Readings

WEEK # TOPICS READINGS
1

Introduction

See the Lecture Summary

No Readings
2

Introduction to stem cells and induced pluripotency

See the Lecture Summary

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.

3

Epigenetic memory and epigenetic states

See the Lecture Summary

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.

4

DNA methylation

See the Lecture Summary

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.

5

DNA methyl-binding proteins

See the Lecture Summary

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.

6

Histone marks and epigenomic sequencing technologies

See the Lecture Summary

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. http://www.jove.com/video/2053

7

Polycomb group proteins

See the Lecture Summary

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

See the Lecture Summary

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.

9

Super enhancers

See the Lecture Summary

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.

10

Non-coding RNA

See the Lecture Summary

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.

11

Modeling complex biological systems & Student paper discussions

See the Lecture Summary

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.

12

Chromatin nuclear topology

See the Lecture Summary

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.

13

Stem Cell Therapy

See the Lecture Summary

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.

14

Final

See the Lecture Summary

No Readings