Skip to main content

Epigenetic Regulation of ES Cell Pluripotency Maintenance

  • Chapter
  • First Online:
Epigenetics, the Environment, and Children’s Health Across Lifespans
  • 1610 Accesses

Abstract

Epigenetic regulation plays an important role in ES cell pluripotency maintenance. Chromatin structure changes, DNA methylation, and noncoding RNAs all contribute to the epigenetic regulation of ES cell pluripotency maintenance. They will be described in detail in this chapter.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Ang, Y. S., Tsai, S. Y., Lee, D. F., Monk, J., Su, J., Ratnakumar, K., Ding, J., Ge, Y., Darr, H., Chang, B., et al. (2011). Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell, 145, 183–197.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Azuara, V., Perry, P., Sauer, S., Spivakov, M., Jorgensen, H. F., John, R. M., Gouti, M., Casanova, M., Warnes, G., Merkenschlager, M., et al. (2006). Chromatin signatures of pluripotent cell lines. Nature Cell Biology, 8, 532–538.

    Article  CAS  PubMed  Google Scholar 

  • Banath, J. P., Banuelos, C. A., Klokov, D., MacPhail, S. M., Lansdorp, P. M., & Olive, P. L. (2009). Explanation for excessive DNA single-strand breaks and endogenous repair foci in pluripotent mouse embryonic stem cells. Experimental Cell Research, 315, 1505–1520.

    Article  CAS  PubMed  Google Scholar 

  • Bar-Nur, O., Russ, H. A., Efrat, S., & Benvenisty, N. (2011). Epigenetic memory and preferential lineage-specific differentiation in induced pluripotent stem cells derived from human pancreatic islet beta cells. Cell Stem Cell, 9, 17–23.

    Article  CAS  PubMed  Google Scholar 

  • Barrero, M. J., Sese, B., Kuebler, B., Bilic, J., Boue, S., Marti, M., & Izpisua Belmonte, J. C. (2013). Macrohistone variants preserve cell identity by preventing the gain of H3K4me2 during reprogramming to pluripotency. Cell Reports, 3, 1005–1011.

    Article  CAS  PubMed  Google Scholar 

  • Barski, A., Cuddapah, S., Cui, K., Roh, T. Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007). High-resolution profiling of histone methylations in the human genome. Cell, 129, 823–837.

    Article  CAS  PubMed  Google Scholar 

  • Basta, J., & Rauchman, M. (2015). The nucleosome remodeling and deacetylase complex in development and disease. Translational Research, 165, 36–47.

    Article  CAS  PubMed  Google Scholar 

  • Benetti, R., Gonzalo, S., Jaco, I., Munoz, P., Gonzalez, S., Schoeftner, S., Murchison, E., Andl, T., Chen, T., Klatt, P., et al. (2008). A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases. Nature Structural and Molecular Biology, 15, 998.

    Article  CAS  PubMed  Google Scholar 

  • Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006). A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell, 125, 315–326.

    Article  CAS  PubMed  Google Scholar 

  • Bhutani, N., Brady, J. J., Damian, M., Sacco, A., Corbel, S. Y., & Blau, H. M. (2010). Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature, 463, 1042–1047.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Biterge, B., & Schneider, R. (2014). Histone variants: Key players of chromatin. Cell and Tissue Research, 356, 457–466.

    Article  CAS  PubMed  Google Scholar 

  • Buschbeck, M., & Di Croce, L. (2010). Approaching the molecular and physiological function of macroH2A variants. Epigenetics, 5, 118–123.

    Article  CAS  PubMed  Google Scholar 

  • Cao, K., Lailler, N., Zhang, Y., Kumar, A., Uppal, K., Liu, Z., Lee, E. K., Wu, H., Medrzycki, M., Pan, C., et al. (2013). High-resolution mapping of h1 linker histone variants in embryonic stem cells. PLoS Genetics, 9, e1003417.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Chamberlain, S. J., Yee, D., & Magnuson, T. (2008). Polycomb repressive complex 2 is dispensable for maintenance of embryonic stem cell pluripotency. Stem Cells, 26, 1496–1505.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Christophorou, M. A., Castelo-Branco, G., Halley-Stott, R. P., Oliveira, C. S., Loos, R., Radzisheuskaya, A., Mowen, K. A., Bertone, P., Silva, J. C., Zernicka-Goetz, M., et al. (2014). Citrullination regulates pluripotency and histone H1 binding to chromatin. Nature, 507, 104–108.

