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'''[[Media:Class intro.ppt|Slides]]''' | '''[[Media:Class intro.ppt|Slides]]''' | ||
'''[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 ]''' | |||
==Week 2: Chromatin Functions to Define Cell State== | ==Week 2: Chromatin Functions to Define Cell State== | ||
==Papers== | ==Papers== | ||
'''[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. | ||
'''[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)]''' | ||
==Week 3: Chromatin Structure and Discovery of Chromatin Modifying Enzymes== | ==Week 3: Chromatin Structure and Discovery of Chromatin Modifying Enzymes== | ||
==Papers== | ==Papers== | ||
'''[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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==Week 4: Methylation and the Emergence of the "Histone Code"== | ==Week 4: Methylation and the Emergence of the "Histone Code"== | ||
==Papers== | ==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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==Week 5: Heritable Gene Expression == | ==Week 5: Heritable Gene Expression == | ||
==Papers== | ==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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==Bonus Materials== | ==Bonus Materials== | ||
'''[http://cancerres.aacrjournals.org/cgi/reprint/65/24/ | '''[http://cancerres.aacrjournals.org/cgi/reprint/65/24/11241 Commentary on the Human Epigenome Project]''' | ||
'''[http://www.genesdev.org/cgi/reprint/18/19/2315 Epigenetics and Cancer Review]''' | '''[http://www.genesdev.org/cgi/reprint/18/19/2315 Epigenetics and Cancer Review]''' | ||
'''[http://www.genesdev.org/cgi/reprint/17/15/1805 Commentary on Rauscher Paper]''' | |||
'''[http://www.nature.com/nature/journal/v412/n6846/pdf/412493a0.pdf Commentary on Kouzarides Paper]''' | |||
==Week 6: Pluripotency Regulators & Stem Cell Differentiation== | ==Week 6: Pluripotency Regulators & Stem Cell Differentiation== | ||
==Papers== | ==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.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]''' | '''[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]''' | ||
==Week 7: Regulation of Early Development by Polycomb Proteins == | |||
==Papers== | |||
'''[http://www.sciencemag.org/cgi/reprint/298/5595/1039.pdf 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. | |||
'''[http://www.genesdev.org/cgi/reprint/20/9/1123 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== | |||
'''[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]''' | |||
'''[http://www.nature.com/nrc/journal/v6/n11/abs/nrc1991.html;jsessionid=A495C7BE623FC8A83A788F5B725B71A7 Review of Polycomb, Stem Cells and Cancer]''' | |||
'''[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]''' | |||
==Week 8: Master Regulators of Differentiation: The story of MyoD== | |||
==Papers== | |||
'''[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]''' | |||
Davis, RL, Weintraub, H, & Lassar, AB (1987). Cell 51:987-1000. | |||
'''[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]''' | |||
Blais, A, Tsikitis, M, Acosta-Alvear, D, Sharan, R, Kluger, Y, & Dynlacht, BD (2005), Genes Dev 19:553-569. | |||
==Bonus Materials== | |||
'''[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]''' | |||
'''[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]''' | |||
'''[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]''' | |||
==Week 9: Transdifferentiation, Dedifferentiation, and the Adoption of Alternate Cell Fates== | |||
==Papers== | |||
'''[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]''' | |||
K Takahashi & S Yamanaka (2006) Cell 126:663-676. | |||
'''[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]''' | |||
Odelberg, SJ, Kollhoff, A, & Keating, MT (2000) Cell 103:1099-1109. | |||
==Bonus Materials== | |||
'''[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]''' | |||
'''[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]''' | |||
'''[http://www.sciencedirect.com/science/MiamiMultiMediaURL/B6WSN-4KM3YVR-1/B6WSN-4KM3YVR-1-H/7051/7d326fc760fcc4cd7ace417485d0035f/mmc1.pdf Supplemental Materials for Takahashi & Yamanaka paper]''' | |||
'''[http://www.nature.com/nature/journal/v441/n7097/pdf/nature04955.pdf Review on nuclear reprogramming and pluripotency]''' | |||
'''[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]''' | |||
==Week 10: The RNAi machinery and chromatin== | |||
==Papers== | |||
'''[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]''' | |||
Morris, KV, Chan, SW-L, Jacobsen, SE, & Looney, DJ (2004) Science 305:1289-1292. | |||
'''[http://www.nature.com/nsmb/journal/v13/n9/pdf/nsmb1142.pdf 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 | |||
'''[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]''' | |||
'''[http://www.nature.com/nature/journal/v431/n7006/pdf/nature02875.pdf RNAi and heterochromatin]''' | |||
==Week 11: When regulators go bad: misregulation of chromatin modifiers in cancer== | |||
==Papers== | |||
'''[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. ]''' | |||
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. | |||
'''[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.]''' | |||
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. |
Latest revision as of 16:10, 24 November 2006
Week 1: Introduction
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
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
Obituary of Alan Wolffe: Champion of Chromatin
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.
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
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
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
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
NIH report on prospects for neural regeneration using stem cells
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
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
Week 9: Transdifferentiation, Dedifferentiation, and the Adoption of Alternate Cell Fates
Papers
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
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
Week 11: When regulators go bad: misregulation of chromatin modifiers in cancer
Papers
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.