2.6. Conclusions. References

Principles of stem cell biology and cancer: future applications and therapeutics. Edited by T. Regad, T. J. Sayers and R. C. Rees. John Wiley & Sons (2015)

Part I. Stem Cells


ESCs provide a unique system in which to study changes in gene expression and chromatin regulation during differentiation. Understanding these mechanisms will not only be relevant to improving the in vitro generation of cell types and tissues useful for regenerative medicine but also provides insights into regulatory pathways that are frequently altered in pathological situations such as cancer. Importantly, the reversibility of the epigenetic marks can offer multiple possibilities for therapeutic intervention.

References:

Aasen, T., Raya, A., Barrero, M.J., Garreta, E., Consiglio, A., Gonzalez, F., et al., 2008. Efficient and rapid generation of induced pluripotent stem cells from human keratinocytes. Nat. Biotechnol. 26, 1276 – 1284.

Adamo, A., Sese, B., Boue, S., Castano, J., Paramonov, I., Barrero, M.J., Izpisua Belmonte, J.C. 2011. LSD1 regulates the balance between self-renewal and differentiation in human embryonic stem cells. Nat. Cell Biol. 13, 652 – 659.

Agger, K., Cloos, P.A., Christensen, J., Pasini, D., Rose, S., Rappsilber, J., et al., 2007. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 449, 731 – 734.

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

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

Barrero, M.J., Sese, B., Marti, M., Izpisua Belmonte, J.C., 2013b. Macro histone variants are critical for the differentiation of human pluripotent cells. J. Biol. Chem. 288, 16 110 – 16 116.

Bйguelin, W., Popovic, R., Teater, M., Jiang, Y., Bunting, K.L., Rosen, M., et al., 2013. EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation. Cancer Cell 23, 677 – 692.

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

Burgold, T., Spreafico, F., De Santa, F., Totaro, M.G., Prosperini, E., Natoli, G., Testa, G., 2008. The histone H3 lysine 27-specific demethylase Jmjd3 is required for neural commitment. PLoS One 3, e3034.

Cao, R., Wang, L., Wang, H., Xia, L., Erdjument-Bromage, H., Tempst, P., et al., 2002. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039 – 1043.

Costa, Y., Ding, J., Theunissen, T.W., Faiola, F., Hore, T.A., Shliaha, P.V., et al., 2013. NANOG-dependent function of TET1 and TET2 in establishment of pluripotency. Nature 495, 370 – 374.

Chen, J., Liu, H., Liu, J., Qi, J., Wei, B., Yang, J., et al., 2013. H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nat. Genet. 45, 34 – 42.

Denissov, S., Hofemeister, H., Marks, H., Kranz, A., Ciotta, G., Singh, S., et al., 2014. Mll2 is required for H3K4 trimethylation on bivalent promoters in embryonic stem cells, whereas Mll1 is redundant. Development 141, 526 – 537.

Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., et al., 2012. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376 – 380.

Doege, C.A., Inoue, K., Yamashita, T., Rhee, D.B., Travis, S., Fujita, R., et al., 2012. Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2. Nature 488, 652 – 655.

Doi, A., Park, I.H., Wen, B., Murakami, P., Aryee, M.J., Irizarry, R., et al., 2009. Differential methylation of tissueand cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat. Genet. 41, 1350 – 1353.

ENCODE Project Consortium. 2011. A user’s guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 9, e1001046.

Epsztejn-Litman, S., Feldman, N., Abu-Remaileh, M., Shufaro, Y., Gerson, A., Ueda, J., et al., 2008. De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes. Nat. Struct. Mol. Biol. 15, 1176 – 1183.

Esteller, M. 2008. Epigenetics in cancer. N. Engl. J. Med. 358, 1148 – 1159.

Farcas, A.M., Blackledge, N.P., Sudbery, I., Long, H.K., Mcgouran, J.F., Rose, N.R., et al., 2012. KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. eLife, 1, e00205.

Feldman, N., Gerson, A., Fang, J., Li, E., Zhang, Y., Shinkai, Y., et al., 2006. G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis. Nat. Cell Biol. 8, 188 – 194.

Feng, B., Ng, J.H., Heng, J.C., Ng, H.H. 2009. Molecules that promote or enhance reprogramming of somatic cells to induced pluripotent stem cells. Cell Stem Cell, 4, 301 – 312.

Filion, G.J., Van Steensel, B. 2010. Reassessing the abundance of H3K9me2 chromatin domains in embryonic stem cells. Nat. Genet. 42, 4; author reply 5 – 6.

