Recommended Readings: Marc Kirschner, Ph.D., May 8th

Friday Lecture Series
Friday, May 8, 2015
3:45 p.m., Caspary Auditorium

Marc W. Kirschner, Ph.D.
John Franklin Enders University Professor,
Professor and Chair,
Department of Systems Biology,
Harvard Medical School

The Origin of Specificity in Regulated Protein Degradation

Recommended Readings

Empirical Articles

Gujral, T. S., Chan, M., Peshkin, L., Sorger, P. K., Kirschner, M. W., & MacBeath, G. (2014). A noncanonical frizzled2 pathway regulates epithelial-mesenchymal transition and metastasis. Cell, 159(4), 844-856. doi: 10.1016/j.cell.2014.10.032.

Lu, Y., Lee, B. H., King, R. W., Finley, D., & Kirschner, M. W. (2015). Substrate degradation by the proteasome: A single-molecule kinetic analysis.Science, 348(6231), 1250834. doi: 10.1126/science.1250834

Lu, Y., Wang, W., & Kirschner, M. W. (2015). Specificity of the anaphase-promoting complex: A single-molecule study. Science, 348(6231), 1248737. doi: 10.1126/science.1248737.

Zhao, R., Deibler, R. W., Lerou, P. H., Ballabeni, A., Heffner, G. C., Cahan, P., … & Daley, G. Q. (2014). A nontranscriptional role for Oct4 in the regulation of mitotic entry. Proceedings of the National Academy of Sciences, 111(44), 15768-15773. doi: 10.1073/pnas.1417518111

Review Papers

Kirschner, M. W. (2005). The meaning of systems biology. Cell, 121(4), 503-504.

Recommended Readings: Ronald Breaker, Ph.D., May 1

Friday Lecture Series
Friday, May 1, 2015
3:45 p.m., Caspary Auditorium

Ronald Breaker, Ph.D.
Henry Ford II Professor,
Professor, Molecular Biophysics and Biochemistry,
Yale University
Investigator, Howard Hughes Medical Institute

Prospects for Riboswitch and Ribozyme Discovery

Empirical Articles

Baker, J. L., Sudarsan, N., Weinberg, Z., Roth, A., Stockbridge, R. B., & Breaker, R. R. (2012). Widespread genetic switches and toxicity resistance proteins for fluoride. Science, 335(6065), 233-235. doi:10.1126/science.1215063

Kim, P. B., Nelson, J. W., & Breaker, R. R. (2015). An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism. Molecular Cell, 57(2), 317-328. doi:10.1016/j.molcel.2015.01.001

Nelson, J. W., Sudarsan, N., Furukawa, K., Weinberg, Z., Wang, J. X., & Breaker, R. R. (2013). Riboswitches in eubacteria sense the second messenger c-di-AMP. Nature Chemical Biology, 9(12), 834-839. doi:10.1038/nchembio.1363

Roth, A., Weinberg, Z., Chen, A. G., Kim, P. B., Ames, T. D., & Breaker, R. R. (2014). A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nature chemical biology, 10(1), 56-60. doi:10.1038/nchembio.1386

Review Papers

Breaker, R. R. (2012). Riboswitches and the RNA world. Cold Spring Harbor Perspectives in Biology, 4(2), a003566. doi:10.1101/cshperspect.a003566

Breaker, R. R., & Joyce, G. F. (2014). The expanding view of RNA and DNA function. Chemistry & Biology, 21(9), 1059-1065. doi:10.1016/j.chembiol.2014.07.008

Recommended Readings: Robert G. Roeder, Ph.D., April 13

Monday Lecture Series
Monday, April 13, 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

Empirical Articles

Jiang, H., Lu, X., Shimada, M., Dou, Y., Tang, Z., & Roeder, R. G. (2013). Regulation of transcription by the MLL2 complex and MLL complex–associated AKAP95. Nature Structural & Molecular Biology, 20(10), 1156-1163. doi:10.1038/nsmb.2656

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. 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

Review Papers

Malik, S., & Roeder, R. G. (2010). The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation. Nature Reviews Genetics, 11(11), 761-772. doi:10.1038/nrg2901

Roeder, R. G. (2005). Transcriptional regulation and the role of diverse coactivators in animal cells. FEBS letters, 579(4), 909-915. doi:10.1016/j.febslet.2004.12.007

