hepatocytes. Curr Pathobiol Rep 2014; 2(1): 11-20. doi: 10.1007/s40139-013-0039-2 PMID: 25650171</mixed-citation></ref><ref id="B173"><label>173.</label><mixed-citation>Lai X, Li Q, Wu F, et al. Epithelial-mesenchymal transition and metabolic switching in cancer: Lessons from somatic cell reprogramming. Front Cell Dev Biol 2020; 8: 760. doi: 10.3389/fcell.2020.00760 PMID: 32850862</mixed-citation></ref><ref id="B174"><label>174.</label><mixed-citation>Takaishi M, Tarutani M, Takeda J, Sano S. Mesenchymal to epithelial transition induced by reprogramming factors attenuates the malignancy of cancer cells. PLoS One 2016; 11(6): e0156904. doi: 10.1371/journal.pone.0156904 PMID: 27258152</mixed-citation></ref><ref id="B175"><label>175.</label><mixed-citation>Liu X, Ding J, Meng L. Oncogene-induced senescence: A double edged sword in cancer. Acta Pharmacol Sin 2018; 39(10): 1553-8. doi: 10.1038/aps.2017.198 PMID: 29620049</mixed-citation></ref><ref id="B176"><label>176.</label><mixed-citation>Paranjpe SS, Veenstra GJC. Establishing pluripotency in early development. Biochim Biophys Acta 2015; 1849(6): 626-36. doi: 10.1016/j.bbagrm.2015.03.006 PMID: 25857441</mixed-citation></ref><ref id="B177"><label>177.</label><mixed-citation>Chin MH, Mason MJ, Xie W, et al. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 2009; 5(1): 111-23. doi: 10.1016/j.stem.2009.06.008 PMID: 19570518</mixed-citation></ref><ref id="B178"><label>178.</label><mixed-citation>Allshire RC, Madhani HD. Ten principles of heterochromatin formation and function. Nat Rev Mol Cell Biol 2018; 19(4): 229-44. doi: 10.1038/nrm.2017.119 PMID: 29235574</mixed-citation></ref><ref id="B179"><label>179.</label><mixed-citation>Lee JH, Hart SR, Skalnik DG. Histone deacetylase activity is required for embryonic stem cell differentiation. Genesis 2004; 38(1): 32-8. doi: 10.1002/gene.10250 PMID: 14755802</mixed-citation></ref><ref id="B180"><label>180.</label><mixed-citation>Polo JM, Anderssen E, Walsh RM, et al. A molecular roadmap of reprogramming somatic cells into iPS cells. Cell 2012; 151(7): 1617-32. doi: 10.1016/j.cell.2012.11.039 PMID: 23260147</mixed-citation></ref><ref id="B181"><label>181.</label><mixed-citation>Lewandowski J, Kurpisz M. Techniques of human embryonic stem cell and induced pluripotent stem cell derivation. Arch Immunol Ther Exp 2016; 64(5): 349-70. doi: 10.1007/s00005-016-0385-y PMID: 26939778</mixed-citation></ref><ref id="B182"><label>182.</label><mixed-citation>van Leeuwen J, Berg DK, Pfeffer PL. Morphological and gene expression changes in cattle embryos from hatched blastocyst to early gastrulation stages after transfer of in vitro produced embryos. PLoS One 2015; 10(6): e0129787. doi: 10.1371/journal.pone.0129787 PMID: 26076128</mixed-citation></ref><ref id="B183"><label>183.</label><mixed-citation>Theunissen TW, Jaenisch R. Mechanisms of gene regulation in human embryos and pluripotent stem cells. Development 2017; 144(24): 4496-509. doi: 10.1242/dev.157404 PMID: 29254992</mixed-citation></ref><ref id="B184"><label>184.</label><mixed-citation>Takahashi K, Yamanaka S. A developmental framework for induced pluripotency. Development 2015; 142(19): 3274-85. doi: 10.1242/dev.114249 PMID: 26443632</mixed-citation></ref><ref id="B185"><label>185.</label><mixed-citation>Vierbuchen T, Ostermeier A, Pang ZP, Kokubu Y, Südhof TC, Wernig M. Direct conversion of fibroblasts to functional neurons by defined factors. Nature 2010; 463(7284): 1035-41. doi: 10.1038/nature08797 PMID: 20107439</mixed-citation></ref><ref id="B186"><label>186.</label><mixed-citation>Chen JX, et al. Inefficient reprogramming of fibroblasts into cardiomyocytes using Gata4, Mef2c, and Tbx5. Circulation research 2012; 111(1): 50-5. doi: 10.1161/CIRCRESAHA.112.270264</mixed-citation></ref><ref id="B187"><label>187.