Recommended Readings: Robert G. Roeder, Ph.D., November 16th

Monday Lecture Series
Monday, November 16, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Robert G. Roeder, Ph.D.
Arnold and Mabel Beckman Professor and Head,
Laboratory of Biochemistry and Molecular Biology,
The Rockefeller University

Transcriptional Regulatory Mechanisms in Animal Cells

Recommended Readings

Cevher, M. A., Shi, Y., Li, D., Chait, B. T., Malik, S., & Roeder, R. G. (2014). Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit. Nature Structural & Molecular Biology, 21(12), 1028-34. doi: 10.1038/nsmb.2914

Deshpande, A. J., Deshpande, A., Sinha, A. U., Chen, L., Chang, J., Cihan, A., … & Armstrong, S. A. (2014). AF10 regulates progressive H3K79 methylation and HOX gene expression in diverse AML subtypes. Cancer Cell, 26(6), 896-908. doi: 10.1016/j.ccell.2014.10.009

Iida, S., Chen, W., Nakadai, T., Ohkuma, Y., & Roeder, R. G. (2015). PRDM16 enhances nuclear receptor-dependent transcription of the brown fat-specific Ucp1 gene through interactions with Mediator subunit MED1. Genes & Development, 29(3), 308-321. doi:10.1101/gad.252809.114

Sabari, B. R., Tang, Z., Huang, H., Yong-Gonzalez, V., Molina, H., Kong, H. E., … & Allis, C. D. (2015). Intracellular Crotonyl-CoA Stimulates Transcription through p300-Catalyzed Histone Crotonylation. Molecular Cell, 58(2), 203-215. doi:10.1016/j.molcel.2015.02.029

Zhang, P., Tu, B., Wang, H., Cao, Z., Tang, M., Zhang, C., … & Zhu, W. G. (2014). Tumor suppressor p53 cooperates with SIRT6 to regulate gluconeogenesis by promoting FoxO1 nuclear exclusion. Proceedings of the National Academy of Sciences, 111(29), 10684-10689. doi:10.1073/pnas.1411026111

Recommended Readings: Seth Darst, Ph.D., November 2nd

Monday Lecture Series
Monday, November 2, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Seth Darst, Ph.D.
Jack Fishman Professor and Head,
Laboratory of Molecular Biophysics,
The Rockefeller University

CarD, an Essential Transcription Factor in Mycobacterium Tuberculosis, Uses a Minor Groove Wedge Mechanism to Stabilize the RNA Polymerase Open Promoter Complex

Recommended Readings

Empirical Articles

Bae, B., Chen, J., Davis, E., Leon, K., Darst, S. A., & Campbell, E. A. (2015). CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex. eLife, e08505. doi:10.7554/eLife.08505

Davis, E., Chen, J., Leon, K., Darst, S. A., & Campbell, E. A. (2014). Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD. Nucleic Acids Research, gku1231. doi: 10.1093/nar/gku1231

Srivastava, D. B., Leon, K., Osmundson, J., Garner, A. L., Weiss, L. A., Westblade, L. F., … & Campbell, E. A. (2013). Structure and function of CarD, an essential mycobacterial transcription factor. Proceedings of the National Academy of Sciences, 110(31), 12619-12624. doi:10.1073/pnas.1308270110

Review Papers

Feklístov, A., Sharon, B. D., Darst, S. A., & Gross, C. A. (2014). Bacterial sigma factors: a historical, structural, and genomic perspective. Annual Review of Microbiology, 68, 357-376. doi:0.1146/annurev-micro-092412-155737

Recommended Readings: John Stamatoyannopoulos, M.D., May 11th

Special Lecture
Monday, May 11, 2015
4:00 p.m., Carson Family Auditorium (CRC)

John Stamatoyannopoulos, M.D.
Associate Professor of Genome Sciences and Medicine,
University Washington School of Medicine

New Insights into Human Genome Function

Recommended Readings

Empirical Articles

ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57-74. doi:10.1038/nature11247

Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., … & Kulkarni, A. (2015). Integrative analysis of 111 reference human epigenomes. Nature, 518(7539), 317-330. doi:10.1038/nature14248

Mayer, A., di Iulio, J., Maleri, S., Eser, U., Vierstra, J., Reynolds, A., … & Churchman, L. S. (2015). Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell, 161(3), 541-554. doi:10.1016/j.cell.2015.03.010

Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., … & Morrissey, C. S. (2014). A comparative encyclopedia of DNA elements in the mouse genome. Nature, 515(7527), 355-364. doi:10.1038/nature13992

Review Paper

Kellis, M., Wold, B., Snyder, M. P., Bernstein, B. E., Kundaje, A., Marinov, G. K., … & Hardison, R. C. (2014). Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences, 111(17), 6131-6138. doi:10.1073/pnas.1318948111

Recommended Readings: Eva Nogales, Ph.D., February 20

Friday Lecture Series
Friday, February 20, 2015
3:45 p.m., Caspary Auditorium

Eva Nogales, Ph.D.
Professor of Biochemistry, Biophysics and Structural Biology,
University of California, Berkeley
Senior Faculty Scientist, Life Sciences Division,
Lawrence Berkeley National Laboratory
Investigator, Howard Hughes Medical Institute

