7.342:Materials

Week 1: Introduction
[[Media:Syllabus v4.doc|Course Syllabus]]

[[Media:Class intro.ppt|Slides]]

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

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)

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

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

Papers
'''[http://www.nature.com/nature/journal/v412/n6846/pdf/412561a0.pdf 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

'''[http://www.genesdev.org/cgi/reprint/17/15/1855 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

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

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.

'''[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
News article on how polycomb proteins regulate cell fate

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]'''

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

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

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

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.

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.