</label><mixed-citation>Sun S, White RR, Fischer KE, Zhang Z, Austad SN, Vijg J. Inducible aging in Hydra oligactis implicates sexual reproduction, loss of stem cells, and genome maintenance as major pathways. Geroscience 2020; 42(4): 1119-32. doi: 10.1007/s11357-020-00214-z PMID: 32578072</mixed-citation></ref><ref id="B188"><label>188.</label><mixed-citation>Yang MM, Wang J, Dong L, et al. Lack of association of C3 gene with uveitis: additional insights into the genetic profile of uveitis regarding complement pathway genes. Sci Rep 2017; 7(1): 879. doi: 10.1038/s41598-017-00833-1 PMID: 28408754</mixed-citation></ref><ref id="B189"><label>189.</label><mixed-citation>Yang N, Zuchero JB, Ahlenius H, et al. Generation of oligodendroglial cells by direct lineage conversion. Nat Biotechnol 2013; 31(5): 434-9. doi: 10.1038/nbt.2564 PMID: 23584610</mixed-citation></ref><ref id="B190"><label>190.</label><mixed-citation>Weltner J, Balboa D, Katayama S, et al. Human pluripotent reprogramming with CRISPR activators. Nat Commun 2018; 9(1): 2643. doi: 10.1038/s41467-018-05067-x PMID: 29980666</mixed-citation></ref><ref id="B191"><label>191.</label><mixed-citation>Aschheim K. Making neurons with microRNAs. Nat Biotechnol 2011; 29(8): 721-2.</mixed-citation></ref><ref id="B192"><label>192.</label><mixed-citation>Jayawardena T, Egemnazarov B, Finch E, Zhang L, Payne J, Pandya K. MicroRNA-mediated in vitro and in vivo direct reprogramming of cardiac fibroblasts to cardiomyocytes. Circ Res 2012; 110(11): 1465-73.</mixed-citation></ref><ref id="B193"><label>193.</label><mixed-citation>Yamamoto K, Kishida T, Sato Y, et al. Direct conversion of human fibroblasts into functional osteoblasts by defined factors. Proc Natl Acad Sci USA 2015; 112(19): 6152-7. doi: 10.1073/pnas.1420713112 PMID: 25918395</mixed-citation></ref><ref id="B194"><label>194.</label><mixed-citation>Xie H, Ye M, Feng R, Graf T. Stepwise reprogramming of B cells into macrophages. Cell 2004; 117(5): 663-76. doi: 10.1016/S0092-8674(04)00419-2 PMID: 15163413</mixed-citation></ref><ref id="B195"><label>195.</label><mixed-citation>Strumpf D, Mao C-A, Yamanaka Y, Ralston A, Chawengsaksophak K, Beck F. Cdx2 is required for correct cell fate specification and differentiation of trophectoderm in the mouse blastocyst. Development 2005; 132(9): 2093-102. doi: 10.1242/dev.01801 PMID: 15788452</mixed-citation></ref><ref id="B196"><label>196.</label><mixed-citation>Xu H, Tsang KS, Chan JCN, et al. The combined expression of Pdx1 and MafA with either Ngn3 or NeuroD improves the differentiation efficiency of mouse embryonic stem cells into insulin-producing cells. Cell Transplant 2013; 22(1): 147-58. doi: 10.3727/096368912X653057 PMID: 22776709</mixed-citation></ref><ref id="B197"><label>197.</label><mixed-citation>Guo Z, Zhang L, Wu Z, Chen Y, Wang F, Chen G. In vivo direct reprogramming of reactive glial cells into functional neurons after brain injury and in an Alzheimers disease model. Cell Stem Cell 2014; 14(2): 188-202. doi: 10.1016/j.stem.2013.12.001 PMID: 24360883</mixed-citation></ref><ref id="B198"><label>198.</label><mixed-citation>Pataskar A, Jung J, Smialowski P, et al. NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program. EMBO J 2016; 35(1): 24-45. doi: 10.15252/embj.201591206 PMID: 26516211</mixed-citation></ref><ref id="B199"><label>199.</label><mixed-citation>Galipeau J, Sensébé L. Mesenchymal stromal cells: Clinical challenges and therapeutic opportunities. Cell Stem Cell 2018; 22(6): 824-33. doi: 10.1016/j.stem.2018.05.004 PMID: 29859173</mixed-citation></ref><ref id="B200"><label>200.