    Article  CAS  PubMed  Google Scholar 

  • Creppe, C., Janich, P., Cantarino, N., Noguera, M., Valero, V., Musulen, E., Douet, J., Posavec, M., Martin-Caballero, J., Sumoy, L., et al. (2012). MacroH2A1 regulates the balance between self-renewal and differentiation commitment in embryonic and adult stem cells. Molecular and Cellular Biology, 32, 1442–1452.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Creyghton, M. P., Markoulaki, S., Levine, S. S., Hanna, J., Lodato, M. A., Sha, K., Young, R. A., Jaenisch, R., & Boyer, L. A. (2008). H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment. Cell, 135, 649–661.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Dinger, M. E., Amaral, P. P., Mercer, T. R., Pang, K. C., Bruce, S. J., Gardiner, B. B., Askarian-Amiri, M. E., Ru, K., Solda, G., Simons, C., et al. (2008). Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Research, 18, 1433–1445.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • dos Santos, R. L., Tosti, L., Radzisheuskaya, A., Caballero, I. M., Kaji, K., Hendrich, B., & Silva, J. C. (2014). MBD3/NuRD facilitates induction of pluripotency in a context-dependent manner. Cell Stem Cell, 15, 102–110.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Erriquez, D., Perini, G., & Ferlini, A. (2013). Non-coding RNAs in muscle dystrophies. International Journal of Molecular Sciences, 14, 19681–19704.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Fazzio, T. G., & Panning, B. (2010). Control of embryonic stem cell identity by nucleosome remodeling enzymes. Current Opinion in Genetics and Development, 20, 500–504.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Fussner, E., Djuric, U., Strauss, M., Hotta, A., Perez-Iratxeta, C., Lanner, F., Dilworth, F. J., Ellis, J., & Bazett-Jones, D. P. (2011). Constitutive heterochromatin reorganization during somatic cell reprogramming. Embo Journal, 30, 1778–1789.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gao, X., Tate, P., Hu, P., Tjian, R., Skarnes, W. C., & Wang, Z. (2008). ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a. Proceedings of the National Academy of Sciences of the United States of America, 105, 6656–6661.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gaspar-Maia, A., Alajem, A., Meshorer, E., & Ramalho-Santos, M. (2011). Open chromatin in pluripotency and reprogramming. Nature Reviews Molecular Cell Biology, 12, 36–47.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gaspar-Maia, A., Qadeer, Z. A., Hasson, D., Ratnakumar, K., Leu, N. A., Leroy, G., Liu, S., Costanzi, C., Valle-Garcia, D., Schaniel, C., et al. (2013). MacroH2A histone variants act as a barrier upon reprogramming towards pluripotency. Nature Communications, 4, 1565.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Glaser, S., Schaft, J., Lubitz, S., Vintersten, K., van der Hoeven, F., Tufteland, K. R., Aasland, R., Anastassiadis, K., Ang, S. L., & Stewart, A. F. (2006). Multiple epigenetic maintenance factors implicated by the loss of Mll2 in mouse development. Development, 133, 1423–1432.

    Article  CAS  PubMed  Google Scholar 

  • Gu, T. P., Guo, F., Yang, H., Wu, H. P., Xu, G. F., Liu, W., Xie, Z. G., Shi, L., He, X., Jin, S. G., et al. (2011). The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature, 477, 606–610.

    Article  CAS  PubMed  Google Scholar 

  • Guidi, C. J., Sands, A. T., Zambrowicz, B. P., Turner, T. K., Demers, D. A., Webster, W., Smith, T. W., Imbalzano, A. N., & Jones, S. N. (2001). Disruption of Ini1 leads to peri-implantation lethality and tumorigenesis in mice. Molecular and Cellular Biology, 21, 3598–3603.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Guo, H., Zhu, P., Yan, L., Li, R., Hu, B., Lian, Y., Yan, J., Ren, X., Lin, S., Li, J., et al. (2014). The DNA methylation landscape of human early embryos. Nature, 511, 606–610.

