7.342:Materials

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