</label><mixed-citation>Karow M, Camp JG, Falk S, et al. Direct pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program. Nat Neurosci 2018; 21(7): 932-40. doi: 10.1038/s41593-018-0168-3 PMID: 29915193</mixed-citation></ref><ref id="B201"><label>201.</label><mixed-citation>Ahfeldt T, Schinzel RT, Lee YK, et al. Programming human pluripotent stem cells into white and brown adipocytes. Nat Cell Biol 2012; 14(2): 209-19. doi: 10.1038/ncb2411 PMID: 22246346</mixed-citation></ref><ref id="B202"><label>202.</label><mixed-citation>Liu XS, Wu H, Ji X, Stelzer Y, Wu X, Czauderna S. Editing DNA methylation in the mammalian genome. Cell 2016; 167(1): 233-47. doi: 10.1016/j.cell.2016.08.056</mixed-citation></ref><ref id="B203"><label>203.</label><mixed-citation>Baumann V, Wiesbeck M, Breunig CT, et al. Targeted removal of epigenetic barriers during transcriptional reprogramming. Nat Commun 2019; 10(1): 2119. doi: 10.1038/s41467-019-10146-8 PMID: 31073172</mixed-citation></ref><ref id="B204"><label>204.</label><mixed-citation>Black JB, Adler AF, Wang HG, et al. Targeted epigenetic remodeling of endogenous loci by CRISPR/Cas9-based transcriptional activators directly converts fibroblasts to neuronal cells. Cell Stem Cell 2016; 19(3): 406-14. doi: 10.1016/j.stem.2016.07.001 PMID: 27524438</mixed-citation></ref><ref id="B205"><label>205.</label><mixed-citation>Hill PWS, Leitch HG, Requena CE, et al. Epigenetic reprogramming enables the transition from primordial germ cell to gonocyte. Nature 2018; 555(7696): 392-6. doi: 10.1038/nature25964 PMID: 29513657</mixed-citation></ref><ref id="B206"><label>206.</label><mixed-citation>Warren L, Wang J. Feeder‐free reprogramming of human fibroblasts with messenger RNA. Curr Protoc Stem Cell Biol 2013; 27(1): 4A.6.1-4A.6.27. doi: 10.1002/9780470151808.sc04a06s27</mixed-citation></ref><ref id="B207"><label>207.</label><mixed-citation>Zhou H. Dissecting transcriptional control by Klf4 in somatic cell reprogramming UCLA Electronic Theses and Dissertations. Los Angeles University of California 2017.</mixed-citation></ref><ref id="B208"><label>208.</label><mixed-citation>Tian Z, Guo F, Biswas S, Deng W. Rationale and methodology of reprogramming for generation of induced pluripotent stem cells and induced neural progenitor cells. Int J Mol Sci 2016; 17(4): 594. doi: 10.3390/ijms17040594 PMID: 27104529</mixed-citation></ref><ref id="B209"><label>209.</label><mixed-citation>Rizzino A, Wuebben EL. Sox2/Oct4: A delicately balanced partnership in pluripotent stem cells and embryogenesis. Biochim Biophys Acta Gene Regul Mech 2016; 1859(6): 780-91. doi: 10.1016/j.bbagrm.2016.03.006 PMID: 26992828</mixed-citation></ref><ref id="B210"><label>210.</label><mixed-citation>Rizzino A. Sox2 and Oct‐3/4: A versatile pair of master regulators that orchestrate the self‐renewal and pluripotency of embryonic stem cells. Wiley Interdiscip Rev Syst Biol Med 2009; 1(2): 228-36. doi: 10.1002/wsbm.12 PMID: 20016762</mixed-citation></ref><ref id="B211"><label>211.</label><mixed-citation>Takahashi K, Tanabe K, Ohnuki M, et al. Induction of pluripotency in human somatic cells via a transient state resembling primitive streak-like mesendoderm. Nat Commun 2014; 5(1): 3678. doi: 10.1038/ncomms4678 PMID: 24759836</mixed-citation></ref><ref id="B212"><label>212.</label><mixed-citation>King HW, Klose RJ. The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells. eLife 2017; 6: e22631. doi: 10.7554/eLife.22631 PMID: 28287392</mixed-citation></ref><ref id="B213"><label>213.