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Introduction to stem cells and induced pluripotency

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Grabarek, J. B., K. Zyzyńska, et al. “ Differential Plasticity of Epiblast and Primitive Endoderm Precursors within the ICM of the Early Mouse Embryo.” Development 139, no. 1 (2012): 129–39.

Takahashi, K., and S. Yamanaka. “ Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors.” Cell 126, no. 4 (2006): 663–76.


Epigenetic memory and epigenetic states

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Kim, K., A. Doi, et al. “ Epigenetic Memory in Induced Pluripotent Stem Cells.” Nature 467, no. 7313 (2010): 285–90.

Gafni, O., L. Weinberger, et al. “ Derivation of Novel Human Ground State Naive Pluripotent Stem Cells.” Nature 504, no. 7479 (2013): 282–6.


DNA methylation

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Okano, M., D. W. Bell, et al. “DNA Methyltransferases Dnmt3a and Dnmt3b are Essential for De Novo Methylation and Mammalian Development.” Cell 99, no. 3 (1999): 247–57.

Bhutani, N., J. J. Brady, et al. “ Reprogramming Towards Pluripotency Requires AID-dependent DNA Demethylation.” Nature 463, no. 7284 (2010): 1042–7.


DNA methyl-binding proteins

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Jones, P. L., G. J. Veenstra, et al. “ Methylated DNA and MeCP2 Recruit Histone Deacetylase to Repress Transcription.” Nature Genetics 19, no. 2 (1998): 187–91.

Guy, J., J. Gan, et al. “ Reversal of Neurological Defects in a Mouse Model of Rett Syndrome.” Science 315, no. 5815 (2007): 1143–7.


Histone marks and epigenomic sequencing technologies

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Mikkelsen, T. S., M. Ku, et al. “ Genome-wide Maps of Chromatin State in Pluripotent and Lineage-Committed Cells.” Nature 448, no. 7153 (2007): 553–60.

Bernstein, B. E., T. S. Mikkelsen, et al. “ A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells.” Cell 125, no. 2 (2006): 315–26.

Buro, L. J., S. Shah, et al. “ Chromatin Immunoprecipitation (ChIP) to Assay Dynamic Histone Modification in Activated Gene Expression in Human Cells.” Journal of Visualized Experiments, no. 41 (2010): e2053.


Polycomb group proteins

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Boyer, L. A., K. Plath, et al. “ Polycomb Complexes Repress Developmental Regulators in Murine Embryonic Stem Cells.” Nature 441, no. 7091 (2006): 349–53.

Sneeringer, C. J., M. P. Scott, et al. “ Coordinated Activities of Wild-type Plus Mutant EZH2 Drive Tumor-Associated Hypertrimethylation of Lysine 27 on Histone H3 (H3K27) in Human B-cell Lymphomas.” Proceedings of the National Academy of Sciences of the United States of America 107, no. 49 (2010): 20980–5.

8 Enhancers

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Visel, A., M. J. Blow, et al. “ ChIP-seq Accurately Predicts Tissue-Specific Activity of Enhancers.” Nature 457, no. 7231 (2009): 854–8.

Rada-Iglesias, A., R. Bajpai, et al. “ A Unique Chromatin Signature Uncovers Early Developmental Enhancers in Humans.” Nature 470, no. 7333 (2010): 279–83.


Super enhancers

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Whyte, W. A., D. A. Orlando, et al. “ Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes.” Cell 153, no. 2 (2013): 307–19.

Lovén, J., H. A. Hoke, et al. “ Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers.” Cell 153, no. 2 (2013): 320–34.


Non-coding RNA

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Guttman, M., I. Amit, et al. “ Chromatin Signature Reveals Over a Thousand Highly Conserved Large Non-Coding RNAs in Mammals.” Nature 458, no. 7235 (2009): 223–7.

Rinn, J. L., M. Kertesz, et al. “ Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs.” Cell 129, no. 7 (2007): 1311–23.


Modeling complex biological systems & Student paper discussions

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Umbach, J. A., K. L. Adams, et al. “ Functional Neuromuscular Junctions Formed by Embryonic Stem Cell-Derived Motor Neurons.” PLoS One 7, no. 5 (2012): e36049.


Chromatin nuclear topology

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Meister, P., B. D. Towbin, et al. “ The Spatial Dynamics of Tissue-Specific Promoters During C. Elegans Development.” Genes & Development 24, no. 8 (2010): 766–82.

Hou, C., L. Li, et al. “ Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains.” Molecular Cell 48, no. 3 (2012): 471–84.


Stem Cell Therapy

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Hanna, J., M. Wernig, et al. “ Treatment of Sickle Cell Anemia Mouse Model with IPS Cells Generated from Autologous Skin.” Science 318, no. 5858 (2007): 1920–3.

Tsuji, O., K. Miura, et al. “ Therapeutic Potential of Appropriately Evaluated Safe-Induced Pluripotent Stem Cells for Spinal Cord Injury.” Proceedings of the National Academy of Sciences of the United States of America 107, no. 28 (2010): 12704–9.



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