7.342:Materials

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'''[[Media:Class intro.ppt|Slides]]'''
'''[[Media:Class intro.ppt|Slides]]'''
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'''[http://www.nature.com/milestones/geneexpression/index.html An Extensive Review of the History of Gene transcription Research and Timeline of Milestones in This Field ]'''
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==Week 2: Chromatin Functions to Define Cell State==
==Week 2: Chromatin Functions to Define Cell State==
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==Papers==
==Papers==
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'''[http://links.jstor.org/sici?sici=0036-8075%2819760903%293%3A193%3A4256%3C848%3ACSIAGH%3E2.0.CO%3B2-8 Chromosomal Subunits in Active Genes Have an Altered Conformation]'''  
'''[http://links.jstor.org/sici?sici=0036-8075%2819760903%293%3A193%3A4256%3C848%3ACSIAGH%3E2.0.CO%3B2-8 Chromosomal Subunits in Active Genes Have an Altered Conformation]'''  
Weintraub, H & Groudine, M. (1976) Science 193, 848-856.
Weintraub, H & Groudine, M. (1976) Science 193, 848-856.
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'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WW3-4J0PF31-G-H&_cdi=7119&_user=501045&_coverDate=01%2F31%2F2006&_sk=%23TOC%237119%232006%23999899998%23614710%23FLA%23display%23Volume_10,_Issue_1,_Pages_1-150_(January_2006)%23tagged%23Volume%23first%3D10%23Issue%23first%3D1%23date%23(January_2006)%23&view=c&_gw=y&wchp=dGLbVlz-zSkWA&md5=e80e81f7283aaaf91e546b750dc88e30&ie=/sdarticle.pdf Hyperdynamic Plasticity of Chromatin Proteins in Pluripotent Embryonic Stem Cells]'''
'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WW3-4J0PF31-G-H&_cdi=7119&_user=501045&_coverDate=01%2F31%2F2006&_sk=%23TOC%237119%232006%23999899998%23614710%23FLA%23display%23Volume_10,_Issue_1,_Pages_1-150_(January_2006)%23tagged%23Volume%23first%3D10%23Issue%23first%3D1%23date%23(January_2006)%23&view=c&_gw=y&wchp=dGLbVlz-zSkWA&md5=e80e81f7283aaaf91e546b750dc88e30&ie=/sdarticle.pdf Hyperdynamic Plasticity of Chromatin Proteins in Pluripotent Embryonic Stem Cells]'''
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'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WSN-4CWYSV0-3F-1&_cdi=7051&_user=501045&_orig=browse&_coverDate=05%2F05%2F1995&_sk=999189996&view=c&wchp=dGLbVtz-zSkWW&md5=8725ca6b88d786976e02f1cc83f3c2ca&ie=/sdarticle.pdf Obituary for Harold Weintraub from Cell, 1995 (by Richard Axel & Tom Maniatis)]'''
'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WSN-4CWYSV0-3F-1&_cdi=7051&_user=501045&_orig=browse&_coverDate=05%2F05%2F1995&_sk=999189996&view=c&wchp=dGLbVtz-zSkWW&md5=8725ca6b88d786976e02f1cc83f3c2ca&ie=/sdarticle.pdf Obituary for Harold Weintraub from Cell, 1995 (by Richard Axel & Tom Maniatis)]'''
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==Week 3: Chromatin Structure and Discovery of Chromatin Modifying Enzymes==
==Week 3: Chromatin Structure and Discovery of Chromatin Modifying Enzymes==
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==Papers==
==Papers==