    Article  CAS  PubMed  Google Scholar 

  • Guttman, M., Donaghey, J., Carey, B. W., Garber, M., Grenier, J. K., Munson, G., Young, G., Lucas, A. B., Ach, R., Bruhn, L., et al. (2011). lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature, 477, 295–300.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Guttman, M., Garber, M., Levin, J. Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M. J., Gnirke, A., Nusbaum, C., et al. (2010). Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotechnology, 28, 503–510.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Habibi, E., Brinkman, A. B., Arand, J., Kroeze, L. I., Kerstens, H. H., Matarese, F., Lepikhov, K., Gut, M., Brun-Heath, I., Hubner, N. C., et al. (2013). Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. Cell Stem Cell, 13, 360–369.

    Article  CAS  PubMed  Google Scholar 

  • Happel, N., & Doenecke, D. (2009). Histone H1 and its isoforms: contribution to chromatin structure and function. Gene, 431, 1–12.

    Article  CAS  PubMed  Google Scholar 

  • Hargreaves, D. C., & Crabtree, G. R. (2011). ATP-dependent chromatin remodeling: Genetics, genomics and mechanisms. Cell Research, 21, 396–420.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Hayakawa, K., Ohgane, J., Tanaka, S., Yagi, S., & Shiota, K. (2012). Oocyte-specific linker histone H1foo is an epigenomic modulator that decondenses chromatin and impairs pluripotency. Epigenetics, 7, 1029–1036.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • He, Y. F., Li, B. Z., Li, Z., Liu, P., Wang, Y., Tang, Q., Ding, J., Jia, Y., Chen, Z., Li, L., et al. (2011). Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science, 333, 1303–1307.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Heo, I., Joo, C., Cho, J., Ha, M., Han, J., & Kim, V. N. (2008). Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. Molecular Cell, 32, 276–284.

    Article  CAS  PubMed  Google Scholar 

  • Ho, L., Jothi, R., Ronan, J. L., Cui, K., Zhao, K., & Crabtree, G. R. (2009a). An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proceedings of the National Academy of Sciences of the United States of America, 106, 5187–5191.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ho, L., Ronan, J. L., Wu, J., Staahl, B. T., Chen, L., Kuo, A., Lessard, J., Nesvizhskii, A. I., Ranish, J., & Crabtree, G. R. (2009b). An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proceedings of the National Academy of Sciences of the United States of America, 106, 5181–5186.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Houbaviy, H. B., Murray, M. F., & Sharp, P. A. (2003). Embryonic stem cell-specific MicroRNAs. Developmental Cell, 5, 351–358.

    Article  CAS  PubMed  Google Scholar 

  • Hu, X., Zhang, L., Mao, S. Q., Li, Z., Chen, J., Zhang, R. R., Wu, H. P., Gao, J., Guo, F., Liu, W., et al. (2014). Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming. Cell Stem Cell, 14, 512–522.

    Article  CAS  PubMed  Google Scholar 

  • Huangfu, D., Maehr, R., Guo, W., Eijkelenboom, A., Snitow, M., Chen, A. E., & Melton, D. A. (2008a). Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nature Biotechnology, 26, 795–797.

    Article  CAS  PubMed  Google Scholar 

  • Huangfu, D., Osafune, K., Maehr, R., Guo, W., Eijkelenboom, A., Chen, S., Muhlestein, W., & Melton, D. A. (2008b). Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2. Nature Biotechnology, 26, 1269–1275.

    Article  CAS  PubMed  Google Scholar 

  • Ito, S., Shen, L., Dai, Q., Wu, S. C., Collins, L. B., Swenberg, J. A., He, C., & Zhang, Y. (2011). Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science, 333, 1300–1303.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Judson, R. L., Babiarz, J. E., Venere, M., & Blelloch, R. (2009). Embryonic stem cell-specific microRNAs promote induced pluripotency. Nature Biotechnology, 27, 459–461.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kafer, G. R., Lehnert, S. A., Pantaleon, M., Kaye, P. L., & Moser, R. J. (2010). Expression of genes coding for histone variants and histone-associated proteins in pluripotent stem cells and mouse preimplantation embryos. Gene Expression Patterns, 10, 299–305.

