Recommended Readings: Frank Grosveld, Ph.D., June 5th

Friday Lecture Series
Friday, June 5, 2015
3:45 p.m., Caspary Auditorium

Frank Grosveld, Ph.D.
Professor and Head,
Department of Cell Biology
Chair, Research School MGC,
Erasmus MC

Transcription Factors and Genomic Architecture

Recommended Readings

Empirical Articles

Ghamari, A., van de Corput, M. P., Thongjuea, S., van Cappellen, W. A., van IJcken, W., van Haren, J., … & Grosveld, F. G. (2013). In vivo live imaging of RNA polymerase II transcription factories in primary cells. Genes & Development, 27(7), 767-777. doi:10.1101/gad.216200.113

Mylona, A., Andrieu-Soler, C., Thongjuea, S., Martella, A., Soler, E., Jorna, R., … & Grosveld, F. (2013). Genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis. Blood, 121(15), 2902-2913. doi:10.1182/blood-2012-11-467654

Nuez, B., Michalovich, D., Bygrave, A., Ploemacher, R., & Grosveld, F. (1995). Defective haematopoiesis in fetal liver resulting from inactivation of the EKLF gene. Nature, 375(6529), 316-318.

Soler, E., Andrieu-Soler, C., de Boer, E., Bryne, J. C., Thongjuea, S., Stadhouders, R., … & Grosveld, F. (2010). The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation. Genes & Development, 24(3), 277-289. doi:10.1101/gad.551810

Stadhouders, R., Thongjuea, S., Andrieu‐Soler, C., Palstra, R. J., Bryne, J. C., van den Heuvel, A., … & Soler, E. (2012). Dynamic long‐range chromatin interactions control Myb proto‐oncogene transcription during erythroid development. The EMBO Journal, 31(4), 986-999. doi:10.1038/emboj.2011.450

Review Papers

Kolovos, P., Knoch, T. A., Grosveld, F. G., Cook, P. R., & Papantonis, A. (2012). Enhancers and silencers: an integrated and simple model for their function. Epigenetics Chromatin, 5(1). doi:10.1186/1756-8935-5-1

Recommended Readings: W. Ian Lipkin, M.D., May 29th

Friday Lecture Series
Friday, May 29, 2015
3:45 p.m., Caspary Auditorium

W. Ian Lipkin, M.D.
John Snow Professor of Epidemiology,
Mailman School of Public Health
Professor of Neurology and Pathology,
College of Physicians and Surgeons
Director, Center for Infection and Immunity, C
Columbia University

Small Game Hunting

Recommended Readings

Empirical Articles

Cox-Foster, D. L., Conlan, S., Holmes, E. C., Palacios, G., Evans, J. D., Moran, N. A., … & Lipkin, W. I. (2007). A metagenomic survey of microbes in honey bee colony collapse disorder. Science, 318(5848), 283-287.

Memish, Z. A., Mishra, N., Olival, K. J., Fagbo, S. F., Kapoor, V., Epstein, J. H., … & Lipkin, W. I. (2013). Middle East respiratory syndrome coronavirus in bats, Saudi Arabia. Emerging Infectious Diseases, 19(11), 1819-1823. doi:10.3201/eid1911.131172

Negredo, A., Palacios, G., Vázquez-Morón, S., González, F., Dopazo, H., Molero, F., … & Tenorio, A. (2011). Discovery of an ebolavirus-like filovirus in europe. PLoS Pathogens, 7(10), e1002304. doi:10.1371/journal.ppat.1002304

Palacios, G., Druce, J., Du, L., Tran, T., Birch, C., Briese, T., … & Lipkin, W. I. (2008). A new arenavirus in a cluster of fatal transplant-associated diseases. New England Journal of Medicine, 358(10), 991-998. doi:10.1056/NEJMoa073785

Review Papers

Lipkin, W. I. (2013). The changing face of pathogen discovery and surveillance. Nature Reviews Microbiology, 11(2), 133-141. doi:10.1038/nrmicro2949

Lipkin, W. I. (2010). Microbe hunting. Microbiology and Molecular Biology Reviews, 74(3), 363-377. doi:10.1128/MMBR.00007-10

Lipkin, W. I., & Anthony, S. J. (2015). Virus hunting. Virology. doi:10.1016/j.virol.2015.02.006

Recommended Readings: Carl H. June, M.D., May 22nd

Friday Lecture Series
Friday, May 22, 2015
3:45 p.m., Caspary Auditorium

Carl H. June, M.D.
Director, Translational Research Program,
Abramson Family Cancer Research Institute
Richard W. Vague Professor in Immunotherapy,
Perelman School of Medicine,
University of Pennsylvania

Adoptive Cell Therapy with Engineered T Cells

Recommended Readings

Empirical Articles

Grupp, S. A., Kalos, M., Barrett, D., Aplenc, R., Porter, D. L., Rheingold, S. R., … & June, C. H. (2013). Chimeric antigen receptor–modified T cells for acute lymphoid leukemia. New England Journal of Medicine, 368(16), 1509-1518.  doi:10.1056/NEJMoa1215134

Kalos, M., Levine, B. L., Porter, D. L., Katz, S., Grupp, S. A., Bagg, A., & June, C. H. (2011). T cells with chimeric antigen receptors have potent antitumor effects and can establish memory in patients with advanced leukemia. Science Translational Medicine, 3(95), 95ra73-95ra73. doi:10.1126/scitranslmed.3002842

Porter, D. L., Levine, B. L., Kalos, M., Bagg, A., & June, C. H. (2011). Chimeric antigen receptor–modified T cells in chronic lymphoid leukemia. New England Journal of Medicine, 365(8), 725-733. doi:10.1056/NEJMoa1103849

Review Papers

June, C. H., Maus, M. V., Plesa, G., Johnson, L. A., Zhao, Y., Levine, B. L., … & Porter, D. L. (2014). Engineered T cells for cancer therapy. Cancer Immunology, Immunotherapy, 63(9), 969-975. doi:10.1007/s00262-014-1568-1

Maus, M. V., Fraietta, J. A., Levine, B. L., Kalos, M., Zhao, Y., & June, C. H. (2014). Adoptive immunotherapy for cancer or viruses. Annual Review of Immunology, 32, 189-225. doi:10.1146/annurev-immunol-032713-120136

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: 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