SWI/SNF Chromatin Remodeling Complex: A New Cofactor in Reprogramming

Stem Cell Reviews and Reports

Volumn 8, Issue 1, 2012, Pages 128-136

  He, Ling ^a   Liu, Huan ^a   Tang, Liling ^a  

^a CHONGQING UNIVERSITY   (China)

Author keywords

Embryonic stem cells; Induced pluripotent stem cells; Pluripotent factors; Reprogramming; SWI SNF

Indexed keywords

MICRORNA; MULTIPROTEIN COMPLEX; NONHISTONE PROTEIN; TRANSCRIPTION FACTOR;

ANIMAL; CELL DIFFERENTIATION; CHROMATIN ASSEMBLY AND DISASSEMBLY; HUMAN; METABOLISM; PHYSIOLOGY; REVIEW; RNA INTERFERENCE; STEM CELL;

ANIMALS; CELL DIFFERENTIATION; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOMAL PROTEINS, NON-HISTONE; HUMANS; MICRORNAS; MULTIPROTEIN COMPLEXES; RNA INTERFERENCE; STEM CELLS; TRANSCRIPTION FACTORS;

IPS;

EID: 84857653600     PISSN: 15508943     EISSN: 15586804     Source Type: Journal    
DOI: 10.1007/s12015-011-9285-z     Document Type: Review

References (72)