    Article  CAS  PubMed  Google Scholar 

  • Kaji, K., Caballero, I. M., MacLeod, R., Nichols, J., Wilson, V. A., & Hendrich, B. (2006). The NuRD component Mbd3 is required for pluripotency of embryonic stem cells. Nature Cell Biology, 8, 285–292.

    Article  CAS  PubMed  Google Scholar 

  • Kaji, K., Nichols, J., & Hendrich, B. (2007). Mbd3, a component of the NuRD co-repressor complex, is required for development of pluripotent cells. Development, 134, 1123–1132.

    Article  CAS  PubMed  Google Scholar 

  • Kidder, B. L., Palmer, S., & Knott, J. G. (2009). SWI/SNF-Brg1 regulates self-renewal and occupies core pluripotency-related genes in embryonic stem cells. Stem Cells, 27, 317–328.

    Article  CAS  PubMed  Google Scholar 

  • Kim, K., Doi, A., Wen, B., Ng, K., Zhao, R., Cahan, P., Kim, J., Aryee, M. J., Ji, H., Ehrlich, L. I., et al. (2010). Epigenetic memory in induced pluripotent stem cells. Nature, 467, 285–290.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kim, J. K., Huh, S. O., Choi, H., Lee, K. S., Shin, D., Lee, C., Nam, J. S., Kim, H., Chung, H., Lee, H. W., et al. (2001). Srg3, a mouse homolog of yeast SWI3, is essential for early embryogenesis and involved in brain development. Molecular and Cellular Biology, 21, 7787–7795.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Klochendler-Yeivin, A., Fiette, L., Barra, J., Muchardt, C., Babinet, C., & Yaniv, M. (2000). The murine SNF5/INI1 chromatin remodeling factor is essential for embryonic development and tumor suppression. EMBO Reports, 1, 500–506.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kumar, M. S., Lu, J., Mercer, K. L., Golub, T. R., & Jacks, T. (2007). Impaired microRNA processing enhances cellular transformation and tumorigenesis. Nature Genetics, 39, 673–677.

    Article  CAS  PubMed  Google Scholar 

  • Leitch, H. G., McEwen, K. R., Turp, A., Encheva, V., Carroll, T., Grabole, N., Mansfield, W., Nashun, B., Knezovich, J. G., Smith, A., et al. (2013). Naive pluripotency is associated with global DNA hypomethylation. Nature Structural and Molecular Biology, 20, 311–316.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Lessard, J. A., & Crabtree, G. R. (2010). Chromatin regulatory mechanisms in pluripotency. Annual Review of Cell and Developmental Biology, 26, 503–532.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Li, B., Pattenden, S. G., Lee, D., Gutierrez, J., Chen, J., Seidel, C., Gerton, J., & Workman, J. L. (2005). Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. Proceedings of the National Academy of Sciences of the United States of America, 102, 18385–18390.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Liang, J., Wan, M., Zhang, Y., Gu, P., Xin, H., Jung, S. Y., Qin, J., Wong, J., Cooney, A. J., Liu, D., et al. (2008). Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells. Nature Cell Biology, 10, 731–739.

    Article  CAS  PubMed  Google Scholar 

  • Lin, M., Pedrosa, E., Shah, A., Hrabovsky, A., Maqbool, S., Zheng, D., & Lachman, H. M. (2011). RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders. PLoS One, 6, e23356.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Lister, R., Pelizzola, M., Kida, Y. S., Hawkins, R. D., Nery, J. R., Hon, G., Antosiewicz-Bourget, J., O’Malley, R., Castanon, R., Klugman, S., et al. (2011). Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature, 471, 68–73.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Loewer, S., Cabili, M. N., Guttman, M., Loh, Y. H., Thomas, K., Park, I. H., Garber, M., Curran, M., Onder, T., Agarwal, S., et al. (2010). Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nature Genetics, 42, 1113–1117.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F., & Richmond, T. J. (1997). Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature, 389, 251–260.

