Recommended Readings: Christopher D. Lima, Ph.D. Friday March 30th, 2018

Friday Lectures

Friday, March 30th, 2018  3:45 p.m.

Caspary Auditorium

Christopher D. Lima, Ph.D.


Structural Biology Program

Memorial Sloan Kettering Cancer Center

Targeting RNA for Degradation by the Eukaryotic RNA Exosome

Recommended Readings:

Empirical Articles

Wasmuth, Elizabeth V.; Lima, Christopher D. (2017). The Rrp6 C-terminal domain binds RNA and activates the nuclear RNA exosome. NUCLEIC ACIDS RESEARCH. 45 (2): 846-860

Januszyk, Kurt; Lima, Christopher D. (2014). The eukaryotic RNA exosome. CURRENT OPINION IN STRUCTURAL BIOLOGY. 24: 132-140

Zinder, John C.; Wasmuth, Elizabeth V.; Lima, Christopher D. (2016). Nuclear RNA Exosome at 3.1 angstrom Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44/Dis3. MOLECULAR CELL. 64 (4): 734-745

Wasmuth, Elizabeth V.; Januszyk, Kurt; Lima, Christopher D. (2014). Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA. NATURE. 511 (7510): 435-+

Wasmuth, Elizabeth V.; Lima, Christopher D. (2012). Exo- and Endoribonucleolytic Activities of Yeast Cytoplasmic and Nuclear RNA Exosomes Are Dependent on the Noncatalytic Core and Central Channel. MOLECULAR CELL. 48 (1): 133-144

Liu, Quansheng; Greimann, Jaclyn C.; Lima, Christopher D. (2006). Reconstitution, activities, and structure of the eukaryotic RNA exosome. CELL. 127 (6): 1223-1237

Review Paper

Zinder, John C.; Lima, Christopher D. (2017). Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors. GENES & DEVELOPMENT. 31 (2): 88-100

Book Chapter

Greimann, Jaclyn C.; Lima, Christopher D. (2008). RECONSTITUTION of RNA Exsomes From Human And Saccharomyces Cerevisiae: Clonning, Expression, Purification, And  Activity Assays. METHODS IN ENZYMOLOGY. 448: 185-210

Recommended Readings: Sanford M. Simon, Ph.D. Monday March 19, 2018

Monday Lectures

Monday, March 19, 2018  4:00 p.m.

Carson Family Auditorium

Sanford M. Simon, Ph.D.

Professor and Head

Laboratory of Cellular Biophysics

The Rockefeller University

ESCRTing Viruses out of the Cell: Lessons from HIV-1

Recommended Readings:

Empirical Articles

Itano, Michelle S.; Arnion, Helene; Wolin, Sandra L.; et al. (2018). Recruitment of 7SL RNA to assembling HIV-1 virus-like particles. TRAFFIC. 19 (1): 36-43

Itano, Michelle S.; Bleck, Marina; Johnson, Daniel S.; et al. (2016). Readily Accessible Multiplane Microscopy: 3D Tracking the HIV-1 Genome in Living Cells. TRAFFIC. 17 (2): 179-186

Bleck, Marina; Itano, Michelle S.; Johnson, Daniel S.; et al. (2014). Temporal and spatial organization of ESCRT protein recruitment during HIV-1 budding. PNAS. 111 (33): 12211-12216

Jouvenet, Nolwenn; Zhadina, Maria; Bieniasz, Paul D.; et al. (2011). Dynamics of ESCRT protein recruitment during retroviral assembly. NATURE CELL BIOLOGY. 13 (4): 394-U124

Jouvenet, Nolwenn; Simon, Sanford M.; Bieniasz, Paul D. (2009). Imaging the interaction of HIV-1 genomes and Gag during assembly of individual viral particles. PNAS. 106 (45): 19114-19119

Jouvenet, Nolwenn; Bieniasz, Paul D.; Simon, Sanford M. (2008). Imaging the biogenesis of individual HIV-1 virions in live cells. NATURE. 454 (7201): 236-240

Review Papers

Jouvenet, Nolwenn; Simon, Sanford M.; Bieniasz, Paul D. (2011). Visualizing HIV-1 Assembly.  JOURNAL OF MOLECULAR BIOLOGY. 410 (4): 501-511

Book Chapter

Woolf, Steven H.; Purnell, Jason Q.; Simon, Sarah M.; et al. (2015). Translating Evidence into Population Health Improvement: Strategies and Barriers. ANNUAL REVIEW OF PUBLIC HEALTH. 36: 463-482


Recommended Readings: Lewis Cantley, Ph.D. Friday March 16, 2018

Friday Lectures

Friday, March 16, 2018  3:45 p.m.