</label><mixed-citation>Respuela P, Nikolić M, Tan M, et al. Foxd3 promotes exit from naive pluripotency through enhancer decommissioning and inhibits germline specification. Cell Stem Cell 2016; 18(1): 118-33. doi: 10.1016/j.stem.2015.09.010 PMID: 26748758</mixed-citation></ref><ref id="B214"><label>214.</label><mixed-citation>Krishnakumar R, Chen AF, Pantovich MG, et al. FOXD3 regulates pluripotent stem cell potential by simultaneously initiating and repressing enhancer activity. Cell Stem Cell 2016; 18(1): 104-17. doi: 10.1016/j.stem.2015.10.003 PMID: 26748757</mixed-citation></ref><ref id="B215"><label>215.</label><mixed-citation>Iturbide A, Pascual-Reguant L, Fargas L, et al. LOXL2 oxidizes methylated TAF10 and controls TFIID-dependent genes during neural progenitor differentiation. Mol Cell 2015; 58(5): 755-66. doi: 10.1016/j.molcel.2015.04.012 PMID: 25959397</mixed-citation></ref><ref id="B216"><label>216.</label><mixed-citation>Hu K. Quick, coordinated and authentic reprogramming of ribosome biogenesis during iPSC reprogramming. Cells 2020; 9(11): 2484. doi: 10.3390/cells9112484 PMID: 33203179</mixed-citation></ref><ref id="B217"><label>217.</label><mixed-citation>Carey BW, Markoulaki S, Hanna JH, et al. Reprogramming factor stoichiometry influences the epigenetic state and biological properties of induced pluripotent stem cells. Cell Stem Cell 2011; 9(6): 588-98. doi: 10.1016/j.stem.2011.11.003 PMID: 22136932</mixed-citation></ref><ref id="B218"><label>218.</label><mixed-citation>Stadtfeld M, Apostolou E, Akutsu H, et al. Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature 2010; 465(7295): 175-81. doi: 10.1038/nature09017 PMID: 20418860</mixed-citation></ref><ref id="B219"><label>219.</label><mixed-citation>Han J, Yuan P, Yang H, et al. Tbx3 improves the germ-line competency of induced pluripotent stem cells. Nature 2010; 463(7284): 1096-100. doi: 10.1038/nature08735 PMID: 20139965</mixed-citation></ref><ref id="B220"><label>220.</label><mixed-citation>Jiang J, Lv W, Ye X, et al. Zscan4 promotes genomic stability during reprogramming and dramatically improves the quality of iPS cells as demonstrated by tetraploid complementation. Cell Res 2013; 23(1): 92-106. doi: 10.1038/cr.2012.157 PMID: 23147797</mixed-citation></ref><ref id="B221"><label>221.</label><mixed-citation>Zhao XY, Lv Z, Li W, Zeng F, Zhou Q. Production of mice using iPS cells and tetraploid complementation. Nat Protoc 2010; 5(5): 963-71. doi: 10.1038/nprot.2010.61 PMID: 20431542</mixed-citation></ref><ref id="B222"><label>222.</label><mixed-citation>Lengner CJ, Gimelbrant AA, Erwin JA, et al. Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations. Cell 2010; 141(5): 872-83. doi: 10.1016/j.cell.2010.04.010 PMID: 20471072</mixed-citation></ref><ref id="B223"><label>223.</label><mixed-citation>Stadtfeld M, Apostolou E, Ferrari F, et al. Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of alliPS cell mice from terminally differentiated B cells. Nat Genet 2012; 44(4): 398-405 S1-S2. doi: 10.1038/ng.1110 PMID: 22387999</mixed-citation></ref><ref id="B224"><label>224.</label><mixed-citation>Yuan X, Wan H, Zhao X, Zhu S, Zhou Q, Ding S. Brief report: Combined chemical treatment enables Oct4-induced reprogramming from mouse embryonic fibroblasts. Stem Cells 2011; 29(3): 549-53. doi: 10.1002/stem.594 PMID: 21425417</mixed-citation></ref><ref id="B225"><label>225.</label><mixed-citation>Omole AE, Fakoya AOJ. Ten years of progress and promise of induced pluripotent stem cells: historical origins, characteristics, mechanisms, limitations, and potential applications. PeerJ 2018; 6: e4370. doi: 10.7717/peerj.4370 PMID: 29770269</mixed-citation></ref><ref id="B226"><label>226.