    Article  CAS  PubMed  Google Scholar 

  • Ma, D. K., Chiang, C. H., Ponnusamy, K., Ming, G. L., & Song, H. (2008). G9a and Jhdm2a regulate embryonic stem cell fusion-induced reprogramming of adult neural stem cells. Stem Cells, 26, 2131–2141.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mak, A. B., Ni, Z., Hewel, J. A., Chen, G. I., Zhong, G., Karamboulas, K., Blakely, K., Smiley, S., Marcon, E., Roudeva, D., et al. (2010). A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency. Molecular and Cellular Proteomics, 9, 811–823.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mali, P., Chou, B. K., Yen, J., Ye, Z., Zou, J., Dowey, S., Brodsky, R. A., Ohm, J. E., Yu, W., Baylin, S. B., et al. (2010). Butyrate greatly enhances derivation of human induced pluripotent stem cells by promoting epigenetic remodeling and the expression of pluripotency-associated genes. Stem Cells, 28, 713–720.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mansour, A. A., Gafni, O., Weinberger, L., Zviran, A., Ayyash, M., Rais, Y., Krupalnik, V., Zerbib, M., Amann-Zalcenstein, D., Maza, I., et al. (2012). The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming. Nature, 488, 409–413.

    Article  CAS  PubMed  Google Scholar 

  • Marson, A., Levine, S. S., Cole, M. F., Frampton, G. M., Brambrink, T., Johnstone, S., Guenther, M. G., Johnston, W. K., Wernig, M., Newman, J., et al. (2008). Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell, 134, 521–533.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mattout, A., Biran, A., & Meshorer, E. (2011). Global epigenetic changes during somatic cell reprogramming to iPS cells. Journal of Molecular Cell Biology, 3, 341–350.

    Article  PubMed  CAS  Google Scholar 

  • Mattout, A., & Meshorer, E. (2010). Chromatin plasticity and genome organization in pluripotent embryonic stem cells. Current Opinion in Cell Biology, 22, 334–341.

    Article  CAS  PubMed  Google Scholar 

  • Melton, C., Judson, R. L., & Blelloch, R. (2010). Opposing microRNA families regulate self-renewal in mouse embryonic stem cells. Nature, 463, 621–626.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Meshorer, E., Yellajoshula, D., George, E., Scambler, P. J., Brown, D. T., & Misteli, T. (2006). Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Developmental Cell, 10, 105–116.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mikkelsen, T. S., Hanna, J., Zhang, X., Ku, M., Wernig, M., Schorderet, P., Bernstein, B. E., Jaenisch, R., Lander, E. S., & Meissner, A. (2008). Dissecting direct reprogramming through integrative genomic analysis. Nature, 454, 49–55.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Nashun, B., Akiyama, T., Suzuki, M. G., & Aoki, F. (2011). Dramatic replacement of histone variants during genome remodeling in nuclear-transferred embryos. Epigenetics, 6, 1489–1497.

    Article  CAS  PubMed  Google Scholar 

  • Nguyen, A. T., & Zhang, Y. (2011). The diverse functions of Dot1 and H3K79 methylation. Genes and Development, 25, 1345–1358.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ohi, Y., Qin, H., Hong, C., Blouin, L., Polo, J. M., Guo, T., Qi, Z., Downey, S. L., Manos, P. D., Rossi, D. J., et al. (2011). Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nature Cell Biology, 13, 541–549.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ohnuki, M., Tanabe, K., Sutou, K., Teramoto, I., Sawamura, Y., Narita, M., Nakamura, M., Tokunaga, Y., Watanabe, A., Yamanaka, S., et al. (2014). Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential. Proceedings of the National Academy of Sciences of the United States of America, 111, 12426–12431.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Onder, T. T., Kara, N., Cherry, A., Sinha, A. U., Zhu, N., Bernt, K. M., Cahan, P., Marcarci, B. O., Unternaehrer, J., Gupta, P. B., et al. (2012). Chromatin-modifying enzymes as modulators of reprogramming. Nature, 483, 598–602.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Pasini, D., Bracken, A. P., Hansen, J. B., Capillo, M., & Helin, K. (2007). The polycomb group protein Suz12 is required for embryonic stem cell differentiation. Molecular and Cellular Biology, 27, 3769–3779.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Pasque, V., Radzisheuskaya, A., Gillich, A., Halley-Stott, R. P., Panamarova, M., Zernicka-Goetz, M., Surani, M. A., & Silva, J. C. (2012). Histone variant macroH2A marks embryonic differentiation in vivo and acts as an epigenetic barrier to induced pluripotency. Journal of Cell Science, 125, 6094–6104.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Pereira, C. F., Piccolo, F. M., Tsubouchi, T., Sauer, S., Ryan, N. K., Bruno, L., Landeira, D., Santos, J., Banito, A., Gil, J., et al. (2010). ESCs require PRC2 to direct the successful reprogramming of differentiated cells toward pluripotency. Cell Stem Cell, 6, 547–556.