Cryo-EM Studies of the Human Transcription Initiation Machinery

Recommended Readings

Cianfrocco, M. a, & Nogales, E. (2013). Regulatory interplay between TFIID’s conformational transitions and its modular interaction with core promoter DNA. Transcription, 4(3), 1–7. doi:10.4161/trns.25291

Cianfrocco, M. A., Kassavetis, G. A., Grob, P., Fang, J., Juven-Gershon, T., Kadonaga, J. T., & Nogales, E. (2013). Human TFIID binds to core promoter DNA in a reorganized structural state. Cell, 152(1-2), 120–131. doi:10.1016/j.cell.2012.12.005

He, Y., Fang, J., Taatjes, D. J., & Nogales, E. (2013). Structural visualization of key steps in human transcription initiation. Nature, 495(7442), 481–486. doi:10.1038/nature11991

Recommended Readings: Jennifer Doudna, Ph.D. September 19

Friday Lecture Series
Friday, September 19, 2014
3:45 p.m., Caspary Auditorium

Jennifer Doudna, Ph.D.
Li Ka Shing Chancellor’s Chair in Biomedical and Health Sciences,
Professor of Biochemistry, Biophysics and Structural Biology,
Departments of Molecular and Cell Biology and Chemistry,
University of California, Berkeley
Investigator, Howard Hughes Medical Institute

CRISPR Systems: A Revolution in Basic Science and Biotechnology

Recommended Readings

Empirical Articles

Haurwitz, R. E., Jinek, M., Wiedenheft, B., Zhou, K., & Doudna, J. a. (2010). Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science, 329(5997), 1355–1358. doi:10.1126/science.1192272

Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C., & Doudna, J. a. (2014). DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature, 507(7490), 62–67. doi:10.1038/nature13011

Wiedenheft, B., Sternberg, S. H., & Doudna, J. a. (2012). RNA-guided genetic silencing systems in bacteria and archaea. Nature, 482(7385), 331–338. doi:10.1038/nature10886

Review Papers

Bhaya, D., Davison, M., & Barrangou, R. (2011). CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annual Review of Genetics, 45, 273–97. doi:10.1146/annurev-genet-110410-132430

Hsu, P. D., Lander, E. S., & Zhang, F. (2014). Development and Applications of CRISPR-Cas9 for Genome Engineering. Cell, 157(6), 1262–1278. doi:10.1016/j.cell.2014.05.010

Recommended Readings: Richard A. Young, Ph.D.

Friday Lecture Series

Cancer Biology Lecture

Transcriptional Control of Cell Identity

Richard A. Young, Ph.D., professor of biology and member,

Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology

May 17, 2013

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Guenther, M. G., & Young, R. A. (2010). Repressive transcription. Science, 329(5988), 150-151

Jaenisch, R., & Young, R. (2008). Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell, 132(4), 567-582

Mazzoni, E. O., Mahony, S., Iacovino, M., Morrison, C. A., Mountoufaris, G., Closser, M., . . . Wichterle, H. (2011). Embryonic stem cell-based mapping of developmental transcriptional programs. Nature Methods, 8(12), 1056-1060

Newman, J. J., & Young, R. A. (2010). Connecting transcriptional control to chromosome structure and human disease. Cold Spring Harbor Symposia on Quantitative Biology 75 , pp. 227-235

Novershtern, N., Subramanian, A., Lawton, L. N., Mak, R. H., Haining, W. N., McConkey, M. E., . . . Ebert, B. L. (2011). Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell, 144(2), 296-309

Young, R. A. (2011). Control of the embryonic stem cell state. Cell, 144(6), 940-954


Recommended Readings: Lee Stirling Churchman, Ph.D.

Monday Lecture Series

Visualizing Transcription at Nucleotide Resolution Using Nascent Transcript Sequencing

Lee Stirling Churchman, Ph.D.

Post Doctoral Researcher, Department of Cellular and Molecular Pharmacology

University of California, San Francisco

April 4, 2011

4:00 – 5:00 p.m.  Caspary Auditorium

Recommended Readings:

Churchman, LS; Weissman, JS.  2011.  Nascent transcript sequencing visualizes transcription at nucleotide resolution. NATURE. 469(7330):368-

Namekawa, SH; Lee, JT.  2011.  Detection of nascent RNA, single-copy DNA and protein localization by immunoFISH in mouse germ cells and preimplantation embryosNATURE Protocols. 6(3): 10.1038/nprot.2010.195

Mortenson, KI; Churchman, LS; Spudich, JA, et al.   2010.  Optimized localization analysis for single-molecule tracking and super-resolution microscopy. NATURE Methods. 7(5):377-U59.

Ingolia, NT; Chaemmaghami, S; Newman, JRS; and Weissman, JS.  2009.  Genome-wide analysis in  vivo of translation with nucleotide resolution using ribosome profiling. SCIENCE. 324(5924):218-223.

Churchman, LS; Okten, Z; Rock, RS et al. 2005.  Single molecule high-resolution colocalization of Cy3 and Cy5 attached to macromolecules measures intramolecular distances through time. PNAS 102(5):1419-1423.

Okten, Z; Churchman, LS; Rock, RS et al. 2004. Myosin VI walks hand-over-hand along actin NATURE Structural & Molecular Biology. 11(9):884-887.