</label><mixed-citation>Ahmadzadeh V, Farajnia S, Baghban R, Rahbarnia L, Zarredar H. CRISPR‐Cas system: Toward a more efficient technology for genome editing and beyond. J Cell Biochem 2019; 120(10): 16379-92. doi: 10.1002/jcb.29140 PMID: 31219653</mixed-citation></ref><ref id="B227"><label>227.</label><mixed-citation>Takahashi S, Kobayashi S, Hiratani I. Epigenetic differences between naïve and primed pluripotent stem cells. Cell Mol Life Sci 2018; 75(7): 1191-203. doi: 10.1007/s00018-017-2703-x PMID: 29134247</mixed-citation></ref><ref id="B228"><label>228.</label><mixed-citation>Kojima Y, Kaufman-Francis K, Studdert JB, et al. The transcriptional and functional properties of mouse epiblast stem cells resemble the anterior primitive streak. Cell Stem Cell 2014; 14(1): 107-20. doi: 10.1016/j.stem.2013.09.014 PMID: 24139757</mixed-citation></ref><ref id="B229"><label>229.</label><mixed-citation>Graf T, Stadtfeld M. Heterogeneity of embryonic and adult stem cells. Cell Stem Cell 2008; 3(5): 480-3. doi: 10.1016/j.stem.2008.10.007 PMID: 18983963</mixed-citation></ref><ref id="B230"><label>230.</label><mixed-citation>Liu G, David BT, Trawczynski M, Fessler RG. Advances in pluripotent stem cells: history, mechanisms, technologies, and applications. Stem Cell Rev Rep 2020; 16(1): 3-32. doi: 10.1007/s12015-019-09935-x PMID: 31760627</mixed-citation></ref><ref id="B231"><label>231.</label><mixed-citation>Volpato V, Webber C. Addressing variability in iPSC-derived models of human disease: Guidelines to promote reproducibility. Dis Model Mech 2020; 13(1): dmm042317. doi: 10.1242/dmm.042317 PMID: 31953356</mixed-citation></ref><ref id="B232"><label>232.</label><mixed-citation>Matoba S, Zhang Y. Somatic cell nuclear transfer reprogramming: mechanisms and applications. Cell Stem Cell 2018; 23(4): 471-85. doi: 10.1016/j.stem.2018.06.018 PMID: 30033121</mixed-citation></ref><ref id="B233"><label>233.</label><mixed-citation>Steichen C, Hannoun Z, Luce E, Hauet T, Dubart-Kupperschmitt A. Genomic integrity of human induced pluripotent stem cells: Reprogramming, differentiation and applications. World J Stem Cells 2019; 11(10): 729-47. doi: 10.4252/wjsc.v11.i10.729 PMID: 31692979</mixed-citation></ref><ref id="B234"><label>234.</label><mixed-citation>Schwartz SD, Tan G, Hosseini H, Nagiel A. Subretinal transplantation of embryonic stem cellderived retinal pigment epithelium for the treatment of macular degeneration: An assessment at 4 years. Invest Ophthalmol Vis Sci 2016; 57(5): ORSFc1-9. doi: 10.1167/iovs.15-18681</mixed-citation></ref><ref id="B235"><label>235.</label><mixed-citation>da Cruz L, Fynes K, Georgiadis O, et al. Phase 1 clinical study of an embryonic stem cellderived retinal pigment epithelium patch in age-related macular degeneration. Nat Biotechnol 2018; 36(4): 328-37. doi: 10.1038/nbt.4114 PMID: 29553577</mixed-citation></ref><ref id="B236"><label>236.</label><mixed-citation>Kudo H, Wada H, Sasaki H, et al. Induction of macrophage-like immunosuppressive cells from mouse ES cells that contribute to prolong allogeneic graft survival. PLoS One 2014; 9(10): e111826. doi: 10.1371/journal.pone.0111826 PMID: 25356669</mixed-citation></ref><ref id="B237"><label>237.</label><mixed-citation>Sasaki H, Wada H, Baghdadi M, et al. New immunosuppressive cell therapy to prolong survival of induced pluripotent stem cellderived allografts. Transplantation 2015; 99(11): 2301-10. doi: 10.1097/TP.0000000000000875 PMID: 26360665</mixed-citation></ref><ref id="B238"><label>238.</label><mixed-citation>Cai S, Hou J, Fujino M, et al. iPSC-derived regulatory dendritic cells inhibit allograft rejection by generating alloantigen-specific regulatory T cells. Stem Cell Reports 2017; 8(5): 1174-89. doi: 10.1016/j.stemcr.2017.03.020 PMID: 28434942</mixed-citation></ref></ref-list></back></article>
