Recommended Readings: Tom Muir, Ph.D. Friday January 25, 2019

Friday Lectures

Friday, January 25, 2019  3:45 p.m

Caspary Auditorium

Tom Muir Ph.D.

Professor of Chemistry and Chair

Department of Chemistry

Princeton University

Painting Chromatin with Synthetic Protein Chemistry


Recommended Readings:

Empirical Articles

Nacev, B.A., Feng, L., Bagert, J.D. Lemiesz, A., et al. (2019). The expanding landscape of ‘oncohistone’ mutations in human cancers. NATURE, in press

Wojcik, Felix; Dann, Geoffrey P.; Beh, Leslie Y.; et al. (2018). Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants. NATURE COMMUNICATIONS. 9

Lu, Chao; Jain, Siddhant U.; Hoelper, Dominik; et al. (2016). Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape. SCIENCE. 352 (6287): 844-849

Nguyen, Uyen T. T.; Bittoval, Lenka; Mueller, Manuel M.; et al. (2014). Accelerated chromatin biochemistry using DNA-barcoded nucteosome libraries. NATURE METHODS. 11 (8): 834-840

Fierz, Beat; Kilic, Sinan; Hieb, Aaron R.; et al. (2012). Stability of Nucleosomes Containing Homogenously Ubiquitylated H2A and H2B Prepared Using Semisynthesis. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 134 (48): 19548-19551

Review Paper

David, Yael; Muir, Tom W. (2017). Emerging Chemistry Strategies for Engineering Native Chromatin. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 139 (27): 9090-9096

Mueller, Manuel M.; Muir, Tom W. (2015). Histones: At the Crossroads of Peptide and Protein Chemistry. CHEMICAL REVIEWS. 115 (6): 2296-2349

Chatterjee, Champak; Muir, Tom W. (2010). Chemical Approaches for Studying Histone Modifications. JOURNAL OF BIOLOGICAL CHEMISTRY. 285 (15): 11045-11050

Book Chapter

Holt, Matthew; Muir, Tom (2015). Application of the Protein Semisynthesis Strategy to the Generation of Modified Chromatin. ANNUAL REVIEW OF BIOCHEMISTRY. 84: 265-290

McGinty, Robert K.; Chatterjee, Champak; Muir, Tom W. (2009). Semisynthesis of Ubiquitylated Proteins. METHODS IN ENZYMOLOGY: NON-NATURAL AMINO ACIDS. 462: 225-243

Recommended Readings: Edith Heard, Ph.D., Friday, April 21, 2017

Friday Lectures

Friday, April 21, 2017   3:45 p.m.

Caspary Auditorium

Edith Heard, Ph.D.

Professor and Chair, Epigenetics and Cellular Memory, Collège de France

Director, Department of Genetics and Developmental Biology

Institut Curie

The Epigenetic Dynamics of X-chromosome Inactivation: Fine-tuning Gene Dosage during Development

Recommended Readings:

da Rocha, Simao T.; Heard, Edith (2017). Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 24(3): 197-204

Borensztein, Maud; Syx, Laurene; Ancelin, Katia; et al. (2017). Xist-dependent imprinted X inactivation and the early developmental consequences of its failure. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 24(3): 226-+

Giorgetti, Luca; Lajoie, Bryan R.; Carter, Ava C.; et al. (2016). Structural organization of the inactive X chromosome in the mouse. NATURE. 535(7613): 575-+

Wu, Hao; Luo, Junjie; Yu, Huimin; et al. (2014). Cellular Resolution Maps of X Chromosome Inactivation: Implications for Neural Development, Function, and Disease. NEURON. 81(1): 103-119

Gendrel, Anne-Valerie; Heard, Edith (2014). Noncoding RNAs and Epigenetic Mechanisms During X-Chromosome Inactivation.  ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY. 30: 561-580

Nora, Elphege P.; Lajoie, Bryan R.; Schulz, Edda G.; et al. (2012). Spatial partitioning of the regulatory landscape of the X-inactivation centre. NATURE. 485(7398): 381-385

Recommended Readings: Anne Brunet, Ph.D., March 11

Friday Lecture Series
Friday, March 11
3:45 p.m., Caspary Auditorium

Anne Brunet, Ph.D.
Michele and Timothy Barakett Endowed Professor,
Department of Genetics,
Stanford University School of Medicine