1. Kim, J. H., Auerbach, J. M., Rodríguez-Gómez, J. A., et al. (2002). Dopamine neurons derived from embryonic stem cells function in an animal model of Parkinson's disease. Nature, 418, 50-56.
2. Liu, S., Qu, Y., Stewart, T. J., et al. (2000). Embryonic stem cells differentiate into oligodendrocytes and myelinate in culture and after spinal cord transplantation. Proceedings of the National Academy of Sciences of the United States of America, 97, 6126-6131.
3. Zhang, F., & Pasumarthi, K. B. (2008). Embryonic stem cell transplantation promise and progress in the treatment of heart cisease. BioDrugs, 22, 361-374.
4. Lumelsky, N., Blondel, O., Laeng, P., Velasco, I., Ravin, R., & McKay, R. (2001). Differentiation of embryonic stem cells to insulin-secreting structures similar to pancreatic islets. Science, 292, 1389-1394.
5. Thomson, J., Itskovitz-Eldor, J., Shapiro, S., et al. (1998). Embryonic stem cell lines derived from human blastocysts. Science, 282, 1145-1147.
6. 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.
7. Cowan, C. A., Atienza, J., Melton, D. A., & Eggan, K. (2005). Nuclear reprogramming of somatic cells after fusion with human embryonic stem cells. Science, 309, 1369-1373.
8. Tada, M., Takahama, Y., Abe, K., Nakatsuji, N., & Tada, T. (2001). Nuclear reprogramming of somatic cells by in vitro hybridization with ES cells. Current Biology, 11, 1553-1558.
9. Maherali, N., Sridharan, R., Xie, W., et al. (2007). Directly reprogrammed fibroblasts show global epigenetic remodelling and widespread tissue contribution. Cell Stem Cell, 1, 55-70.
10. Okita, K., Ichisaka, T., & Yamanaka, S. (2007). Generation of germline competent induced pluripotent stem cells. Nature, 448, 313-317.
11. Wernig, M., Meissner, A., Foreman, R., et al. (2007). In vitro reprogramming of fibroblasts into a pluripotent ES cell-like state. Nature, 448, 318-324.
12. Takahashi, K., Tanabe, K., & Ohnuki, M. (2007). Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell, 131, 861-872.
13. Takahashi, K., & Yamanaka, S. (2006). Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell, 126, 663-676.
14. Singhal, N., Graumann, J., Wu, G., et al. (2010). Chromatin-remodeling components of the BAF complex facilitate reprogramming. Cell, 141, 943-955.
15. Yu, J., Vodyanik, M., Smuga-Otto, K., et al. (2007). Induced pluripotent stem cell lines derived from human somatic cells. Science, 318, 1917-1920.
16. Markoulaki, S., Hanna, J., Beard, C., et al. (2009). Transgenic mice with defined combinations of drug-inducible reprogramming factors. Nature Biotechnology, 27, 169-171.
17. Heng, J., Feng, B., Han, J., et al. (2010). The nuclear receptor Nr5a2 can replace Oct4 in the reprogramming of murine somatic cells to pluripotent Cells. Cell Stem Cell, 6, 167-174.
18. Lyssiotis, C., Foreman, R., Staerk, J., et al. (2009). Reprogramming of murine fibroblasts to induced pluripotent stem cells with chemical complementation of Klf4. Proceedings of the National Academy of Sciences of the United States of America, 106, 8912-8917.
19. Ichida, J., Blanchard, J., Lam, K., et al. (2009). A small-molecule inhibitor of Tgf-b signaling replaces Sox2 in reprogramming by inducing Nanog. Cell Stem Cell, 5, 491-503.
20. Yuan, X., Wan, H., Zhao, X., Zhu, S., Zhou, Q., & Ding, S. (2011). Brief report: Combined chemical treatment enables oct4-induced reprogramming from mouse embryonic fibroblasts. Stem Cells, 29, 549-553.
21. Picanço-Castro, V., Russo-Carbolante, E., Reis, L., et al. (2011). Pluripotent reprogramming of fibroblasts by lentiviralmediated insertion of SOX2, C-MYC, and TCL-1A. Stem Cells and Development, 20, 169-180.
22. Han, J., Yuan, P., Yang, H., et al. (2010). Tbx3 improves the germ-line competency of induced pluripotent stem cells. Nature, 463, 1096-1100.
23. Zhao, Y., Yin, X., Qin, H., et al. (2008). Two supporting factors greatly improve the efficiency of human iPSC generation. Cell Stem Cell, 3, 475-479.
24. Kim, J., Zaehres, H., Wu, G., et al. (2008). Pluripotent stem cells induced from adult neural stem cells by reprogramming with two factors. Nature, 454, 646-650.
