| WEEK # | TOPICS | READINGS |
|---|---|---|
| 1 |
Introduction to the course | No Readings |
| 2 |
The discovery of RNA interference |
Paper 1Fire, A., S. Xu, et al. "Potent and Specific Genetic Interference by Double-stranded RNA in Caenorhabditis Elegans." Nature 391, no. 6669 (1998): 806–11. Paper 2Waterhouse, P. M., M. Kertesz, et al. "Virus Resistance and Gene Silencing in Plants can be Induced by Simultaneous Expression of Sense and Antisense RNA." Proceedings of the National Academy of Sciences of the United States of America 95, no. 23 (1998): 13959–64. |
| 3 |
Endogenous miRNA |
Paper 1Lee, R. C., R. L. Feinbaum, et al. "The C. Elegans Heterochronic Gene lin-4 Encodes Small RNAs with Antisense Complementarity to lin-14." Cell 75, no. 5 (1993): 843–54. Paper 2Pasquinelli, A. E., B. J. Reinhart, et al. "Conservation of the Sequence and Temporal Expression of let-7 Heterochronic Regulatory RNA." Nature 408, no. 6808 (2000): 86–9. |
| 4 |
miRNA biogenesis pathway |
Paper 1Grishok, A., A. E. Pasquinelli, et al. "Genes and Mechanisms Related to RNA Interference Regulate Expression of the Small Temporal RNAs that Control C. elegans Developmental Timing." Cell 106, no. 1 (2001): 23–34. Paper 2Hammond, S. M., S. Boettcher, et al. "Argonaute2, A Link between Genetic and Biochemical Analyses of RNAi." Nature 293, no. 5532 (2001): 1146–50. |
| 5 |
Harnessing RNAi as a tool |
Paper 1Elbashir, S. M., J. Harborth, et al. "Duplexes of 21-nucleotide RNAs Mediate RNA Interference in Cultured Mammalian Cells." Nature 411, no. 6836 (2001): 494–8. Paper 2Brummelkamp, T. R., R. Bernards, et al. "A System for Stable Expression of Short Interfering RNAs in Mammalian Cells." Nature 296, no. 5567 (2002): 550–53. |
| 6 |
miRNAs in development |
Paper 1Zhao, Y., J. F. Ransom, et al. "Dysregulation of Cardiogenesis, Cardiac Conduction, and Cell Cycle in Mice Lacking miRNA-1-2." Cell 129, no. 2 (2007): 303–17. Paper 2Xiao, C., D. P. Calado, et al. "MiR-150 Controls B Cell Differentiation by Targeting the Transcription Factor c-Myb." Cell 131, no. 1 (2007): 146–59. |
| 7 |
miRNAs in cancer: tumor suppressors and oncogenes |
Paper 1He, L., J. M. Thomson, et al. "A MicroRNA Polycistron as a Potential Human Oncogene." Nature 435, no. 3552 (2005): 828–33. Paper 2Kumar, M. S., S. J. Erkeland, et al. "Suppression of Non-small Cell Lung Tumor Development by the Let-7 MicroRNA Family." Proceedings of the National Academy of Sciences of the United States of America 105, no. 10 (2008): 3903–8. |
| 8 |
RNAi therapeutics |
Paper 1Soutschek, J., A. Akinc, et al. "Therapeutic Silencing of an Endogenous Gene by Systemic Administration of Modified siRNAs." Nature 432, no. 3121 (2004): 173–8. Paper 2Elmén, J., M. Lindow, et al. "LNA-mediated MicroRNA Silencing in Non-human Primates." Nature 452, no. 6783 (2008): 896–9. |
| 9 |
Visit to Alnylam | No Readings |
| 10 |
Other classes of small noncoding RNAs: piRNAs |
Paper 1Aravin, A. A., R. Sachidanandam, et al. "Developmentally Regulated piRNA Clusters Implicate MILI in Transposon Control." Science 316, no. 5825 (2007): 744–7. Paper 2Khurana, J. S., J. Wang, et al. "Adaptation to P Element Transposon Invasion in Drosophila Melanogaster." Cell 147, no. 7 (2011): 1551–63. |
| 11 |
Long noncoding RNAs: XIST |
Paper 1Brockdorff, N., A. Ashworth, et al. "The Product of the Mouse Xist Gene is a 15 kb Inactive X-Specific Transcript Containing no Conserved ORF and Located in the Nucleus." Cell 71, no. 3 (1992): 515–26. Paper 2Zhao, J., B. K. Sun, et al. "Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome." Science 322, no. 5902 (2008): 750–6. |
| 12 |
Long noncoding RNAs: lincRNAs |
Paper 1Guttman, M., I. Amit, et al. "Chromatin Signature Reveals Over a Thousand Highly Conserved Large Non-coding RNAs in Mammals." Nature 458, no. 7672 (2009): 223–7. Paper 2Rinn, 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. |
| 13 |
Final class—Oral presentations | No Readings |