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'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WSN-41BD76P-6-F&_cdi=7051&_user=501045&_coverDate=03%2F22%2F1996&_sk=%23TOC%237051%231996%23999159993%23212301%23FLA%23display%23Volume_84,_Issue_6,_Pages_813-951_(22_March_1996)%23tagged%23Volume%23first%3D84%23Issue%23first%3D6%23Pages%23first%3D813%23last%3D951%23date%23(22_March_1996)%23&view=c&_gw=y&wchp=dGLzVzz-zSkzV&md5=38b674a66018612a4fd60216fe39b167&ie=/sdarticle.pdf Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation.]'''  
'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WSN-41BD76P-6-F&_cdi=7051&_user=501045&_coverDate=03%2F22%2F1996&_sk=%23TOC%237051%231996%23999159993%23212301%23FLA%23display%23Volume_84,_Issue_6,_Pages_813-951_(22_March_1996)%23tagged%23Volume%23first%3D84%23Issue%23first%3D6%23Pages%23first%3D813%23last%3D951%23date%23(22_March_1996)%23&view=c&_gw=y&wchp=dGLzVzz-zSkzV&md5=38b674a66018612a4fd60216fe39b167&ie=/sdarticle.pdf Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation.]'''  
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Taunton, J., Hassig, C. A., and Schreiber, S. L. (1996). Science 272, 408-411.
Taunton, J., Hassig, C. A., and Schreiber, S. L. (1996). Science 272, 408-411.
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==Week 4: Methylation and the Emergence of the "Histone Code"==
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==Bonus Materials==
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'''[http://www.sciencemag.org/cgi/content/full/275/5297/155 Commentary on HAT Discovery]'''
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==Papers==
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'''[http://www.nature.com/nrc/journal/v1/n3/pdf/nrc1201-194a.pdf Review on HDACs and Cancer]'''
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'''[http://www.sciencemag.org/cgi/reprint/293/5532/1065.pdf Obituary of Alan Wolffe: Champion of Chromatin]'''
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'''[http://www.pnas.org/cgi/reprint/103/17/6425 Profile of C. David Allis]'''
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==Week 4: Methylation and the Emergence of the "Histone Code"==
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==Papers==
'''[http://www.nature.com/nature/journal/v410/n6824/pdf/410116a0.pdf Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins.]'''  
'''[http://www.nature.com/nature/journal/v410/n6824/pdf/410116a0.pdf Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins.]'''  
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Wysocka, J., Swigut, T., Milne, T. A., Dou, Y., Zhang, X., Burlingame, A. L., Roeder, R. G., Brivanlou, A. H., and Allis, C. D. (2005). Cell 121, 859-872.
Wysocka, J., Swigut, T., Milne, T. A., Dou, Y., Zhang, X., Burlingame, A. L., Roeder, R. G., Brivanlou, A. H., and Allis, C. D. (2005). Cell 121, 859-872.
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==Bonus Materials==
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==Week 5: Heritable Gene Expression ==
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'''[http://www.sciencemag.org/cgi/reprint/293/5532/1074.pdf Translating the Histone Code]'''
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'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VRW-47WD9YF-2-9&_cdi=6245&_user=501045&_orig=search&_coverDate=04%2F30%2F2003&_qd=1&_sk=999849997&view=c&_alid=469601740&_rdoc=1&wchp=dGLbVlb-zSkWW&md5=5e5733b16519ef2e3e57b155dc3c05be&ie=/sdarticle.pdf Histone Code and Chromatin Cross-Talk]'''
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==Papers==
 