25. Kim, J., Sebastiano, V., Wu, G., et al. (2009). Oct4-induced pluripotency in adult neural stem cells. Cell, 136, 411-419.
26. Kim, J., Greber, B., Araúzo-Bravo, M., et al. (2009). Direct reprogramming of human neural stem cells by OCT4. Nature, 461, 649-653.
27. Hanna, J., Markoulaki, S., Schorderet, P., et al. (2008). Direct reprogramming of terminally differentiated mature B lymphocytes to pluripotency. Cell, 133, 250-264.
28. Tomioka, I., Maeda, T., Shimada, H., et al. (2010). Generating induced pluripotent stem cells from common marmoset (Callithrix jacchus) fetal liver cells using defined factors, including Lin28. Genes to Cells, 15, 959-969.
29. Chambers, I., Colby, D., Robertson, M., et al. (2003). Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell, 113, 643-655.
30. Lavial, F., Acloque, H., Bertocchini, F., et al. (2007). The Oct4 homologue PouV and Nanog regulate pluripotency in chicken embryonic stem cells. Development, 134, 3549-3563.
31. Mitsui, K., Tokuzawa, Y., Itoh, H., Segawa, K., et al. (2003). The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell, 113, 631-642.
32. Yamaguchi, S., Kimura, H., Tada, M., et al. (2005). Nanog expression in mouse germ cell development. Gene Expression, 5, 639-646.
33. 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.
34. Silva, J., Nichols, J., Theunissen, T., et al. (2009). Nanog is the gateway to the pluripotent ground state. Cell, 138, 722-737.
35. Feng, B., Jiang, J., Kraus, P., et al. (2009). Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb. Nature Cell Biology, 11, 197-203.
36. Imbalzano, A. N., Kwon, H., Green, M. R., & Kingston, R. E. (1994). Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature, 370, 481-485.
37. Kwon, H., Imbalzano, A. N., Khavari, P. A., Kingston, R. E., & Green, M. R. (1994). Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex. Nature, 370, 477-481.
38. Wang, W., Xue, Y., Zhou, S., Kuo, A., Cairns, B. R., & Crabtree, G. R. (1996). Diversity and specialization of mammalian SWI/SNF complexes. Genes & Development, 10, 2117-2130.
39. Wang, G. G., Allis, C. D., & Chi, P. (2007a). Chromatin remodeling and cancer, part II: ATP-dependent chromatin remodeling. Trends in Molecular Medicine, 13, 373-380.
40. Martens, J. A., & Winston, F. (2002). Evidence that Swi/Snf directly represses transcription in S. cerevisiae. Genes & Development, 16, 2231-2236.
41. Batsché, E., Yaniv, M., & Muchardt, C. (2006). The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nature Structural and Molecular Biology, 13, 22-29.
42. Becker, P. B., & Horz, W. (2002). ATP-dependent nucleosome modeling. Annual Review of Biochemistry, 71, 247-273.
43. Wang, G. G., Allis, C. D., & Chi, P. (2007b). Chromatin remodeling and cancer, part I: covalent histone modifications. Trends in Molecular Medicine, 13, 363-372.
44. Gangaraju, V. K., & Bartholomew, B. (2007). Mechanisms of ATP dependent chromatin remodeling. Mutation Research, 618, 3-17.
45. Smith, C. L., Horowitz-Scherer, R., Flanagan, J. F., Woodcock, C. L., & Peterson, C. L. (2003). Structural analysis of the yeast SWI/SNF chromatin remodeling complex. Nature Structural Biology, 10, 141-145.
46. Monahan, B. J., Villén, J., Marguerat, S., Bähler, J., Gygi, S. P., & Winston, F. (2008). Yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast. Nature Structural Biology, 15, 873-880.
47. Du, J., Nasir, I., Benton, B. K., Kladde, M. P., & Laurent, B. C. (1998). Sth1p, a Saccharomyces cerevisiae Snf2p/Swi2p homolog, is an essential ATPase in RSC and differs from Snf/Swi in its interactions with histones and chromatin-associated proteins. Genetics, 150, 987-1005.
48. Mohrmann, L., & Verrijzer, C. P. (2005). Composition and functional specificity of SWI2/SNF2 class chromatin remodeling complexes. Biochimica et Biophysica Acta, 1681, 59-73.
49. Kadam, S., McAlpine, G. S., Phelan, M. L., Kingston, R. E., Jones, K. A., & Emerson, B. M. (2000). Functional selectivity of recombinant mammalian SWI/SNF subunits. Genes & Development, 14, 2441-2451.
