Recommended Readings: Mitzi Kuroda, Ph.D., November 20th

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

Mitzi Kuroda, Ph.D.
Professor of Medicine,
Departments of Genetics and Medicine,
Brigham & Women’s Hospital,
Harvard Medical School

Nucleation and Spreading of Chromatin Domains in Epigenetic Models and in Cancer

Recommended Readings

Empirical Articles 

Alekseyenko, A. A., Gorchakov, A. A., Kharchenko, P. V., & Kuroda, M. I. (2014). Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification. Proceedings of the National Academy of Sciences, 111(7), 2488-2493. doi: 10.1073/pnas.1400648111

Alekseyenko, A. A., Gorchakov, A. A., Zee, B. M., Fuchs, S. M., Kharchenko, P. V., & Kuroda, M. I. (2014). Heterochromatin-associated interactions of Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs. Genes & Development, 28(13), 1445-1460. doi: 10.1101/gad.241950.114

Alekseyenko, A. A., Walsh, E. M., Wang, X., Grayson, A. R., Hsi, P. T., Kharchenko, P. V., … & French, C. A. (2015). The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains. Genes & Development, 29(14), 1507-1523. doi: 10.1101/gad.267583.115

Review Paper

McElroy, K. A., Kang, H., & Kuroda, M. I. (2014). Are we there yet? Initial targeting of the Male-Specific Lethal and Polycomb group chromatin complexes in Drosophila. Open biology, 4(3), 140006. doi: 10.1098/rsob.140006

Recommended Readings: Joanna Wysocka, Ph.D., November 13th

Friday Lecture Series
Friday, November 13, 2015
3:45 p.m., Caspary Auditorium

Joanna Wysocka, Ph.D.
Department of Chemical and Systems Biology,
Department of Developmental Biology,
Stanford University

On Peculiarities of Being a Human: Gene Regulatory Mechanisms in Human Development and Evolution

Recommended Readings

Empirical Articles

Buecker, C., Srinivasan, R., Wu, Z., Calo, E., Acampora, D., Faial, T., … & Wysocka, J. (2014). Reorganization of enhancer patterns in transition from naive to primed pluripoteny. Cell Stem Cell, 14(6), 838-853. doi:10.1016/j.stem.2014.04.003

Grow, E. J., Flynn, R. A., Chavez, S. L., Bayless, N. L., Wossidlo, M., Wesche, D. J., … & Wysocka, J. (2015). Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature. 522(7555), 221-225. doi:10.1038/nature14308

Prescott, S. L., Srinivasan, R., Marchetto, M. C., Grishina, I., Narvaiza, I., Selleri, L., … & Wysocka, J. (2015). Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. Cell, 163(1), 68-83. doi:10.1016/j.cell.2015.08.036

Review Papers

Calo, E., & Wysocka, J. (2013). Modification of enhancer chromatin: what, how, and why?. Molecular Cell, 49(5), 825-837. doi:10.1016/j.molcel.2013.01.038

Buecker, C., & Wysocka, J. (2012). Enhancers as information integration hubs in development: lessons from genomics. Trends in Genetics, 28(6), 276-284. doi:10.1016/j.tig.2012.02.008

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: Jeffrey V. Ravetch, M.D., Ph.D., November 9th

Monday Lecture Series
Monday, November 9, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Jeffrey V. Ravetch, M.D., Ph.D.
Theresa and Eugene M. Lang Professor and Head,
Laboratory of Molecular Genetics and Immunology,
The Rockefeller University

Diversification of antibody effector function

Recommended Readings

Empirical Articles

Bournazos, S., Klein, F., Pietzsch, J., Seaman, M. S., Nussenzweig, M. C., & Ravetch, J. V. (2014). Broadly neutralizing anti-HIV-1 antibodies require Fc effector functions for in vivo activity. Cell, 158(6), 1243-1253. doi: 10.1016/j.cell.2014.08.023

DiLillo, D. J., & Ravetch, J. V. (2015). Differential Fc-receptor engagement drives an anti-tumor vaccinal effect. Cell, 161(5), 1035-1045. doi:10.1016/j.cell.2015.04.016

Fiebiger, B. M., Maamary, J., Pincetic, A., & Ravetch, J. V. (2015). Protection in antibody-and T cell-mediated autoimmune diseases by antiinflammatory IgG Fcs requires type II FcRs. Proceedings of the National Academy of Sciences, 112(18), E2385-E2394. doi:10.1073/pnas.1505292112

Wang, T. T., Maamary, J., Tan, G. S., Bournazos, S., Davis, C. W., Krammer, F., … & Ravetch, J. V. (2015). Anti-HA glycoforms drive B cell affinity selection and determine influenza vaccine efficacy. Cell, 162(1), 160-169. doi:10.1016/j.cell.2015.06.026

Review Papers

Bournazos, S., DiLillo, D. J., & Ravetch, J. V. (2015). The role of Fc–FcγR interactions in IgG-mediated microbial neutralization. The Journal of Experimental Medicine, 212(9), 1361-1369. doi:10.1084/jem.20151267

Pincetic, A., Bournazos, S., DiLillo, D. J., Maamary, J., Wang, T. T., Dahan, R., … & Ravetch, J. V. (2014). Type I and type II Fc receptors regulate innate and adaptive immunity. Nature Immunology, 15(8), 707-716. doi:10.1038/ni.2939

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: Winrich Freiwald, Ph.D., October 30th

Friday Lecture Series
Friday, October 30, 2015
3:45 p.m., Carson Family Auditorium (CRC)

Winrich Freiwald, Ph.D.
Assistant Professor,
Laboratory of Neural Systems,
The Rockefeller University

Face to Face: New Vistas on the Neural Mechanisms of Social Cognition

Recommended Readings

Empirical Articles

Fisher, C., & Freiwald, W. A. (2015). Contrasting specializations for facial motion within the macaque face-processing system. Current Biology, 25(2), 261-266. doi:10.1016/j.cub.2014.11.038.

Meyers, E. M., Borzello, M., Freiwald, W. A., & Tsao, D. (2015). Intelligent information loss: The coding of facial identity, head pose, and non-face information in the Macaque face patch system. The Journal of Neuroscience, 35(18), 7069-7081. doi:10.1523/JNEUROSCI.3086-14.2015.

Polosecki, P., Moeller, S., Schweers, N., Romanski, L. M., Tsao, D. Y., & Freiwald, W. A. (2013). Faces in motion: selectivity of macaque and human face processing areas for dynamic stimuli. The Journal of Neuroscience, 33(29), 11768-11773. doi: 10.1523/JNEUROSCI.5402-11.2013.

Schwiedrzik, C. M., Zarco, W., Everling, S., & Freiwald, W. A. (2015). Face patch resting state networks link face processing to social cognition. PLoS Biology, 13(9), e1002245. doi:10.1371/journal.pbio.1002245

Review Papers

Brecht, M., & Freiwald, W. A. (2012). The many facets of facial interactions in mammals. Current Opinion in Neurobiology, 22(2), 259-266. doi:10.1371/journal.pbio.1002245.