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==Week 5: Heritable Gene Expression ==
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==Papers==
'''[http://www.nature.com/nature/journal/v412/n6846/pdf/412561a0.pdf Rb targets histone H3 methylation and HP1 to promoters. ]'''  
'''[http://www.nature.com/nature/journal/v412/n6846/pdf/412561a0.pdf Rb targets histone H3 methylation and HP1 to promoters. ]'''  
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Ayyanathan, K., Lechner, M. S., Bell, P., Maul, G. G., Schultz, D. C., Yamada, Y., Tanaka, K., Torigoe, K., and Rauscher, F. J., 3rd (2003). Genes Dev 17, 1855-1869.
Ayyanathan, K., Lechner, M. S., Bell, P., Maul, G. G., Schultz, D. C., Yamada, Y., Tanaka, K., Torigoe, K., and Rauscher, F. J., 3rd (2003). Genes Dev 17, 1855-1869.
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==Bonus Materials==
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==Week 6: Pluripotency Regulators & Stem Cell Differentiation==
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'''[http://cancerres.aacrjournals.org/cgi/reprint/65/24/11241 Commentary on the Human Epigenome Project]'''
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'''[http://www.genesdev.org/cgi/reprint/18/19/2315 Epigenetics and Cancer Review]'''
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==Papers==
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'''[http://www.genesdev.org/cgi/reprint/17/15/1805 Commentary on Rauscher Paper]'''
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'''[http://www.nature.com/nature/journal/v412/n6846/pdf/412493a0.pdf Commentary on Kouzarides Paper]'''
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==Week 6: Pluripotency Regulators & Stem Cell Differentiation==
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==Papers==
'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WSN-48RX9V5-G-K&_cdi=7051&_user=501045&_orig=browse&_coverDate=05%2F30%2F2003&_sk=998869994&view=c&wchp=dGLbVzz-zSkWb&md5=c2e6afc325591c27d086226fb2ccb17a&ie=/sdarticle.pdf Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells.]'''
'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WSN-48RX9V5-G-K&_cdi=7051&_user=501045&_orig=browse&_coverDate=05%2F30%2F2003&_sk=998869994&view=c&wchp=dGLbVzz-zSkWb&md5=c2e6afc325591c27d086226fb2ccb17a&ie=/sdarticle.pdf Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells.]'''
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'''[http://www.sciencemag.org/cgi/content/full/283/5407/1468?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1&FIRSTINDEX=0&volume=283&firstpage=1468&resourcetype=HWCIT Perspective on potential uses for ES cells and issues they raise]'''
'''[http://www.sciencemag.org/cgi/content/full/283/5407/1468?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1&FIRSTINDEX=0&volume=283&firstpage=1468&resourcetype=HWCIT Perspective on potential uses for ES cells and issues they raise]'''
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'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VS0-4KPN9SM-1-5&_cdi=6248&_user=501045&_orig=browse&_coverDate=10%2F31%2F2006&_sk=999839994&view=c&wchp=dGLbVlz-zSkWb&md5=6147ac8cb2806bcc2c3690c676718e00&ie=/sdarticle.pdf Recent review on the current state of understanding of the molecular factors which contribute to pluripotency]'''
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'''[http://stemcells.nih.gov/info/scireport/chapter8.asp NIH report on prospects for neural regeneration using stem cells]'''
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'''[http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2005/09/26/MNG95EU12N1.DTL Article from the San Francisco Chronicle about when human trials of stem cell therapies for neurodegenerative disorders might happen]'''
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==Week 7: Regulation of Early Development by Polycomb Proteins ==
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==Papers==
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'''[http://www.sciencemag.org/cgi/reprint/298/5595/1039.pdf Role of histone H3 lysine 27 methylation in Polycomb-group silencing ]'''
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Cao, R., Wang, L., Wang, H., Xia, L., Erdjument-Bromage, H., Tempst, P., Jones, R. S., and Zhang, Y. (2002). Science 298, 1039-1043.
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'''[http://www.genesdev.org/cgi/reprint/20/9/1123 Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. ]'''
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Bracken, A. P., Dietrich, N., Pasini, D., Hansen, K. H., and Helin, K. (2006).  Genes Dev 20, 1123-1136.
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==Bonus Materials==
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'''[http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2006/04/30/MNGPJIFKP51.DTL&feed=rss.news News article on how polycomb proteins regulate cell fate]'''
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'''[http://www.nature.com/nrc/journal/v6/n11/abs/nrc1991.html;jsessionid=A495C7BE623FC8A83A788F5B725B71A7 Review of Polycomb, Stem Cells and Cancer]'''
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'''[http://flybase.bio.indiana.edu/allied-data/lk/interactive-fly/polycomb/polycmb1.htm Link to polycomb information from the interactive fly resource. This is a good interface to research drosophila proteins and genetics]'''
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==Week 8: Master Regulators of Differentiation: The story of MyoD==
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==Papers==
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'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WSN-4C590NY-4G-3&_cdi=7051&_user=501045&_orig=browse&_coverDate=12%2F24%2F1987&_sk=999489993&view=c&wchp=dGLbVzz-zSkWA&md5=6218d593f5ebc82953764da16a118ebc&ie=/sdarticle.pdf Expression of a single transfected cDNA converts fibroblasts to myoblasts]'''
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Davis, RL, Weintraub, H, & Lassar, AB (1987). Cell 51:987-1000.
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'''[http://www.genesdev.org/cgi/reprint/19/5/553?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&author1=Dynlacht%2C+B&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT An initial blueprint for myogenic differentiation]'''