    Article  CAS  PubMed  Google Scholar 

  • Petruk, S., Sedkov, Y., Johnston, D. M., Hodgson, J. W., Black, K. L., Kovermann, S. K., Beck, S., Canaani, E., Brock, H. W., & Mazo, A. (2012). TrxG and PcG proteins but not methylated histones remain associated with DNA through replication. Cell, 150, 922–933.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Polo, J. M., Liu, S., Figueroa, M. E., Kulalert, W., Eminli, S., Tan, K. Y., Apostolou, E., Stadtfeld, M., Li, Y., Shioda, T., et al. (2010). Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. Nature Biotechnology, 28, 848–855.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Rangasamy, D., Berven, L., Ridgway, P., & Tremethick, D. J. (2003). Pericentric heterochromatin becomes enriched with H2A.Z during early mammalian development. EMBO Journal, 22, 1599–1607.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Rothbart, S. B., & Strahl, B. D. (2014). Interpreting the language of histone and DNA modifications. Biochimica et Biophysica Acta, 1839, 627–643.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Rybak, A., Fuchs, H., Smirnova, L., Brandt, C., Pohl, E. E., Nitsch, R., & Wulczyn, F. G. (2008). A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment. Nature Cell Biology, 10, 987–993.

    Article  CAS  PubMed  Google Scholar 

  • Schuettengruber, B., Martinez, A. M., Iovino, N., & Cavalli, G. (2011). Trithorax group proteins: Switching genes on and keeping them active. Nature Reviews Molecular Cell Biology, 12, 799–814.

    Article  CAS  PubMed  Google Scholar 

  • Sheik Mohamed, J., Gaughwin, P. M., Lim, B., Robson, P., & Lipovich, L. (2010). Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. RNA, 16, 324–337.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Shen, X., Liu, Y., Hsu, Y. J., Fujiwara, Y., Kim, J., Mao, X., Yuan, G. C., & Orkin, S. H. (2008). EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Molecular Cell, 32, 491–502.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Shi, Y., Desponts, C., Do, J. T., Hahm, H. S., Scholer, H. R., & Ding, S. (2008). Induction of pluripotent stem cells from mouse embryonic fibroblasts by Oct4 and Klf4 with small-molecule compounds. Cell Stem Cell, 3, 568–574.

    Article  CAS  PubMed  Google Scholar 

  • Shimbo, T., Du, Y., Grimm, S. A., Dhasarathy, A., Mav, D., Shah, R. R., Shi, H., & Wade, P. A. (2013). MBD3 localizes at promoters, gene bodies and enhancers of active genes. PLoS Genetics, 9, e1004028.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Simonsson, S., & Gurdon, J. (2004). DNA demethylation is necessary for the epigenetic reprogramming of somatic cell nuclei. Nature Cell Biology, 6, 984–990.

    Article  CAS  PubMed  Google Scholar 

  • Singhal, N., Graumann, J., Wu, G., Arauzo-Bravo, M. J., Han, D. W., Greber, B., Gentile, L., Mann, M., & Scholer, H. R. (2010). Chromatin-remodeling components of the BAF complex facilitate reprogramming. Cell, 141, 943–955.