Epigenetic and Metabolic Regulation of Aging

Recommended Readings

Empirical Articles

Benayoun, B. A., Pollina, E. A., Ucar, D., Mahmoudi, S., Karra, K., Wong, E. D., … & Brunet, A. (2014). H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell, 158(3), 673-688. doi: 10.1016/j.cell.2014.06.027

Greer, E. L., Maures, T. J., Hauswirth, A. G., Green, E. M., Leeman, D. S., Maro, G. S., … & Brunet, A. (2010). Members of the H3K4 trimethylation complex regulate lifespan in a germline-dependent manner in C. elegans. Nature, 466(7304), 383-387. doi: 10.1038/nature09195

Greer, E. L., Maures, T. J., Ucar, D., Hauswirth, A. G., Mancini, E., Lim, J. P., … & Brunet, A. (2011). Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans. Nature, 479(7373), 365-371. doi: 10.1038/nature10572

Review Papers

Benayoun, B. A., Pollina, E. A., & Brunet, A. (2015). Epigenetic regulation of ageing: linking environmental inputs to genomic stability. Nature Reviews Molecular Cell Biology, 16(10), 593-610. doi:10.1038/nrm4048

Lim, J. P., & Brunet, A. (2013). Bridging the transgenerational gap with epigenetic memory. Trends in Genetics, 29(3), 176-186. doi: 10.1016/j.tig.2012.12.008

Recommended Readings: Brian Liau, Ph.D., February 3

Special Seminar
Wednesday, February 3, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Brian Liau, Ph.D.
Jane Coffins Child Memorial Fund Postdoctoral Fellow,
Department of Pathology,
Massachusetts General Hospital,
Harvard Medical School

Chemical Epigenetics: Discovering Chromatin Mediated Mechanisms in Cancer Using Small Molecules

Recommended Reading

Flavahan, W. A., Drier, Y., Liau, B. B., Gillespie, S. M., Venteicher, A. S., Stemmer-Rachamimov, A. O., … & Bernstein, B. E. (2015). Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature. doi: 10.1038/nature16490

Pelish, H. E., Liau, B. B., Nitulescu, I. I., Tangpeerachaikul, A., Poss, Z. C., Da Silva, D. H., … & Du, K. (2015). Mediator kinase inhibition further activates super-enhancer-associated genes in AML. Nature, 526(7572), 273-276. doi: 10.1038/nature14904

van Galen, P., Viny, A. D., Ram, O., Ryan, R. J., Cotton, M. J., Donohue, L., … & Carroll, K. M. (2015). A Multiplexed system for quantitative comparisons of chromatin landscapes. Molecular Cell. doi: 10.1016/j.molcel.2015.11.003.

Recommended Readings: Tom Muir, Ph.D., March 27

Friday Lecture Series
Friday, March 27, 2015
3:45 p.m., Caspary Auditorium

Tom Muir, Ph.D.
Van Zandt Williams Jr. Class of ‘65 Professor of Chemistry,
Chair, Department of chemistry
Princeton University

‘Houdini’ Proteins: Discovery and Applications of Ultrafast Inteins

Recommended Readings

Empirical Articles

Shah, N. H., Dann, G. P., Vila-Perelló, M., Liu, Z., & Muir, T. W. (2012). Ultrafast protein splicing is common among cyanobacterial split inteins: Implications for protein engineering. Journal of the American Chemical Society, 134(28), 11338–11341. doi:10.1021/ja303226x

Shah, N. H., Eryilmaz, E., Cowburn, D., & Muir, T. W. (2013). Naturally split inteins assemble through a “capture and collapse” mechanism. Journal of the American Chemical Society, 135(49), 18673–18681. doi:10.1021/ja4104364

Shah, N. H., Vila-Perelló, M., & Muir, T. W. (2011). Kinetic control of one-pot trans-splicing reactions by using a wild-type and designed split intein. Angewandte Chemie, 50(290, 6511–6515. doi:10.1002/anie.201102909

Vila-Perelló, M., Liu, Z., Shah, N. H., Willis, J. A., Idoyaga, J., & Muir, T. W. (2013). Streamlined expressed protein ligation using split inteins. Journal of the American Chemical Society, 135(1), 286–292. doi:10.1021/ja309126m