Caspary Auditorium

Lewis Cantley, Ph.D.

Meyer Director of the Sandra and Edward Meyer Cancer Center


Professor of Cancer Biology in Medicine

Weill Cornell Medicine and New York-Presbyterian Hospital

PI 3-Kinase: Linking Obesity, Insulin Resistance, and Cancer

Recommended Readings:

Empirical Articles

Liu H, Murphy CJ, Karreth FA, Emdal KB, White FM, Elemento O, Toker A, Wulf GM, Cantley LC. (2018). Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer. CANCER DISCOVERY. 8 (3):354-369

Waldhart, Althea N.; Dykstra, Holly; Peck, Anderson S.; et al. (2017).  Phosphorylation of TXNIP by AKT Mediates Acute Influx of Glucose in Response to Insulin. CELL REPORTS. 19 (10)2005-2013

Croessmann S, Sheehan JH, Lee KM, Sliwoski G, et al. (2017). PIK3CA C2 Domain Deletions Hyperactivate Phosphoinositide 3-kinase (PI3K), Generate Oncogene Dependence, and Are Exquisitely Sensitive to PI3Kα Inhibitors. CLINICAL CANCER RESEARCH. doi: 10.1158/1078-0432.CCR-17-2141

Fruman, David A.; Chiu, Honyin; Hopkins, Benjamin D.; et al. (2017). The PI3K Pathway in Human Disease. CELL. 170 (4)605-635 

Thorpe, Lauren M.; Spangle, Jennifer M.; Ohlson, Carolynn E.; et al. (2017). PI3K-p110 alpha mediates the oncogenic activity induced by loss of the novel tumor suppressorPI3K-p85 alpha. PNAS.114 (27)7095-7100

Juvekar, Ashish; Hu, Hai; Yadegarynia, Sina; et al. (2016). Phosphoinositide 3-kinase inhibitors induce DNA damage through nucleoside depletion. PNAS. 113 (30): E4338-E4347

Review Papers

Fruman, David A.; Chiu, Honyin; Hopkins, Benjamin D.; et al. (2017). The PI3K Pathway in Human Disease. CELL. 170 (4): 605-635

Heiden, Matthew G. Vander; Cantley, Lewis C.; Thompson, Craig B. (2009). Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation. SCIENCE. 324 (5930): 1029-1033

Yuan, T. L.; Cantley, L. C. (2008). PI3K pathway alterations in cancer: variations on a theme. ONCOGENE. 27 (41): 5497-5510

Book Chapter

Lien, Evan C.; Lyssiotis, Costas A.; Cantley, Lewis C. (2016). Metabolic Reprogramming by the PI3K-Akt-mTOR Pathway in Cancer. METABOLISM IN CANCER. 207: 39-72

Yuan, Tina L.; Cantley, Lewis C. (2010). Phosphoinositide 3-kinase in Health and Disease Volume 1 Introduction. PHOSPHOINOSITIDE 3-KINASE IN HEALTH AND DISEASE, VOL1. Current Topics in Microbiology and Immunology. 346: 1-7


Recommended Readings: Michael Greenberg, Ph.D. Friday March 9th, 2018

Friday Lectures

Friday, March 9th, 2018  3:45 p.m.

Caspary Auditorium

Michael Greenberg, Ph.D.

