The readings listed below are associated with the discussion sessions only, and not the lecture sessions. The session numbers in this table correspond to the discussion sessions listed in the syllabus section.

2 Discussion: Genome and systems biology Nishiyama, A., L. Xin, A. A. Sharov, and M. Thomas, et al. “Uncovering Early Response of Gene Regulatory Networks in ESCs by Systematic Induction of Transcription Factors.Cell Stem Cell 5 (2009): 420-33.
4 Discussion: Cell cycle Li, S., S. Makovets, T. Matsuguchi, J. D. Blethrow, K. M. Shokat, and E. H. Blackburn. “Cdk1-Dependent Phosphorylation of Cdc13 Coordinates Telomere Elongation During Cell-Cycle rogression.Cell 136 (2009): 50-61.
6 Discussion: Transcriptional regulation

Takahashi, K., and S. Yamanaka. “Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors.” Cell 126 (2006): 663–76.

Okita, K., M. Nakagawa, H. Hyenjong , T. Ichisaka, and S. Yamanaka  “Generation of Mouse Induced Pluripotent Stem Cells Without Viral Vectors.” Science 322 (2008): 949-53.

8 Discussion: Transcription and chromatin modification Ezhkova, E., H. A. Pasolli, J. S. Parker, N. Stokes, I. H. Su, G. Hannon, A. Tarakhovsky, and E. Fuchs. “Ezh2 Orchestrates Gene Expression for the Stepwise Differentiation of Tissue-Specific Stem Cells.” Cell 136 (2009): 1122-35.
10 Discussion: Chromosomes/replication

Wang, X., J. W. Tsai, J. H. Imai, W. N. Lian, R. B. Vallee, and S. H. Shi. “Asymmetric Centrosome Inheritance Maintains Neural Progenitors in the Neocortex.” Nature 461 (2009): 947-55.

Falconer, E., E. A. Chavez, A. Henderson, S. S. Poon, S. McKinney, L. Brown, D. G. Huntsman, and P. M. Lansdorp. “Identification of Sister Chromatids by DNA Template Strand Sequences.” Nature 463 (2010): 93-7.

12 Discussion: Epigenetics Iliopoulos, D., H. A. Hirsch, and K. Struhl. “An Epigenetic Switch Involving NF-kappaB, Lin28, Let-7 MicroRNA, and IL6 Links Inflammation to Cell Transformation.” Cell 139 (2009): 693-706.
14 Discussion: Nuclear structure/export Wickramasinghe, V. O., P. I. A. McMurtrie, A. D. Mills, Y. Takei, S. Penrhyn-Lowe, Y. Amagase, S. Main, J. Marr, M. Stewart, and R. A. Laskey. “mRNA Export from Mammalian Cell Nuclei Is Dependent on GANP.” Current Biology 20 (2010): 25-31.
16 Discussion: Chromatin and gene expression I

Hadjur, S., L. M. Williams, N. K. Ryan, B. S. Cobb, T. Sexton, P. Fraser, A. G. Fisher, and M. Merkenschlager. “Cohesins Form Chromosomal Cis-Interactions at the Developmentally Regulated IFNG Locus.” Nature 460 (2009): 410-13.

Lieberman-Aiden, E., N. L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy, A. Telling, I. Amit, B. R. Lajoie, P. J. Sabo, M. O. Dorschner, R. Sandstrom, B. Bernstein, M. A. Bender, M. Groudine, A. Gnirke, J. Stamatoyannopoulos, L. A. Mirny , E. S. Lander, and J. Dekker. “Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome.Science 326 (2009): 289-93.

18 Discussion: Chromatin and gene expression II Hartley, P. D., and H. D. Madhani. “Mechanisms That Specify Promoter Nucleosome Location and Identity.” Cell 137 (2009): 445-58.
20 Discussion: Alternative splicing and polyadenylation

Zhang, C., Z. Zhang, J. Castle, S. Sun, J. Johnson, A. R. Krainer, and M. Q. Zhang. “Defining the Regulatory Network of the Tissue-Specific Splicing Factors Fox-1 and Fox-2.” Genes Dev 22 (2008): 2550-63.

Lee, J. -A., Z. Z. Tang, and D. L. Black. “An Inducible Change in Fox-1/A2BP1 Splicing Modulates the Alternative Splicing of Downstream Neuronal Target Exons.” Genes Dev 23 (2009): 2284-93.

22 Discussion: RNA interference and microRNAs Gu, W., M. Shirayama, D. Conte, Jr., J. Vasale, P. J. Batista, J. M. Claycomb, J. J. Moresco, E. M. Youngman, J. Keys, M. J. Stoltz, C. C. Chen, D. A. Chaves, S. Duan, K.D. Kasschau, N. Fahlgren, J. R. III Yates, S. Mitani, J. C. Carrington, and C. C. Mello. “Distinct Argonaute-Mediated 22G-RNA Pathways Direct Genome Surveillance in the C. elegans Germline.” Mol Cell 36 (2009): 231-44.
24 Discussion: RNA interference and transcription

Klattenhoff, C., H. Xi, C. Li, S. Lee, J. Xu, J. S. Khurana, F. Zhang, N. Schultz, B. S. Koppetsch, A. Nowosielska, H. Seitz, P. D. Zamore, Z. Weng, and W. E. Theurkauf. “The Drosophila HP1 Homolog Rhino Is Required for Transposon Silencing and piRNA Production by Dual-Strand Clusters.” Cell 138 (2009): 1137-49.

Course Info

As Taught In
Spring 2010