The see-saw of differentiation: Tipping the chromatin balance

Molecular Interventions

Volumn 8, Issue 1, 2008, Pages 15-18

  Muegge, Kathrin ^a   Xi, Sichuan ^a   Geiman, Theresa ^a  

^a SAIC FREDERICK INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DOPAMINE; HISTONE H2A; HISTONE H2B; HISTONE H3; HISTONE H4; MYC PROTEIN; RNA;

ACETYLATION; CANCER GENE THERAPY; CARCINOGENICITY; CELL DIFFERENTIATION; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN STRUCTURE; DEGENERATIVE DISEASE; DIABETES MELLITUS; DISEASE TRANSMISSION; DNA METHYLATION; DNA PACKAGING; EPIGENETICS; EXPERIMENTAL MOUSE; GENE REPLACEMENT THERAPY; GERM LINE GENE THERAPY; HEART INFARCTION; HEART MUSCLE CELL; HUMAN; HUMAN CELL CULTURE; HUMAN GENOME; MAMMAL; MOLECULAR INTERACTION; MOLECULAR MECHANICS; MOLECULAR THERAPY; NERVE CELL; NONHUMAN; NUCLEOSOME; PHENOTYPIC VARIATION; PLURIPOTENT STEM CELL; PROTEIN METHYLATION; PROTEIN PHOSPHORYLATION; REVIEW; RNA TRANSCRIPTION; SICKLE CELL ANEMIA; SKIN FIBROBLAST; SPINAL CORD INJURY; TERATOMA; TRANSCRIPTION REGULATION;

ANIMALS; CELL DEDIFFERENTIATION; CELL DIFFERENTIATION; CHROMATIN; DNA METHYLATION; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION; GENETIC MARKERS; HISTONES; HUMANS; METHYLATION; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 40849085190     PISSN: 15340384     EISSN: 15432548     Source Type: Journal    
DOI: 10.1124/mi.8.1.4     Document Type: Review

References (33)