Fragola, G., Germain, P.L., Laise, P., Cuomo, A., Blasimme, A., Gross, F., et al., 2013. Cell reprogramming requires silencing of a core subset of polycomb targets. PLoS Genet. 9, e1003292.

Gao, Y., Chen, J., Li, K., Wu, T., Huang, B., Liu, W., et al., 2013. Replacement of Oct4 by Tet1 during iPSC induction reveals an important role of DNA methylation and hydroxymethylation in reprogramming. Cell Stem Cell 12, 453 – 469.

Gaspar-Maia, A., Alajem, A., Polesso, F., Sridharan, R., Mason, M.J., Heidersbach, A., et al., 2009. Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature 460, 863 – 868.

Gifford, C.A., Ziller, M.J., Gu, H., Trapnell, C., Donaghey, J., Tsankov, A., et al., 2013. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell 153, 1149 – 1163.

Guo, J.U., Su, Y., Zhong, C., Ming, G.-L., Song, H. 2011. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 145, 423 – 434.

Guo, J.U., Su, Y., Shin, J.H., Shin, J., Li, H., Xie, B., et al., 2013. Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nat. Neurosci. 17, 215 – 222.

He, J., Shen, L., Wan, M., Taranova, O., Wu, H., Zhang, Y. 2013. Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes. Nat. Cell Biol. 15, 373 – 384.

Hnisz, D., Abraham, B.J., Lee, T.I., Lau, A., Saint-Andrй, V., Sigova, A.A., et al., 2013. Super-enhancers in the control of cell identity and disease. Cell 155, 934 – 947.

Hu, D., Garruss, A.S., Gao, X., Morgan, M.A., Cook, M., Smith, E.R., Shilatifard, A. 2013, The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells. Nat. Struct. Mol. Biol. 20, 1093 – 1097.

Kieffer-Kwon, K.-R., Tang, Z., Mathe, E., Qian, J., Sung, M.-H., Li, G., et al., 2013. Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell 155, 1507 – 1520.

Koche, R.P., Smith, Z.D., Adli, M., Gu, H., Ku, M., Gnirke, A., et al., 2011. Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell 8, 96 – 105.

Mansour, A.A., Gafni, O., Weinberger, L., Zviran, A., Ayyash, M., Rais, Y., et al., 2013. The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming. Nature 488, 409 – 413.

Marks, H., Kalkan, T., Menafra, R., Denissov, S., Jones, K., Hofemeister, H., et al., 2012. The transcriptional and epigenomic foundations of ground state pluripotency. Cell 149, 590 – 604.

Mikkelsen, T.S., Ku, M., Jaffe, D.B., Issac, B., Lieberman, E., Giannoukos, G., et al., 2007. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553 – 560.

Min, I.M., Waterfall, J.J., Core, L.J., Munroe, R.J., Schimenti, J., Lis, J.T. 2011. Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. Genes Dev. 25, 742 – 754.

Morey, L., Pascual, G., Cozzuto, L., Roma, G., Wutz, A., Benitah, S.A., Di Croce, L. 2012. Nonoverlapping functions of the Polycomb group Cbx family of proteins in embryonic stem cells. Cell Stem Cell 10, 47 – 62.

Nishiyama, A., Xin, L., Sharov, A.A., Thomas, M., Mowrer, G., Meyers, E., et al., 2009. Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors. Cell Stem Cell 5, 420 – 433.

Niwa, H., Toyooka, Y., Shimosato, D., Strumpf, D., Takahashi, K., Yagi, R., Rossant, J. 2005. Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation. Cell 123, 917 – 929.

Nora, E.P., Lajoie, B.R., Schulz, E.G., Giorgetti, L., Okamoto, I., Servant, N., et al., 2012. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485, 381 – 385.

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. Mol. Cell Biol. 27, 3769 – 3779.

Rodriguez-Paredes, M., Esteller, M. 2011. Cancer epigenetics reaches mainstream oncology. Nat. Med. 17, 330 – 339.

Ron-Bigger, S., Bar-Nur, O., Isaac, S., Bocker, M., Lyko, F., Eden, A. 2010. Aberrant epigenetic silencing of tumor suppressor genes is reversed by direct reprogramming. Stem Cells 28, 1349 – 1354.

Shen, X., Liu, Y., Hsu, Y.J., Fujiwara, Y., Kim, J., Mao, X., et al., 2008. EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Mol. Cell 32, 491 – 502.

Shin, H., Liu, T., Manrai, A.K., Liu, X.S. 2009. CEAS: cis-regulatory element annotation system. Bioinformatics 25, 2605 – 2606.

Singhal, N., Graumann, J., Wu, G., Arauzo-Bravo, M.J., Han, D.W., Greber, B., et al., 2010. Chromatin-remodeling components of the BAF complex facilitate reprogramming. Cell 141, 943 – 955.