Review Papers

Eryilma, E., Shah, N. H., Muir, T. W., & Cowburn, D. (2014). Structural and dynamical features of Inteins and implications on protein splicing. Journal of Biological Chemistry, 289(21), 14506–14511. doi:10.1074/jbc.R113.540302

Shah, N. H., & Muir, T. W. (2014). Inteins: Nature’s Gift to Protein Chemists. Chemical Science, 5(1), 446–461. doi:10.1016/j.biotechadv.2011.08.021.Secreted

Recommended Readings: Frederick Cross Ph.D. September 23, 2013

Monday Lecture Series
A Fast Route to Cell Cycle Control in the Plant Superkingdom
Frederick Cross, Ph.D.
Professor, Laboratory of Cell Cycle Genetics
The Rockefeller University
4:00 p.m. – 5:00 p.m. Carson Family Auditorium (CRC)
Refreshments: 3:45 p.m. – 4:00 p.m., Lower Level Greenberg Building (CRC) 

Recommended Readings:

Review Papers

Bloom, J., & Cross, F. R. (2007). Multiple levels of cyclin specificity in cell-cycle control. Nature Reviews Molecular and Cell Biology, 8(2), 1491–1560. doi:10.1038/nrm2105

Cross, F. R., Buchler, N. E., & Skotheim, J. M. (2011). Evolution of networks and sequences in eukaryotic cell cycle control. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 366(1584), 3532–3544. doi:10.1098/rstb.2011.0078

Harris, E. (2001). Chlamydomonas as a model organism. Annual Review of Plant Biology, 52, 363–406. doi:10.1146/annurev.arplant.52.1.363

Empirical Papers

Bisova, K., Krylov, D. M., & Umen, J. G. (2005). Genome-wide annotation and expression profiling of cell cycle regulatory genes in Chlamydomonas reinhardtii. Plant Physiology, 137, 475–491. doi:10.1104/pp.104.054155.G1-S-G2-M

Fang, S.-C., de los Reyes, C., & Umen, J. G. (2006). Cell size checkpoint control by the retinoblastoma tumor suppressor pathway. PLoS Genetics, 2(10), e167. doi:10.1371/journal.pgen.0020167

Koff, a, Cross, F., Fisher, a, Schumacher, J., Leguellec, K., Philippe, M., & Roberts, J. M. (1991). Human cyclin E, a new cyclin that interacts with two members of the CDC2 gene family. Cell, 66(6), 1217–1228.

Olson, B. J. S. C., Oberholzer, M., Li, Y., Zones, J. M., Kohli, H. S., Bisova, K., … Umen, J. G. (2010). Regulation of the Chlamydomonas cell cycle by a stable, chromatin-associated retinoblastoma tumor suppressor complex. The Plant Cell, 22(10), 3331–3347. doi:10.1105/tpc.110.076067

Richardson, H. E., Wittenberg, C., Cross, F., & Reed, S. I. (1989). An essential G1 function for cyclin-like proteins in yeast. Cell, 59(6), 1127–1133.

Erez Lieberman-Aiden Ph.D. Wednesday, April 4, 2012

How the Genome Folds

Erez Aiden  Ph.D.

Fellow, Harvard Society of Fellows

Prinicpal Investigator, Laboratory-at-Large

Harvard University

Visiting Faculty, Google

4:00 Wednesday, April 4, 2012  Refreshments Abby Lounge 3:45

Caspary Auditorium 

Recommended Readings

Zhang Y; McCord RP, Ho YJ; et al.  2012.  Spatial organization of the mouse genome and its role in recurrent chromosomal translocationsCell. 148(5):908-921.  DOI: 10.1016/j.cell.2012.02.002

Sung MH and  GL Hager.  2011.  More to Hi-C than meets the eye.  Nature Genetics.  43(11):1047-1048.  DOI: 10.1038/ng.984

Yaffe E and A Tanay.  2011.  Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nature Genetics.  43(11):1059-U40.  DOI: 10.1038/ng.947