    Article  CAS  PubMed  Google Scholar 

  • Slany, R. K. (2009). The molecular biology of mixed lineage leukemia. Haematologica, 94, 984–993.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Smith, Z. D., Chan, M. M., Humm, K. C., Karnik, R., Mekhoubad, S., Regev, A., Eggan, K., & Meissner, A. (2014). DNA methylation dynamics of the human preimplantation embryo. Nature, 511, 611–615.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Smith, Z. D., Chan, M. M., Mikkelsen, T. S., Gu, H., Gnirke, A., Regev, A., & Meissner, A. (2012). A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature, 484, 339–344.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sridharan, R., Gonzales-Cope, M., Chronis, C., Bonora, G., McKee, R., Huang, C., Patel, S., Lopez, D., Mishra, N., Pellegrini, M., et al. (2013). Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1gamma in reprogramming to pluripotency. Nature Cell Biology, 15, 872–882.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Stadtfeld, M., Apostolou, E., Akutsu, H., Fukuda, A., Follett, P., Natesan, S., Kono, T., Shioda, T., & Hochedlinger, K. (2010). Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature, 465, 175–181.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Stoller, J. Z., Huang, L., Tan, C. C., Huang, F., Zhou, D. D., Yang, J., Gelb, B. D., & Epstein, J. A. (2010). Ash2l interacts with Tbx1 and is required during early embryogenesis. Experimental Biology and Medicine (Maywood, N.J.), 235, 569–576.

    Article  CAS  Google Scholar 

  • Stummvoll, G. H., Fritsch, R. D., Meyer, B., Hoefler, E., Aringer, M., Smolen, J. S., & Steiner, G. (2009). Characterisation of cellular and humoral autoimmune responses to histone H1 and core histones in human systemic lupus erythaematosus. Annals of the Rheumatic Diseases, 68, 110–116.

    Article  CAS  PubMed  Google Scholar 

  • Taberlay, P. C., Kelly, T. K., Liu, C. C., You, J. S., De Carvalho, D. D., Miranda, T. B., Zhou, X. J., Liang, G., & Jones, P. A. (2011). Polycomb-repressed genes have permissive enhancers that initiate reprogramming. Cell, 147, 1283–1294.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Tahiliani, M., Koh, K. P., Shen, Y., Pastor, W. A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L. M., Liu, D. R., Aravind, L., et al. (2009). Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science, 324, 930–935.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Takashima, Y., Guo, G., Loos, R., Nichols, J., Ficz, G., Krueger, F., Oxley, D., Santos, F., Clarke, J., Mansfield, W., et al. (2014). Resetting transcription factor control circuitry toward ground-state pluripotency in human. Cell, 158, 1254–1269.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Talbert, P. B., & Henikoff, S. (2010). Histone variants--ancient wrap artists of the epigenome. Nature Reviews Molecular Cell Biology, 11, 264–275.

    Article  CAS  PubMed  Google Scholar 

  • Terme, J. M., Sese, B., Millan-Arino, L., Mayor, R., Izpisua Belmonte, J. C., Barrero, M. J., & Jordan, A. (2011). Histone H1 variants are differentially expressed and incorporated into chromatin during differentiation and reprogramming to pluripotency. The Journal of Biological Chemistry, 286, 35347–35357.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Turinetto, V., & Giachino, C. (2015). Histone variants as emerging regulators of embryonic stem cell identity. Epigenetics, 10, 563–573.

    Article  PubMed  Google Scholar 

  • Turinetto, V., Orlando, L., Sanchez-Ripoll, Y., Kumpfmueller, B., Storm, M. P., Porcedda, P., Minieri, V., Saviozzi, S., Accomasso, L., Cibrario Rocchietti, E., et al. (2012). High basal gammaH2AX levels sustain self-renewal of mouse embryonic and induced pluripotent stem cells. Stem Cells, 30, 1414–1423.

    Article  CAS  PubMed  Google Scholar 

  • van Attikum, H., Fritsch, O., & Gasser, S. M. (2007). Distinct roles for SWR1 and INO80 chromatin remodeling complexes at chromosomal double-strand breaks. EMBO Journal, 26, 4113–4125.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Vastenhouw, N. L., & Schier, A. F. (2012). Bivalent histone modifications in early embryogenesis. Current Opinion in Cell Biology, 24, 374–386.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Venkatesh, S., Smolle, M., Li, H., Gogol, M. M., Saint, M., Kumar, S., Natarajan, K., & Workman, J. L. (2012). Set2 methylation of histone H3 lysine 36 suppresses histone exchange on transcribed genes. Nature, 489, 452–455.