1. Bernstein, B.E., Mikkelsen, T.S., Xie et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315-326 (2006). Bernstein and Lander were the first to show the simultaneous presence of the H3K27me silencing mark and H3K4me activation mark at highly conserved sequences in ES cells.
2. Mikkelsen, T.S., Ku, M., Jaffe, D.B. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560 (2007). This study shows the presence of a bivalent histone modification mark present at developmental genes poised for transcription. The mark resolves largely in either H3K4me or H3K27me upon differentiation of ES cells.
3. Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6-21 (2002).
4. Kouzarides, T. Chromatin modifications and their function. Cell 128, 693-705 (2007).
5. Berger, S.L. The complex language of chromatin regulation during transcription. Nature 447, 407-412 (2007).
6. Encode Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816 (2007). The ENCODE (Encyclopedia of DNA Elements) project aims to characterize functional elements in the human genome. Integrating data of many public data bases the consortium addresses also questions with respect e.g. to transcripts, transcription factor binding, histone modifications or higher order chromatin structure.
7. Ringrose, L. and Paro, R. Polycomb/Trithorax response elements and epigenetic memory of cell identity. Development 134, 223-232 (2007).
8. Santos-Rosa, H., Schneider, R., Bernstein, B.E., Karabetsou, N., Morillon, A., Weise, C., Schreiber, S.L., Mellor, J., and Kouzarides, T. Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin. Mol. Cell. 12, 1325-1332 (2003).
9. Wysocka, J., Swigut, T., Xiao, H. et al. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature 442, 31-32 (2006).
10. Francis, N.J., Kingston, R.E., and Woodcock, C.L. Chromatin compaction by a polycomb group protein complex. Science 306, 1574-1577 (2004).
11. Widschwendter, M., Fiegl, H., Egle, D. et al. Epigenetic stem cell signature in cancer. Nat. Genet. 39, 157-158 (2007).
12. Schlesinger, Y., Straussman, R., Keshet, I. et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat. Genet. 39, 232-236 (2007).
13. Vire, E., Brenner, C., Deplus, R. et al. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439, 871-874 (2006).
14. Xi, S., Zhu, H., Xu, H., Schmidtmann, A., Geiman, T.M., and Muegge. K. Lsh controls Hox gene silencing during development. Proc. Natl. Acad. Sci. U.S.A. 104, 14366-14371 (2007).
15. Agger, K., Cloos, P.A., Christensen, J. et al. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 449, 731-734 (2007).
16. Lan, F., Bayliss, P.E., Rinn, J.L. et al. A histone H3 lysine 27 demethylase regulates animal posterior development. Nature 449, 689-694 (2007).
17. Takahashi, K. and Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663-676 (2006). Yamanaka's group were the first to show that the expression of only four transcription factors in murine skin cells can induce the manufacture of pluripotent stem cells.
18. Okita, K., Ichisaka, T., and Yamanaka, S. Generation of germline-competent induced pluripotent stem cells. Nature 448, 313-317 (2007). This study proves that the induced stem cells are truly pluripotent and can be transmitted through the germ line to the next generation.
19. Wernig, M., Meissner, A., Foreman, R., Brambrink, T., Ku, M., Hochedlinger, K., Bernstein, B.E., and Jaenisch, R. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature 448, 318-324 (2007).
20. Takahashi, K., Tanabe, K., Ohnuki, M., Narita, M., Ichisaka, T., Tomoda, K., and Yamanaka, S. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861-872 (2007) This work demonstrates that also human skin cells can be used to induce pluripotent cells.
21. Park, I.H., Zhao, R., West, J.A., Yabuuchi, A., Huo, H., Ince, T.A., Lerou, P.H., Lensch, M.W., and Daley, G.Q. Reprogramming of human somatic cells to pluripotency with defined factors. Nature 451, 141-146 (2008).
22. Yu, J., Vodyanik, M.A., Smuga-Otto, K. et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 318, 1917-1820 (2007).
23. Nakagawa, M., Koyanagi, M., Tanabe, K. et al. Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts. Nat. Biotechnol. 442, 86-90 (2007). Yamanaka's group improves the technique of iPS by omitting the potential tumorigenic c-myc expression vector.
24. Hanna, J., Wernig, M., Markoulaki, S. et al. Treatment of sickle cell anemia mouse model with iPS cells generated from autologous skin. Science 318,1920-1923 (2007). Jaenisch's group is the first to use the iPS for treatment of a murine sickle cell anemia model, proving, in principle, that iPS can be therapeutically useful.
25. Andersson K.E. and Christ G.J. Regenerative pharmacology: The future is now. Mol. Interv. 7, 79-86 (2007).
26. Klimanskaya, I., Rosenthal, N., and Lanza, R. Derive and conquer: Sourcing and differentiating. Nat. Rev. Drug Discov. Dec 14; [Epub ahead of print] (2007).
27. Fairchild, P.J., Robertson, N.J., Minger, S.L., and Waldmann, H. Embryonic stem cells: Protecting pluripotency from alloreactivity. Curr. Opin. Immunol. 19, 596-602 (2007).
28. Filipczyk, A.A., Passier, R., Rochat, A., and Mummery, C.L. Regulation of cardiomyocyte differentiation of embryonic stem cells by extracellular signalling. Cell. Mol. Life Sci. 64, 704-718 (2007).
29. Keirstead, H.S., Nistor, G., Bernal, G., Totoiu, M., Cloutier, F., Sharp, K., and Steward, O. Human embryonic stem cell-derived oligodendrocyte progenitor cell transplants remyelinate and restore locomotion after spinal cord injury. J. Neurosci. 25, 4694-4705 (2005).
30. Lee, H., Shamy, G.A., Elkabetz, Y., Schofield, C.M., Harrsion, N.L., Panagiotakos, G., Socci, N.D., Tabar, V., and Studer, L. Directed differentiation and transplantation of human embryonic stem cell-derived motoneurons. Stem Cells 25, 1931-1939 (2007).
31. Lee, J.P., Jeyakumar, M., Gonzalez, R. et al. Stem cells act through multiple mechanisms to benefit mice with neurodegenerative metabolic disease. Nat. Med. 13, 439-447 (2007).
32. Lees, J.G. and Tuch, B.E. Conversion of embryonic stem cells into pancreatic beta-cell surrogates guided by ontogeny. Regen. Med. 1, 327-336 (2006).
33. Carpenter, M., Rao, M.S., Freed, W., and Zeng, X. Derivation and characterization of neuronal precursors and dopaminergic neurons from human embryonic stem cells in vitro. Methods Mol. Biol. 331,153-167 (2006).