Recommended Readings: Agata Smogorzewska, M.D., Ph.D., April 24

Friday Lecture Series
Friday, April 24, 2015
3:45 p.m., Caspary Auditorium

Agata Smogorzewska, M.D., Ph.D.
Assistant Professor and Head,
Laboratory of Genome Maintenance,
The Rockefeller University

DNA Interstrand Crosslink Repair: from Genetics to Mechanism

Recommended Readings

Empirical Articles

Flynn, E. K., Kamat, A., Lach, F. P., Donovan, F. X., Kimble, D. C., Narisu, N., … & Chandrasekharappa, S. C. (2014). Comprehensive analysis of pathogenic deletion variants in Fanconi anemia genes. Human Mutation, 35(11), 1342-1353. doi:10.1002/humu.22680

Kim, Y., Spitz, G. S., Veturi, U., Lach, F. P., Auerbach, A. D., & Smogorzewska, A. (2013). Regulation of multiple DNA repair pathways by the Fanconi anemia protein SLX4. Blood, 121(1), 54-63. doi:10.1182/blood-2012-07-441212

Ouyang, J., Garner, E., Hallet, A., Nguyen, H. D., Rickman, K. A., Gill, G., … & Zou, L. (2015). Noncovalent interactions with SUMO and ubiquitin orchestrate distinct functions of the SLX4 complex in genome maintenance. Molecular Cell, 57(1), 108-122. doi:10.1016/j.molcel.2014.11.015

Wang, R., Persky, N. S., Yoo, B., Ouerfelli, O., Smogorzewska, A., Elledge, S. J., & Pavletich, N. P. (2014). Mechanism of DNA interstrand cross-link processing by repair nuclease FAN1. Science, 346(6213), 1127-1130. doi:10.1126/science.1258973

Review Paper

Kottemann, M. C., & Smogorzewska, A. (2013). Fanconi anaemia and the repair of Watson and Crick DNA crosslinks. Nature, 493(7432), 356-363. doi:10.1038/nature11863

Recommended Readings: A. James Hudspeth, M.D., Ph.D., April 27

Monday Lecture Series
Monday, April 27, 2015
4:00 p.m., Carson Family Auditorium (CRC)

A. James Hudspeth, M.D., Ph.D.
F.M. Kirby Professor and Head,
Laboratory of Sensory Neuroscience,
The Rockefeller University
Investigator, Howard Hughes Medical Institute

Making an Effort to Listen: the Active Process of the Cochlea

Recommended Readings

Empirical Articles

Fisher, J. A., Nin, F., Reichenbach, T., Uthaiah, R. C., & Hudspeth, A. J. (2012). The spatial pattern of cochlear amplification. Neuron, 76(5), 989-997. doi:10.1016/j.neuron.2012.09.031

Jacobo, A., & Hudspeth, A. J. (2014). Reaction–diffusion model of hair-bundle morphogenesis. Proceedings of the National Academy of Sciences, 111(43), 15444-15449. doi:10.1073/pnas.1417420111

Maoiléidigh, D. Ó., & Hudspeth, A. J. (2013). Effects of cochlear loading on the motility of active outer hair cells. Proceedings of the National Academy of Sciences, 110(14), 5474-5479. doi:10.1073/pnas.1302911110

Nin, F., Reichenbach, T., Fisher, J. A., & Hudspeth, A. J. (2012). Contribution of active hair-bundle motility to nonlinear amplification in the mammalian cochlea. Proceedings of the National Academy of Sciences, 109(51), 21076-21080. doi:10.1073/pnas.1219379110

Review Papers

Hudspeth, A. J. (2015). The energetic ear. Daedalus, 144(1), 42-52. doi:10.1162/DAED_a_00316

Hudspeth, A. J. (2014). Integrating the active process of hair cells with cochlear function. Nature Reviews Neuroscience, 15(9), 600-614. doi:10.1038/nrn3786

Recommended Readings: Michael W. Young, Ph.D., April 20

Monday Lecture Series
Monday, April 20, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Michael W. Young, Ph.D.
Vice President for Academic Affairs,
Richard and Jeanne Fisher Professor and Head,
Laboratory of Genetics,
The Rockefeller University

Genes that Regulate Sleep and Circadian Rhythms

Recommended Readings

Empirical Articles

Levy, C., Zoltowski, B. D., Jones, A. R., Vaidya, A. T., Top, D., Widom, J., … & Leys, D. (2013). Updated structure of Drosophila cryptochrome. Nature, 495(7441), E3-E4. doi:10.1038/nature11995.

