Week 1: Introduction
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
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.
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
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.
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"
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.
Translating the Histone Code
Histone Code and Chromatin Cross-Talk
Week 5: Heritable Gene Expression
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.
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
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.
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
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.
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
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.
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
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.
Reviews on the role of RNA in chromatin modifications
RNA meets chromatin
RNAi and heterochromatin
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
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.