    Article  CAS  PubMed  Google Scholar 

  • Viswanathan, S. R., Daley, G. Q., & Gregory, R. I. (2008). Selective blockade of microRNA processing by Lin28. Science, 320, 97–100.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wade, P. A., Gegonne, A., Jones, P. L., Ballestar, E., Aubry, F., & Wolffe, A. P. (1999). Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nature Genetics, 23, 62–66.

    CAS  PubMed  Google Scholar 

  • Wang, Y., Baskerville, S., Shenoy, A., Babiarz, J. E., Baehner, L., & Blelloch, R. (2008). Embryonic stem cell-specific microRNAs regulate the G1-S transition and promote rapid proliferation. Nature Genetics, 40, 1478–1483.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wang, T., Chen, K., Zeng, X., Yang, J., Wu, Y., Shi, X., Qin, B., Zeng, L., Esteban, M. A., Pan, G., et al. (2011). The histone demethylases Jhdm1a/1b enhance somatic cell reprogramming in a vitamin-C-dependent manner. Cell Stem Cell, 9, 575–587.

    Article  CAS  PubMed  Google Scholar 

  • Wang, L., Du, Y., Ward, J. M., Shimbo, T., Lackford, B., Zheng, X., Miao, Y. L., Zhou, B., Han, L., Fargo, D. C., et al. (2014a). INO80 facilitates pluripotency gene activation in embryonic stem cell self-renewal, reprogramming, and blastocyst development. Cell Stem Cell, 14, 575–591.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wang, L., Zhang, J., Duan, J., Gao, X., Zhu, W., Lu, X., Yang, L., Li, G., Ci, W., Li, W., et al. (2014b). Programming and inheritance of parental DNA methylomes in mammals. Cell, 157, 979–991.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Whyte, W. A., Bilodeau, S., Orlando, D. A., Hoke, H. A., Frampton, G. M., Foster, C. T., Cowley, S. M., & Young, R. A. (2012). Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature, 482, 221–225.

    PubMed Central  CAS  PubMed  Google Scholar 

  • Woodcock, C. L. (2005). A milestone in the odyssey of higher-order chromatin structure. Nature Structural and Molecular Biology, 12, 639–640.

    Article  CAS  PubMed  Google Scholar 

  • Wu, T., Liu, Y., Wen, D., Tseng, Z., Tahmasian, M., Zhong, M., Rafii, S., Stadtfeld, M., Hochedlinger, K., & Xiao, A. (2014). Histone variant H2A.X deposition pattern serves as a functional epigenetic mark for distinguishing the developmental potentials of iPSCs. Cell Stem Cell, 15, 281–294.

    Article  CAS  PubMed  Google Scholar 

  • Zhang, Z., Jones, A., Sun, C. W., Li, C., Chang, C. W., Joo, H. Y., Dai, Q., Mysliwiec, M. R., Wu, L. C., Guo, Y., et al. (2011). PRC2 complexes with JARID2, MTF2, and esPRC2p48 in ES cells to modulate ES cell pluripotency and somatic cell reprogramming. Stem Cells, 29, 229–240.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ping Hu Ph.D. .

Editor information

Editors and Affiliations

Abbreviations

Abbreviations

BAF:

Brahma-associated factor

CpG:

Cytosine-guanine nucleotide-rich sequence

DNMT:

DNA methyltransferase

ES Cells:

Embryonic stem cell

HP1α:

Heterochromatin protein 1α

iPS Cells:

Induced pluripotent stem cells

ICM:

Inner cell mass

INO80 chromatin remodeling complex:

A chromatin remodeling complex

lncRNA:

Long noncoding RNA

NODE:

Nanog and Oct4-associated deacetylase

ncRNA:

Noncoding RNA

NuRD:

Nucleosome remodeling and deacetylase

c-Myc:

Oncogene master regulator

PcG:

Polycomb group protein

TrxG:

Trithorax group protein

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Hu, P. (2016). Epigenetic Regulation of ES Cell Pluripotency Maintenance. In: Hollar, D. (eds) Epigenetics, the Environment, and Children’s Health Across Lifespans. Springer, Cham. https://doi.org/10.1007/978-3-319-25325-1_9

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-25325-1_9

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-25323-7

  • Online ISBN: 978-3-319-25325-1

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics