Recommended Readings: Luciano Marraffini, Ph.D., Friday October 20th, 2017

Friday Lectures

Friday, October 20, 2017  3:45 p.m.

Caspary Auditorium

Luciano Marraffini, Ph.D.

Associate Professor and Head

Laboratory of Bacteriology

The Rockefeller University

CRISPR-Cas, Acquired Immunity in Prokaryotes


Recommended Readings:

Niewoehner, Ole; Garcia-Doval, Carmela; Rostol, Jakob T.; et al. (2017). Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers.  NATURE. 548 (7669): 543-+

Modell, Joshua W.; Jiang, Wenyan; Marraffini, Luciano A. (2017). CRISPR-Cas systems exploit viral DNA injection to establish and maintain adaptive immunity. NATURE. 544 (7648): 101-+  

Marraffini, Luciano A. (2017). Sensing danger. PNAS. 114 (1): 15-16

Heler, Robert; Wright, Addison V.; Vucelja, Marija; et al. (2017). Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response. MOLECULAR CELL. 65 (1): 168-175

Marraffini, Luciano A. (2015). CRISPR-Cas immunity in prokaryotes. NATURE. 526 (7571): 55-61

McGinn, Jon; Marraffini, Luciano A. (2016). CRISPR-Cas Systems Optimize Their Immune Response by Specifying the Site of Spacer Integration. MOLECULAR CELL. 64 (3): 616-623

Barrangou, Rodolphe; Marraffini, Luciano A. (2014). CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity. MOLECULAR CELL. 54 (2): 234-244

Cong, Le; Ran, F. Ann; Cox, David; et al. (2013). Multiplex Genome Engineering Using CRISPR/Cas Systems.  SCIENCE. 339 (6121): 819-823



Recommended Readings: Emmanuelle Charpentier, Ph.D., January 22

Friday Lecture Series
Friday, January 22, 2016
3:45 p.m., Caspary Auditorium

Emmanuelle Charpentier, Ph.D.
Professor, Department of Regulation in Infection Biology
Director, Max Planck Institute for Infection Biology;
Visiting Professor, Laboratory for Molecular Infection Medicine Sweden, Umeå University

The Transformative Genome Engineering Technology CRISPR-Cas9: Lessons Learned from bacteria

Recommended Reading

Empirical Articles

Chylinski, K., Le Rhun, A., & Charpentier, E. (2013). The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biology, 10(5), 726-737. doi:10.4161/rna.24321

Fonfara, I., Le Rhun, A., Chylinski, K., Makarova, K. S., Lécrivain, A. L., Bzdrenga, J., … & Charpentier, E. (2014). Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic acids research, 42(4), 2577-2590. doi:10.1093/nar/gkt1074.

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012). A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096), 816-821. doi:10.1126/science.1225829.

Review Papers

Charpentier, E., Richter, H., van der Oost, J., & White, M. F. (2015). Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. FEMS Microbiology Reviews, 39(3), 428-441. doi:10.1093/femsre/fuv023.

Chylinski, K., Makarova, K. S., Charpentier, E., & Koonin, E. V. (2014). Classification and evolution of type II CRISPR-Cas systems. Nucleic acids research, 42(10), 6091-6105. doi:10.1093/nar/gku241

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: 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: Shixin Liu, Ph.D. September 29

Special Seminar
Monday, September 29, 2014
4:00 p.m., Carson Family Auditorium

Shixin Liu, Ph.D.
Postdoctoral Fellow,
California Institute for Quantitative Biosciences (QB3),
University of California, Berkeley

Visualization and Manipulation of Single Biomolecular Machines

Recommended Readings

Empirical Articles

Chistol, G., Liu, S., Hetherington, C. L., Moffitt, J. R., Grimes, S., Jardine, P. J., & Bustamante, C. (2012). High degree of coordination and division of labor among subunits in a homomeric ring ATPase. Cell, 151(5), 1017–1028. doi:10.1016/j.cell.2012.10.031

Liu, S., Abbondanzieri, E., & Rausch, J. (2008). Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates. Science, 322(5904):1092-1097. doi: 10.1126/science.1163108.

Liu, S., Chistol, G., Hetherington, C. L., Tafoya, S., Aathavan, K., Schnitzbauer, J., … Bustamante, C. (2014). A viral packaging motor varies its DNA rotation and step size to preserve subunit coordination as the capsid fills. Cell, 157(3), 702–713. doi:10.1016/j.cell.2014.02.034

Liu, S., Harada, B. T., Miller, J. T., Le Grice, S. F. J., & Zhuang, X. (2010). Initiation complex dynamics direct the transitions between distinct phases of early HIV reverse transcription. Nature Structural & Molecular Biology, 17(12), 1453–60. doi:10.1038/nsmb.1937

Review Papers

Liu, S., Chistol, G., & Bustamante, C. (2014). Mechanical operation and intersubunit coordination of ring-shaped molecular motors: insights from single-molecule studies. Biophysical Journal, 106(9), 1844–58. doi:10.1016/j.bpj.2014.03.029

Recommended Readings: Zhijian ‘James’ Chen, Ph.D. September 26

Friday Lecture Series
Friday, September 26, 2014
3:45 p.m., Caspary Auditorium

Zhijian “James” Chen, Ph.D.
George L. MacGregor Distinguished Chair in Biomedical Sciences,
Director, Center for Inflammation,
Research Professor, Department of Molecular Biology,

The University of Texas Southwestern Medical Center
Investigator, Howard Hughes Medical Institute

Enemy Within – Immune and Autoimmune Responses to cytosolic DNA and RNA

Recommended Readings

Empirical Articles

Gao, D., Wu, J., Wu, Y.-T., Du, F., Aroh, C., Yan, N., … Chen, Z. J. (2013). Cyclic GMP-AMP synthase is an innate immune sensor of HIV and other retroviruses. Science, 341(6148), 903–906. doi:10.1126/science.1240933

Li, X.-D., Wu, J., Gao, D., Wang, H., Sun, L., & Chen, Z. J. (2013). Pivotal roles of cGAS-cGAMP signaling in antiviral defense and immune adjuvant effects. Science, 341(6152), 1390–1394. doi:10.1126/science.1244040

Sun, L., Wu, J., Du, F., Chen, X., & Chen, Z. J. (2013). Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway. Science, 339(6121), 786–791. doi:10.1126/science.1232458

Zeng, W., Sun, L., Jiang, X., Chen, X., Hou, F., Adhikari, A., … Chen, Z. J. (2010). Reconstitution of the RIG-I pathway reveals a signaling role of unanchored polyubiquitin chains in innate immunity. Cell, 141(2), 315–330. doi:10.1016/j.cell.2010.03.029

Review Papers

Cai, X., Chiu, Y.-H., & Chen, Z. J. (2014). The cGAS-cGAMP-STING pathway of cytosolic DNA sensing and signaling. Molecular Cell, 54(2), 289–296. doi:10.1016/j.molcel.2014.03.040

Wu, J., & Chen, Z. J. (2014). Innate immune sensing and signaling of cytosolic nucleic acids. Annual Review of Immunology, 32, 461–88. doi:10.1146/annurev-immunol-032713-120156

Recommended Readings: Jennifer Doudna, Ph.D. September 19

Friday Lecture Series
Friday, September 19, 2014
3:45 p.m., Caspary Auditorium

Jennifer Doudna, Ph.D.
Li Ka Shing Chancellor’s Chair in Biomedical and Health Sciences,
Professor of Biochemistry, Biophysics and Structural Biology,
Departments of Molecular and Cell Biology and Chemistry,
University of California, Berkeley
Investigator, Howard Hughes Medical Institute

CRISPR Systems: A Revolution in Basic Science and Biotechnology

Recommended Readings

Empirical Articles

Haurwitz, R. E., Jinek, M., Wiedenheft, B., Zhou, K., & Doudna, J. a. (2010). Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science, 329(5997), 1355–1358. doi:10.1126/science.1192272

Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C., & Doudna, J. a. (2014). DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature, 507(7490), 62–67. doi:10.1038/nature13011

Wiedenheft, B., Sternberg, S. H., & Doudna, J. a. (2012). RNA-guided genetic silencing systems in bacteria and archaea. Nature, 482(7385), 331–338. doi:10.1038/nature10886

Review Papers

Bhaya, D., Davison, M., & Barrangou, R. (2011). CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annual Review of Genetics, 45, 273–97. doi:10.1146/annurev-genet-110410-132430