Fudenberg G; Getz G; Meyerson M; et al.  2011.  High order chromatic architecture shapes the landscape of chromosomal alterations in cancer.   Nature Biotechnology. 29(12):1109-U75.  DOI: 10.1038/nbt.2049

Lieberman-Aiden E; van Berkum NL; Williams L; et al.  2009.  Comprehenesive mapping of long-range interactions reveals folding principles of the human genomeScience.  326(5950):289-293.  DOI: 10.1126/science.1181369

Guelen L; Pagie L; Brasset E; et al.  Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions.   Nature.  453(7197):948-U83.  DOI: 10.1038/nature06947

Rada-Iglesias A; Ameur A; Kapronov P; et al.  2008.  Whole-genome maps opf USA and USF2 binding and histone H3 acetylation reveal new aspects of prmotoer structure and candidate genes for common human disorders.  Genome Research.  18(3):380-392.  DOI: 10.1101/gr.6880908

Xiao G; Wang X; and Ab Khodursky.  2011.  Modeling three-dimensional chromosome structures using gene expression data. Journal of the American Statistical Association.  106(493):61-72.  DOI: 10.1198/jasa.2010/ap09504   Please request copy from Markus Library.

Recommended Readings: Howard Chang, M.D., Ph.D.

Friday Lecture Series

Genome Regulation by Long Noncoding RNA

Howard Chang, M.D., Ph.D., early career scientist,

Howard Hughes Medical Institute; professor of dermatology,

Stanford University School of Medicine, member, Stanford Cancer Center and Stanford Institute for Stem Cell Biology and Regenerative Medicine

February 10, 2012

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

Caspary Auditorium


Recommended Readings:

Hung, T., Y. Wang, M. F. Lin, A. K. Koegel, Y. Kotake, G. D. Grant, H. M. Horlings, et al. 2011. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nature genetics 43, (7): 621-629

Rinn, J. L., M. Kertesz, J. K. Wang, S. L. Squazzo, X. Xu, S. A. Brugmann, L. H. Goodnough, et al. 2007. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, (7): 1311-1323

Tsai, M. -C, O. Manor, Y. Wan, N. Mosammaparast, J. K. Wang, F. Lan, Y. Shi, E. Segal, and H. Y. Chang. 2010. Long noncoding RNA as modular scaffold of histone modification complexes. Science 329, (5992): 689-693

Wang, K., and H. Chang. 2011. Molecular mechanisms of long noncoding RNAs. Molecular cell 43, (6): 904-914

Wang, K. C., Y. W. Yang, B. Liu, A. Sanyal, R. Corces-Zimmerman, Y. Chen, B. R. Lajoie, et al. 2011. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, (7341): 120-126


Recommended Readings: Gerald Crabtree, M.D.; June 5, 2009

Friday Lecture Series

“Understanding the Words of Chromatin Remodeling”

Gerald Crabtree, M.D.

Stanford University

June 5, 2009

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

Caspary Auditorium

Recommended Articles:

Wu, J. I., J. Lessard, and G. R. Crabtree. 2009. Understanding the words of chromatin regulation. Cell. 136(2):200-206.


Lessard, J., J. I. Wu, J. A. Ranish, M. Wan, M. M. Winslow, B. T. Staahl, H. Wu, R. Aebersold, I. A. Graef, and G. R. Crabtree. 2007. An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron. 55(2):201-215.


Chi, T. H., M. Wan, P. P. Lee, K. Akashi, D. Metzger, P. Chambon, C. B. Wilson, and G. R. Crabtree. 2003. Sequential roles of brg, the ATPase subunit of BAF chromatin remodeling complexes, in thymocyte development. Immunity. 19(2):169-182.


Rando, O. J., T. H. Chi, and G. R. Crabtree. 2003. Second messenger control of chromatin remodeling. Nature structural biology. 10(2):81-83.


Wu, J. I., J. Lessard, I. A. Olave, Z. Qiu, A. Ghosh, I. A. Graef, and G. R. Crabtree. 2007. Regulation of dendritic development by neuron-specific chromatin remodeling complexes. Neuron. 56(1):94-108.


Olave, I. A., Reck-Peterson, S. L., and Crabtree, G. R. 2002. Nuclear actin and actin-related proteins in chromatin remodeling. Annual Review of Biochemistry. 71:755-781.