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Blais, A, Tsikitis, M, Acosta-Alvear, D, Sharan, R, Kluger, Y, & Dynlacht, BD (2005), Genes Dev 19:553-569.
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==Bonus Materials==
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'''[http://dev.biologists.org/cgi/reprint/132/12/2685?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=132&firstpage=2685&resourcetype=HWCIT Recent review on MyoD and how it functions as a 'master switch' in development]'''
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'''[http://links.jstor.org/sici?sici=0036-8075%2819910215%293%3A251%3A4995%3C761%3ATMGFNP%3E2.0.CO%3B2-K An early review considering how MyoD functions as a 'nodal point' for information flow during muscle specification]'''
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'''[http://www.pnas.org/cgi/reprint/86/14/5434?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=86&firstpage=5434&resourcetype=HWCIT Original paper showing MyoD is capable of transdifferentiating a variety of different cell types into muscle]'''
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==Week 9: Transdifferentiation, Dedifferentiation, and the Adoption of Alternate Cell Fates==
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==Papers==
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'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WSN-4KM3YVR-1-J&_cdi=7051&_user=501045&_orig=search&_coverDate=08%2F25%2F2006&_sk=998739995&view=c&wchp=dGLbVtb-zSkzk&md5=7e436ed3ce0bdc140a574e376736182e&ie=/sdarticle.pdf Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors]'''
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K Takahashi & S Yamanaka (2006) Cell 126:663-676.
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'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WSN-426YK0V-D-K&_cdi=7051&_user=501045&_orig=search&_coverDate=12%2F22%2F2000&_sk=998969992&view=c&wchp=dGLzVlz-zSkWA&md5=e1be9670cf0621ae3c7b174b6abc8170&ie=/sdarticle.pdf Dedifferentiation of mammalian myotubes induced by msx1]'''
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Odelberg, SJ, Kollhoff, A, & Keating, MT (2000) Cell 103:1099-1109.
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==Bonus Materials==
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'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WSN-4KR3KCP-B-3&_cdi=7051&_user=501045&_orig=browse&_coverDate=08%2F25%2F2006&_sk=998739995&view=c&wchp=dGLbVtz-zSkzk&md5=80b22253332366d5a0521466dec0e03c&ie=/sdarticle.pdf Commentary on Takahashi & Yamanaka paper]'''
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'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VRT-42RMMY4-F-5&_cdi=6243&_user=501045&_orig=search&_coverDate=03%2F20%2F2001&_sk=999889993&view=c&wchp=dGLzVzz-zSkzS&md5=ba32c3f0508b7f4e6821df7d4ba03ae4&ie=/sdarticle.pdf Commentary on Odelberg paper]'''
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'''[http://www.sciencedirect.com/science/MiamiMultiMediaURL/B6WSN-4KM3YVR-1/B6WSN-4KM3YVR-1-H/7051/7d326fc760fcc4cd7ace417485d0035f/mmc1.pdf Supplemental Materials for Takahashi & Yamanaka paper]'''
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'''[http://www.nature.com/nature/journal/v441/n7097/pdf/nature04955.pdf Review on nuclear reprogramming and pluripotency]'''
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'''[http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WX0-46T3XWD-6-5&_cdi=7144&_user=501045&_orig=search&_coverDate=10%2F31%2F2002&_sk=999869994&view=c&wchp=dGLbVtz-zSkWb&md5=e2dd774be58abadded13850314204c62&ie=/sdarticle.pdf Review on muscle regeneration and dedifferentiation]'''
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==Week 10: The RNAi machinery and chromatin==
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==Papers==
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'''[http://www.sciencemag.org/cgi/reprint/305/5688/1289.pdf?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1&FIRSTINDEX=0&volume=305&firstpage=1289&resourcetype=HWCIT Small interfering RNA-induced transcriptional gene silencing in human cells]'''
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Morris, KV, Chan, SW-L, Jacobsen, SE, & Looney, DJ (2004) Science 305:1289-1292.
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'''[http://www.nature.com/nsmb/journal/v13/n9/pdf/nsmb1142.pdf Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells]'''
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Kim, DH, Villeneuve, LM, Morris, KV, & Rossi, JJ (2006) Nat Struct Mol Biol 13:793-797.
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==Bonus materials==
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Reviews on the role of RNA in chromatin modifications
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'''[http://www.genesdev.org/cgi/reprint/19/14/1635?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=1&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=19&firstpage=1635&resourcetype=HWCIT RNA meets chromatin]'''
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'''[http://www.nature.com/nature/journal/v431/n7006/pdf/nature02875.pdf RNAi and heterochromatin]'''
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==Week 11: When regulators go bad: misregulation of chromatin modifiers in cancer==
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==Papers==
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'''[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v391/n6669/full/391815a0_fs.html&content_filetype=pdf Fusion proteins of the retinoic acid receptor-alpha recruit histone deacetylase in promyelocytic leukaemia. ]'''
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Grignani, F., De Matteis, S., Nervi, C., Tomassoni, L., Gelmetti, V., Cioce, M., Fanelli, M., Ruthardt, M., Ferrara, F. F., Zamir, I., et al. (1998). Nature 391, 815-818.
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'''[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4G0KCXX-6&_coverDate=04%2F22%2F2005&_alid=495126267&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=7051&_sort=d&view=c&_acct=C000022659&_version=1&_urlVersion=0&_userid=501045&md5=ad3e9def36d5399f1a452fc8168d3095 hDOT1L links histone methylation to leukemogenesis.]'''
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Okada, Y., Feng, Q., Lin, Y., Jiang, Q., Li, Y., Coffield, V. M., Su, L., Xu, G., and Zhang, Y. (2005). Cell 121, 167-178.