Department Chair and Nathan Marsh Pusey Professor

Department of Neurobiology

Harvard Medical School

How Nature and Nurture Conspire to Control Brain Development and Function

Recommended Readings:

Empirical Articles

Kalish, Brian T.; Cheadle, Lucas; Hrvatin, Sinisa; et al. (2018). Single-cell transcriptomics of the developing lateral geniculate nucleus reveals insights into circuit assembly and refinement. PNAS. 115 (5): E1051-E1060

Hrvatin, Sinisa; Hochbaum, Daniel R.; Nagy, M. Aurel; et al. (2018). Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex. NATURE NEUROSCIENCE. 21 (1): 120-+

Gabel, Harrison W.; Kinde, Benyam; Stroud, Hume; et al. (2015). Disruption of DNA-methylation-dependent long gene repression in Rett syndrome. NATURE. 522 (7554): 89-U221

Malik, Athar N.; Vierbuchen, Thomas; Hemberg, Martin; et al. (2014). Genome-wide identification and characterization of functional neuronal activity-dependent enhancers. NATURE NEUROSCIENCE. 17 (10): 1330-1339

West, Anne E.; Greenberg, Michael E. (2011). Neuronal Activity-Regulated Gene Transcription in Synapse Development and Cognitive Function. COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY. 3 (6)

Greer, Paul L.; Hanayama, Rikinari; Bloodgood, Brenda L.; et al. (2010). The Angelman Syndrome Protein Ube3A Regulates Synapse Development by Ubiquitinating Arc. CELL. 140 (5): 704-716

Review Papers

Hardingham, Giles E.; Pruunsild, Priit; Greenberg, Michael E.; et al. (2018). Lineage divergence of activity-driven transcription and evolution of cognitive ability. NATURE REVIEWS NEUROSCIENCE. 19 (1): 9-15

Ebert, Daniel H.; Greenberg, Michael E. (2013). Activity-dependent neuronal signalling and autism spectrum disorder. NATURE. 493 (7432): 327-337

Book Chapter

Flavell, Steven W.; Greenberg, Michael E. (2008). Signaling mechanisms linking neuronal activity to gene expression and plasticity of the nervous system. ANNUAL REVIEW OF NEUROSCIENCE. 31: 563-590


Recommended Readings: Philip Cole, M.D., Ph.D. Friday December 8th, 2017

Friday Lectures

Friday, December 8, 2017  3:45 p.m.

Caspary Auditorium

Philip Cole, M.D., Ph.D.


Department of Medicine, Biological Chemistry and Molecular Pharmacology

Harvard Medical School

Targeting Reversible Lysine Acetylation with Designed Small Molecules


Recommended Readings:

Empirical Articles

Boija, Ann; Mahat, Dig Bijay; Zare, Aman; et al. (2017). CBP Regulates Recruitment and Release of PromoterProximal RNA Polymerase II.  MOLECULAR CELL. 68 (3): 491-+

Lasko, Loren M.; Jakob, Clarissa G.; Edalji, Rohinton P.; et al. (2017). Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours. NATURE. 550 (7674): 128-+

Maksimoska, Jasna; Segura-Pena, Dario; Cole, Philip A.; et al. (2014). Structure of the p300 Histone Acetyltransferase Bound to Acetyl-Coenzyme A and Its Analogues. BIOCHEMISTRY. 53 (21): 3415-3422

Bowers, Erin M.; Yan, Gai; Mukherjee, Chandrani; et al. (2010). Virtual Ligand Screening of the p300/CBP Histone Acetyltransferase: Identification of a Selective Small Molecule Inhibitor.  CHEMISTRY & BIOLOGY. 17 (5): 471-482

Dancy, Beverley M.; Crump, Nicholas T.; Peterson, Daniel J.; et al. (2012). Live-Cell Studies of p300/CBP Histone Acetyltransferase Activity and Inhibition. CHEMBIOCHEM. 13 (14): 2113-2121

Liu, Xin; Wang, Ling; Zhao, Kehao; et al. (2008). The structural basis of protein acetylation by the p300/CBP transcriptional coactivator. NATURE. 451 (7180): 846-850

Review Papers

Dancy, Beverley M.; Cole, Philip A. (2013). Protein Lysine Acetylation by p300/CBP. CHEMICAL REVIEWS. 115 (6): 2419-2452

Cole, Philip A. (2008). Chemical probes for histone-modifying enzymes.  NATURE CHEMICAL BIOLOGY. 4 (10): 590-597

Recommended Readings: Ali H. Brivanlou, Ph.D. Monday November 20th, 2017

Monday Lectures

Monday, November 20, 2017  3:45 p.m.