Soufi, A., Donahue, G., Zaret, K.S. 2012. Facilitators and impediments of the pluripotency reprogramming factors’ initial engagement with the genome. Cell 151, 994 – 1004.

Spruijt, C.G., Gnerlich, F., Smits, A.H., Pfaffeneder, T., Jansen, P.W., Bauer, C., et al., 2013. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 152, 1146 – 1159.

Sridharan, R., Tchieu, J., Mason, M.J., Yachechko, R., Kuoy, E., Horvath, S., et al., 2009. Role of the murine reprogramming factors in the induction of pluripotency. Cell 136, 364 – 377.

Sridharan, R., Gonzales-Cope, M., Chronis, C., Bonora, G., Mckee, R., Huang, C., et al., 2013. Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1gamma in reprogramming to pluripotency. Nat. Cell Biol. 15, 872 – 882.

Stock, J.K., Giadrossi, S., Casanova, M., Brookes, E., Vidal, M., Koseki, H., et al., 2007. Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nat. Cell Biol. 9, 1428 – 1435.

Tahiliani, M., Koh, K.P., Shen, Y., Pastor, W.A., Bandukwala, H., Brudno, Y., et al., 2009. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930 – 935.

Takahashi, K., Yamanaka, S. 2006. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663 – 676.

Tee, W.-W., Shen, S.S., Oksuz, O., Narendra, V., Reinberg, D. 2014. Erk1/2 activity promotes chromatin features and RNAPII phosphorylation at developmental promoters in mouse ESCs. Cell 156, 678 – 690.

Terme, J.M., Sese, B., Millan-Arino, L., Mayor, R., 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. J. Biol. Chem. 286, 35 347 – 35 357.

Trowbridge, J.J., Sinha, A.U., Zhu, N., Li, M., Armstrong, S.A., Orkin, S.H. 2012. Haploinsufficiency of Dnmt1 impairs leukemia stem cell function through derepression of bivalent chromatin domains. Genes Dev. 26, 344 – 349.

Vastenhouw, N.L., Zhang, Y., Woods, I.G., Imam, F., Regev, A., Liu, X.S., et al., 2010. Chromatin signature of embryonic pluripotency is established during genome activation. Nature 464, 922 – 926.

Voigt, P., Leroy, G., Drury, W.J., Zee, B.M., Son, J., Beck, D.B., et al., 2012. Asymmetrically modified nucleosomes. Cell 151, 181 – 193.

Wen, B., Wu, H., Shinkai, Y., Irizarry, R.A., Feinberg, A.P. 2009. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat. Genet. 41, 246 – 250.

Whyte, W.A., Orlando, D.A., Hnisz, D., Abraham, B.J., Lin, C.Y., Kagey, M.H., et al., 2013. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307 – 319.

Widschwendter, M., Fiegl, H., Egle, D., Mueller-Holzner, E., Spizzo, G., Marth, C., et al., 2007. Epigenetic stem cell signature in cancer. Nat. Genet. 39, 157 – 158.

Wilmut, I., Schnieke, A.E., Mcwhir, J., Kind, A.J., Campbell, K.H. 1997. Viable offspring derived from fetal and adult mammalian cells. Nature 385, 810 – 813.

Wu, H., D’Alessio, A.C., Ito, S., Xia, K., Wang, Z., Cui, K., et al., 2011. Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 473, 389 – 393.

Wu, X., Johansen, J.V., Helin, K. 2013. Fbxl10/Kdm2b recruits polycomb repressive complex 1 to CpG islands and regulates H2A ubiquitylation. Mol. Cell 49, 1134 – 1146.

Xie, R., Everett, L.J., Lim, H.W., Patel, N.A., Schug, J., Kroon, E., et al., 2013a. Dynamic chromatin remodeling mediated by polycomb proteins orchestrates pancreatic differentiation of human embryonic stem cells. Cell Stem Cell 12, 224 – 237.

Xie, W., Schultz, M.D., Lister, R., Hou, Z., Rajagopal, N., Ray, P., et al., 2013b. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134 – 1148.

Yildirim, O., Li, R., Hung, J.H., Chen, P.B., Dong, X., Ee, L.S., et al., 2011. Mbd3/ NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell 147, 1498 – 1510.

Zaret, K.S., Carroll, J.S. 2011. Pioneer transcription factors: establishing competence for gene expression. Genes Dev. 25, 2227 – 2241.

Zhu, J., Adli, M., Zou, J.Y., Verstappen, G., Coyne, M., Zhang, X., et al., 2013. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152, 642 – 654.

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