Current revision

7.342: Reading the Blueprint of Life: Transcription, Stem Cells, & Differentiation

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Contents

Week 1: Introduction

Course Syllabus

Slides

An Extensive Review of the History of Gene transcription Research and Timeline of Milestones in This Field


Week 2: Chromatin Functions to Define Cell State

Papers

Chromosomal Subunits in Active Genes Have an Altered Conformation

Weintraub, H & Groudine, M. (1976) Science 193, 848-856.

Hyperdynamic Plasticity of Chromatin Proteins in Pluripotent Embryonic Stem Cells

Meshorer, E, Yellajoshula, D, George, E, Scambler, PJ, Brown, DT, & Misteli, T. (2006) Dev Cell 10, 105-116.

Bonus Materials

Commentary on Meshorer et al paper

Supplemental Data for Meshorer et al paper

Obituary for Harold Weintraub from Molecular Biology of the Cell, 1995 (by Marc Kirschner)

Obituary for Harold Weintraub from Cell, 1995 (by Richard Axel & Tom Maniatis)


Week 3: Chromatin Structure and Discovery of Chromatin Modifying Enzymes

Papers

Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation.

Brownell, J. E., Zhou, J., Ranalli, T., Kobayashi, R., Edmondson, D. G., Roth, S. Y., and Allis, C. D. (1996). Cell 84, 843-851.

A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p.

Taunton, J., Hassig, C. A., and Schreiber, S. L. (1996). Science 272, 408-411.

Bonus Materials

Commentary on HAT Discovery

Review on HDACs and Cancer

Obituary of Alan Wolffe: Champion of Chromatin

Profile of C. David Allis


Week 4: Methylation and the Emergence of the "Histone Code"

Papers

Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins.

Lachner, M., O'Carroll, D., Rea, S., Mechtler, K., and Jenuwein, T. (2001). Nature 410, 116-120.

WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development.

Wysocka, J., Swigut, T., Milne, T. A., Dou, Y., Zhang, X., Burlingame, A. L., Roeder, R. G., Brivanlou, A. H., and Allis, C. D. (2005). Cell 121, 859-872.

Bonus Materials

Translating the Histone Code

Histone Code and Chromatin Cross-Talk


Week 5: Heritable Gene Expression

Papers

Rb targets histone H3 methylation and HP1 to promoters.

Nielsen, S. J., Schneider, R., Bauer, U. M., Bannister, A. J., Morrison, A., O'Carroll, D., Firestein, R., Cleary, M., Jenuwein, T., Herrera, R. E., and Kouzarides, T. (2001). Nature 412, 561-565

Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation.

Ayyanathan, K., Lechner, M. S., Bell, P., Maul, G. G., Schultz, D. C., Yamada, Y., Tanaka, K., Torigoe, K., and Rauscher, F. J., 3rd (2003). Genes Dev 17, 1855-1869.