Carson Family Auditorium

Ali H. Brivanlou, Ph.D.

Robert and Harriet Heilbrunnand Professor and Head

Laboratory of Stem Cell Biology and Molecular Embryology

The Rockefeller University


Self-organization of Spatial Patterns in Artificial Human Embryos and Organoids

Recommended Readings:


Patrick Monahan.

Empirical Articles

Deglincerti, Alessia; Croft, Gist F.; Pietila, Lauren N.; et al. (2016). Self-organization of the in vitro attached human embryo. NATURE.  533 (7602): 251-+

Etoc, Fred; Metzger, Jakob; Ruzo, Albert; et al. (2016). A Balance between Secreted Inhibitors and Edge Sensing Controls Gastruloid Self-Organization. DEVELOPMENTAL CELL. 39 (3): 302-315  

Haremaki, Tomomi; Deglincerti, Alessia; Brivanlou, Ali H. (2015). Huntingtin is required for ciliogenesis and neurogenesis during early Xenopus development. DEVELOPMENTAL BIOLOGY. 408 (2): 305-315

Warmflash, Aryeh; Sorre, Benoit; Etoc, Fred; et al. (2014). A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. NATURE METHODS. 11 (8): 847-854

Bedzhov, Ivan; Leung, Chuen Yan; Bialecka, Monika; et al. (2014). In vitro culture of mouse blastocysts beyond the implantation stages. NATURE PROTOCOLS.  9 (12): 2732-2739

Review Paper

Simunovic, Mijo; Brivanlou, Ali H. (2017). Embryoids, organoids and gastruloids: new approaches to understanding embryogenesis.  DEVELOPMENT. 144 (6): 976-985

Clevers, Hans (2016). Modeling Development and Disease with Organoids. CELL. 165 (7): 1586-1597


Recommended Readings: Anja Groth, Ph.D., Friday October 13th, 2017

Friday Lectures

Friday, October 13, 2017  3:45 p.m.

Caspary Auditorium

Anja Groth, Ph.D.

Professor and Group Leader

Biotech Research and Innovation Centre (BRIC)

 University of Copenhagen

Chromatin Replication and Epigenome Maintenance


Recommended Readings:

Hammond, Colin M.; Stromme, Caroline B.; Huang, Hongda; et al. (2017). Histone chaperone networks shaping chromatin function. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 18 (3): 141-158

Saredi, Giulia; Huang, Hongda; Hammond, Colin M.; et al. (2016). H4K20me0 marks post-replicative chromatin and recruits the TONSL-MMS22L DNA repair complex. NATURE. 534 (7609): 714-+   

Alabert, Constance; Barth, Teresa K.; Reveron-Gomez, Nazaret; et al. (2015). Two distinct modes for propagation of histone PTMs across the cell cycle. GENES & DEVELOPMENT 29 (6): 585-590

Huang, Hongda; Stromme, Caroline B.; Saredi, Giulia; et al. (2015). A unique binding mode enables MCM2 to chaperone histones H3-H4 at replication forks. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 22 (8): 618-626

Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Bau; et al. (2014). Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components.  NATURE CELL BIOLOGY. 16 (3): 281-+

Alabert, Constance; Groth, Anja (2012). Chromatin replication and epigenome maintenance. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 13 (3): 153-167



Recommended Readings: Kenneth Zaret, Ph.D., Friday May 26th, 2017

Friday Lectures

Friday, May 26, 2017  3:45 p.m.

Caspary Auditorium

Kenneth Zaret, Ph.D.