50. Yan, Z., Cui, K., Murray, D. M., et al. (2005). PBAF chromatin-remodeling complex requires a novel specificity subunit, BAF200, to regulate expression of selective interferon-responsive genes. Genes & Development, 19, 1662-1667.
51. Wang, W. (2003). The SWI/SNF family of ATP-dependent chromatin remodeler: similar mechanisms for diverse functions. Current Topics Microbiology and Immunology, 274, 143-169.
52. Roberts, C. W., & Orkin, S. H. (2004). The SWI/SNF complex-chromatin and cancer. Nature Reviews Cancer, 4, 133-142.
53. Tang, L. L., Nogales, E., & Ciferri, C. (2010). Structure and function of SWI/SNF chromatin remodeling complexes and mechanistic implications for transcription. Progress in Biophysics and Molecular Biology, 102, 122-128.
54. Mak, A. B., Ni, Z., Hewel, J. A., et al. (2010). A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency. Molecular & Cellular Proteomics, 9, 811-823.
55. Ho, L., Jothi, R., Ronan, J. L., Cui, K., Zhao, K., & Crabtree, G. R. (2009). 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.
56. Bultman, S. J., Gebuhr, T. C., Pan, H., & Svoboda, P. (2006). Maternal BRG1 regulates zygotic genome activation in the mouse. Genes & Development, 20, 1744-1754.
57. Kidder, B. L., Palmer, S., & Knott, J. G. (2009). SWI/SNF-Brg1 regulates self-renewal and occupiescore pluripotency-related genes in embryonic stem cells. Stem Cells, 27, 317-328.
58. Yan, Z., Wang, Z., Sharova, L., et al. (2008). BAF250B-associated SWI/SNF chromatin-remodeling complex is required to maintain undifferentiated mouse embryonic stem cells. Stem Cells, 26, 1155-1165.
59. de la Serna, I. L., Ohkawa, Y., Higashi, C., et al. (2006). The microphthalmia-associated transcription factor requires SWI/SNF enzymes to activate melanocyte-specific genes. Journal of Biological Chemistry, 281, 20233-20241.
60. Young, D. W., Pratap, J., Javed, A., et al. (2005). SWI/SNF chromatin remodeling complex is obligatory for BMP2-induced, Runx2-dependent skeletal gene expression that controls osteoblast differentiation. Journal of Cellular Biochemistry, 94, 720-730.
61. Cheng, S. W., Davies, K. P., Yung, E., Beltran, R. J., Yu, J., & Kalpana, G. V. (1999). Beltran c-MYC interacts with INI1/hSNF5 and requires the SWI/SNF complex for transactivation function. Nature Genetics, 22, 102-105.
62. Singh, A. M., & Dalton, S. (2009). The cell cycle and Myc intersect with mechanisms that regulate pluripotency and reprogramming. Cell Stem Cell, 5, 141-149.
63. Inoue, H., Giannakopoulos, S., Parkhurst, C. N., et al. (2011). Target genes of the largest human SWI/SNF complex subunit control cell growth. Biochemical Journal, 434, 83-92.
64. Saladi, S. V., & de la Serna, I. L. (2010). ATP dependent chromatin remodeling enzymes in embryonic stem cells. Stem Cell Reviews, 6, 62-73.
65. Reisman, D., Glaros, S., & Thompson, E. A. (2009). The SWI/SNF complex and cancer. Oncogene, 28, 1653-1668.
66. Bultman, S., Gebuhr, T., Yee, D., et al. (2000). A Brg1 null mutation in the mouse reveals functional differences among mammalian SWI/SNF complexes. Molecular Cell, 6, 1287-1295.
67. Sridharan, R., Tchieu, J., Mason, M. J., et al. (2009). Role of the murine reprogramming factors in the induction of pluripotency. Cell, 136, 364-377.
68. Sims, H. I., Baughman, C. B., & Schnitzler, G. R. (2008). Human SWI/SNF directs sequence-specific chromatin changes on promoter polynucleosomes. Nucleic Acids Research, 36, 6118-6131.
69. Sims, H. I., Lane, J. M., Ulyanova, N. P., & Schnitzler, G. R. (2007). Human SWI/SNF drives sequence-directed repositioning of nucleosomes on c-Myc promoter DNA minicircles. Biochemistry, 46, 11377-11388.
70. Xu, N., Papagiannakopoulos, T., Pan, G., Thomson, J. A., & Kosik, K. S. (2009). MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells. Cell, 137, 647-658.
71. Lin, S. L., Chang, D. C., Lin, C. H., Ying, S. Y., Leu, D., & Wu, D. T. (2011). Regulation of somatic cell reprogramming through inducible mir-302 expression. Nucleic Acids Research, 39, 1054-1065.
72. Yoo, A. S., Staahl, B. T., Chen, L., & Crabtree, G. R. (2009). MicroRNA-mediated switching of chromatin-remodelling complexes in neural development. Nature, 460, 642-646.