Rogulja, D., & Young, M. W. (2012). Control of sleep by cyclin A and its regulator. Science, 335(6076), 1617-1621. doi:10.1126/science.1212476.

Stavropoulos, N., & Young, M. W. (2011). insomniac and Cullin-3 regulate sleep and wakefulness in Drosophila. Neuron, 72(6), 964-976. doi:10.1016/j.neuron.2011.12.003.

Zoltowski, B. D., Vaidya, A. T., Top, D., Widom, J., Young, M. W., & Crane, B. R. (2011). Structure of full-length Drosophila cryptochrome. Nature, 480(7377), 396-399. doi:10.1038/nature10618.

Review Papers

Boothroyd, C. E., & Young, M. W. (2008). The in (put)s and out (put)s of the Drosophila circadian clock. Annals of the New York Academy of Sciences, 1129(1), 350-357. doi:10.1196/annals.1417.006

Crane, B. R., & Young, M. W. (2014). Interactive features of proteins composing eukaryotic circadian clocks. Annual Review of Biochemistry, 83, 191-219. doi:10.1146/annurev-biochem-060713-035644

Recommended Readings: David Baker, Ph.D., April 29

Special Lecture Series
Wednesday, April 29, 2015
3:45 p.m., Carson Family Auditorium (CRC)

David Baker, Ph.D.,
Professor of Biochemistry,
University of Washington
Investigator, Howard Hughes Medical Institute

Post-Evolutionary Biology: Design of Novel Protein Structures, Functions and Assemblies

Recommended Readings

Empirical Articles

Bradley, P., Misura, K. M., & Baker, D. (2005). Toward high-resolution de novo structure prediction for small proteins. Science, 309(5742), 1868-1871.

Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., … & Popović, Z. (2010). Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-760. doi:10.1038/nature09304

Eiben, C. B., Siegel, J. B., Bale, J. B., Cooper, S., Khatib, F., Shen, B. W., … & Baker, D. (2012). Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nature Biotechnology, 30(2), 190-192. doi:10.1038/nbt.2109

Jiang, L., Althoff, E. A., Clemente, F. R., Doyle, L., Röthlisberger, D., Zanghellini, A., … & Baker, D. (2008). De novo computational design of retro-aldol enzymes. Science, 319(5868), 1387-1391. doi:10.1126/science.1152692

Review Papers

Adams, P. D., Baker, D., Brunger, A. T., Das, R., DiMaio, F., Read, R. J., … & Terwilliger, T. C. (2013). Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annual Review of Biophysics, 42, 265-287.doi: 10.1146/annurev-biophys-083012-130253

Das, R., & Baker, D. (2008). Macromolecular modeling with Rosetta. Annual Review of Biophysics, 77, 363-382. doi:10.1146/annurev.biochem.77.062906.171838

Recommended Readings: David Tollervey, Ph.D., April 10

Friday Lecture Series
Friday, April 10, 2015
3:45 p.m., Caspary Auditorium

David Tollervey, Ph.D.,
Wellcome Trust Centre for Cell Biology,
University of Edinburgh

Lighting Up RNA Interactions

Recommended Readings

Empirical Articles

Granneman, S., Kudla, G., Petfalski, E., & Tollervey, D. (2009). Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs. Proceedings of the National Academy of Sciences, 106(24), 9613-9618. doi:10.1073/pnas.0901997106

Helwak, A., Kudla, G., Dudnakova, T., & Tollervey, D. (2013). Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell, 153(3), 654-665. doi:10.1016/j.cell.2013.03.043

Helwak, A., & Tollervey, D. (2014). Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH). Nature Protocols, 9(3), 711-728. doi:10.1038/nprot.2014.043

Tuck, A. C., & Tollervey, D. (2013). A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs. Cell, 154(5), 996-1009. doi:10.1016/j.cell.2013.07.047

Review Papers

Schneider, C., & Tollervey, D. (2013). Threading the barrel of the RNA exosome. Trends in Biochemical Sciences, 38(10), 485-493. doi:10.1016/j.tibs.2013.06.013

Tuck, A. C., & Tollervey, D. (2011). RNA in pieces. Trends in Genetics, 27(10), 422-432. doi:10.1016/j.tig.2011.06.001