Joseph Leidy Professor, Department of Cell and Developmental Biology

Director, Institute for Regenerative Medicine

Perelman School of Medicine, University of Pennsylvania

Overcoming Chromatin Barriers to Control Cell Fate

Recommended Readings:

Zaret, Kenneth S.; Lerner, Jonathan; Iwafuchi-Doi, Makiko (2016). Chromatin Scanning by Dynamic Binding of Pioneer Factors. MOLECULAR CELL. 62 (5): 665-667

Zaret, Kenneth S.; Mango, Susan E. (2016). Pioneer transcription factors, chromatin dynamics, and cell fate control. CURRENT OPINION IN GENETICS & DEVELOPMENT. 37: 76-81

Iwafuchi-Doi, Makiko; Donahue, Greg; Kakumanu, Akshay; et al. (2016). The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation. MOLECULAR CELL. 62(1): 79-91

Soufi, Abdenour; Garcia, Meilin Fernandez; Jaroszewicz, Artur; et al. (2015). Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming. CELL. 161(3): 555-568

Zaret, Kenneth S.; Carroll, Jason S. (2011). Pioneer transcription factors: establishing competence for gene expression. GENES & DEVELOPMENT. 25 (21): 2227-2241


Recommended Readings: Michael P. Rout, Ph.D., Monday May 15th, 2017

Monday Lectures

Monday, May 15, 2017  3:45 p.m.

Carson Family Auditorium

Michael P. Rout, Ph.D.

 Professor and Head,

Laboratory of Cellular and Structural Biology

The Rockefeller University

Getting the Hole Picture: Structure-Function Mapping of the Nuclear Pore Complex

Recommended Readings:

Timney, Benjamin L.; Raveh, Barak; Mironska, Roxana; et al. (2016). Simple rules for passive diffusion through the nuclear pore complex. JOURNAL OF CELL BIOLOGY. 215(1): 57-76

Raveh, Barak; Karp, Jerome M.; Sparks, Samuel; et al. (2016). Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA . 113(18): E2489-E2497

Fernandez-Martinez, Javier; Kim, Seung Joong; Shi, Yi; et al. (2016). Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. CELL. 167(5): 1215-+

Tu, Li-Chun; Fu, Guo; Zilman, Anton; et al. (2013). Large cargo transport by nuclear pores: implications for the spatial organization of FG-nucleoporins.EMBO JOURNAL. 32(24): 3220-3230

Fernandez-Martinez, Javier; Phillips, Jeremy; Sekedat, Matthew D.; et al. (2012). Structure-function mapping of a heptameric module in the nuclear pore complex. JOURNAL OF CELL BIOLOGY. 196(4): 419-434

Grossman, Einat; Medalia, Ohad; Zwerger, Monika (2012). Functional Architecture of the Nuclear Pore Complex. ANNUAL REVIEW OF BIOPHYSICS. 41: 557-584

Recommended Readings: Sue Biggins, Ph.D., Friday May 5th, 2017

Friday Lectures

Friday, May 5th, 2017   3:45 p.m.

Caspary Auditorium

Sue Biggins, Ph.D.

Member and Associate Director

Division of Basic Sciences

Fred Hutchinson Cancer Research Center

Sensing Tension at Kinetochores

Recommended Readings: 

Miller, Matthew P.; Asbury, Charles L.; Biggins, Sue (2016). A TOG Protein Confers Tension Sensitivity to Kinetochore-Microtubule Attachments. CELL. 165(6): 1428-1439

Musacchio, Andrea (2015). The Molecular Biology of Spindle Assembly Checkpoint Signaling Dynamics. CURRENT BIOLOGY.  25(20): R1002-R1018

Biggins, Sue (2015). Under tension: Kinetochores and Basic Research. GENETICS. 200(3): 681-682

London, Nitobe; Biggins, Sue (2014). Signalling dynamics in the spindle checkpoint response. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 15 (11): 735-747

Sarangapani, Krishna K.; Duro, Eris; Deng, Yi; et al. (2014). Sister kinetochores are mechanically fused during meiosis I in yeast. SCIENCE. 346(6206): 248-251

Biggins, Sue (2013). The Composition, Functions, and Regulation of the Budding Yeast Kinetochore. GENETICS. 194(4): 817-846

Gonen, Shane; Akiyoshi, Bungo; Iadanza, Matthew G.; et al. (2012). The structure of purified kinetochores reveals multiple microtubule-attachment sites. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 19( 9): 925-929