Bonus Materials

Commentary on the Human Epigenome Project

Epigenetics and Cancer Review

Commentary on Rauscher Paper

Commentary on Kouzarides Paper


Week 6: Pluripotency Regulators & Stem Cell Differentiation

Papers

Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells.

Chambers, I, Colby, D, Robertson, M, Nichols, J, Lee, S, Tweedle, S, & Smith, A. (2003). Cell 113, 643-655.

Directed differentiation of embryonic stem cells into motor neurons.

Wichterle, H, Lieberam, I, Porter, JA, & Jessell, TM. (2002). Cell 110, 385-397.

Bonus Materials

Commentary on Chambers et al paper

Perspective on potential uses for ES cells and issues they raise

Recent review on the current state of understanding of the molecular factors which contribute to pluripotency

NIH report on prospects for neural regeneration using stem cells

Article from the San Francisco Chronicle about when human trials of stem cell therapies for neurodegenerative disorders might happen


Week 7: Regulation of Early Development by Polycomb Proteins

Papers

Role of histone H3 lysine 27 methylation in Polycomb-group silencing

Cao, R., Wang, L., Wang, H., Xia, L., Erdjument-Bromage, H., Tempst, P., Jones, R. S., and Zhang, Y. (2002). Science 298, 1039-1043.

Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions.

Bracken, A. P., Dietrich, N., Pasini, D., Hansen, K. H., and Helin, K. (2006). Genes Dev 20, 1123-1136.

Bonus Materials

News article on how polycomb proteins regulate cell fate

Review of Polycomb, Stem Cells and Cancer

Link to polycomb information from the interactive fly resource. This is a good interface to research drosophila proteins and genetics


Week 8: Master Regulators of Differentiation: The story of MyoD

Papers

Expression of a single transfected cDNA converts fibroblasts to myoblasts

Davis, RL, Weintraub, H, & Lassar, AB (1987). Cell 51:987-1000.

An initial blueprint for myogenic differentiation

Blais, A, Tsikitis, M, Acosta-Alvear, D, Sharan, R, Kluger, Y, & Dynlacht, BD (2005), Genes Dev 19:553-569.

Bonus Materials

Recent review on MyoD and how it functions as a 'master switch' in development

An early review considering how MyoD functions as a 'nodal point' for information flow during muscle specification

Original paper showing MyoD is capable of transdifferentiating a variety of different cell types into muscle


Week 9: Transdifferentiation, Dedifferentiation, and the Adoption of Alternate Cell Fates

Papers

Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors

K Takahashi & S Yamanaka (2006) Cell 126:663-676.

Dedifferentiation of mammalian myotubes induced by msx1

Odelberg, SJ, Kollhoff, A, & Keating, MT (2000) Cell 103:1099-1109.

Bonus Materials

Commentary on Takahashi & Yamanaka paper

Commentary on Odelberg paper

Supplemental Materials for Takahashi & Yamanaka paper

Review on nuclear reprogramming and pluripotency

Review on muscle regeneration and dedifferentiation


Week 10: The RNAi machinery and chromatin

Papers

Small interfering RNA-induced transcriptional gene silencing in human cells

Morris, KV, Chan, SW-L, Jacobsen, SE, & Looney, DJ (2004) Science 305:1289-1292.

Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells

Kim, DH, Villeneuve, LM, Morris, KV, & Rossi, JJ (2006) Nat Struct Mol Biol 13:793-797.

Bonus materials

Reviews on the role of RNA in chromatin modifications

RNA meets chromatin

RNAi and heterochromatin


Week 11: When regulators go bad: misregulation of chromatin modifiers in cancer

Papers

Fusion proteins of the retinoic acid receptor-alpha recruit histone deacetylase in promyelocytic leukaemia.

Grignani, F., De Matteis, S., Nervi, C., Tomassoni, L., Gelmetti, V., Cioce, M., Fanelli, M., Ruthardt, M., Ferrara, F. F., Zamir, I., et al. (1998). Nature 391, 815-818.

hDOT1L links histone methylation to leukemogenesis.

Okada, Y., Feng, Q., Lin, Y., Jiang, Q., Li, Y., Coffield, V. M., Su, L., Xu, G., and Zhang, Y. (2005). Cell 121, 167-178.
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