Hsu, P. D., Lander, E. S., & Zhang, F. (2014). Development and Applications of CRISPR-Cas9 for Genome Engineering. Cell, 157(6), 1262–1278. doi:10.1016/j.cell.2014.05.010

Recommended Readings: Wei Yang, Ph.D. March 10

Monday, March 10, 2014
4:00 p.m., Carson Family Auditorium

Wei Yang, Ph.D.
Senior Investigator and Section Chief
Department of Molecular Biology
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health

Human DNA polymerase η: from Chemistry to Cancer Biology

Recommended Readings:

Empirical Articles

Biertümpfel, C., Zhao, Y., Kondo, Y., Ramón-Maiques, S., Gregory, M., Lee, J. Y., … Yang, W. (2010). Structure and mechanism of human DNA polymerase η. Nature, 465(7301), 1044–1048. doi:10.1038/nature09196

Nakamura, T., Zhao, Y., Yamagata, Y., Hua, Y., & Yang, W. (2012). Watching DNA polymerase η make a phosphodiester bond. Nature, 487(7406), 196–201. doi:10.1038/nature11181

Zhao, Y., Biertümpfel, C., Gregory, M. T., Hua, Y.-J., Hanaoka, F., & Yang, W. (2012). Structural basis of human DNA polymerase η-mediated chemoresistance to cisplatin. Proceedings of the National Academy of Sciences of the United States of America, 109(19), 7269–7274. doi:10.1073/pnas.1202681109

Zhao, Y., Gregory, M. T., Biertümpfel, C., Hua, Y., Hanaoka, F., & Yang, W. (2013). Mechanism of somatic hypermutation at the WA motif by human DNA polymerase η. Proceedings of the National Academy of Sciences of the United States of America, 110(20), 8146–8151. doi:10.1073/pnas.1303126110

Review Papers

Lange, S. S., Takata, K., & Wood, R. D. (2011). DNA polymerases and cancer. Nature Reviews Cancer, 11(2), 96–110. doi:10.1038/nrc2998

Sale, J. E., Lehmann, A. R., & Woodgate, R. (2012). Y-family DNA polymerases and their role in tolerance of cellular DNA damage. Nature Reviews Molecular Cell Biology, 13(3), 141–152. doi:10.1038/nrm3289

Yang, W. (2003). Damage repair DNA polymerases Y. Current Opinion in Structural Biology, 13(1), 23–30. doi:10.1016/S0959-440X(02)00003-9

Recommended Readings: Harmit S. Malik, Ph.D.

Friday Lecture Series

Genetic Conflicts: Beyond the Usual Suspects

Harmit S. Malik, Ph.D., principal investigator, basic sciences division,

Fred Hutchinson Cancer Research Center;

early career scientist, Howard Hughes Medical Institute

December 13, 2013

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

Caspary Auditorium

Recommended Readings

Malik, H. S. (2009). Evolution of TRIM antiviral genes in primate genomes. Retrovirology, 6(SUPPL. 2)

Malik, H. S., & Bayes, J. J. (2006). Genetic conflicts during meiosis and the evolutionary origins of centromere complexity. Biochemical Society Transactions, 34(4), 569-573

Malik, H. S., & Henikoff, S. (2002). Conflict begets complexity: The evolution of centromeres. Current Opinion in Genetics and Development, 12(6), 711-718

Moran, J. V., & Malik, H. S. (2009). Diamonds and rust: How transposable elements influence mammalian genomes. conference on mobile elements in mammalian genomes. EMBO Reports, 10(12), 1306-1310

Oliver, P. L., Goodstadt, L., Bayes, J. J., Birtle, Z., Roach, K. C., Phadnis, N., . . . Ponting, C. P. (2009). Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genetics, 5(12)

Vermaak, D., & Malik, H. S. (2009). Multiple roles for heterochromatin protein 1 genes in drosophila. Annual Review of Genetic 43 , pp. 467-492


Recommended Readings: Bonnie Bassler, Ph.D.

Friday Lecture Series

Manipulating Quorum Sensing to Control Bacterial Pathogenesis

Bonnie Bassler, Ph.D., Squibb Professor in Molecular Biology and director,

Council on Science and Technology,

Princeton University

October 11, 2013

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

Caspary Auditorium

Recommended Readings

Bassler, B., & Vogel, J. (2013). Bacterial regulatory mechanisms: The gene and beyond. Current Opinion in Microbiology, 16(2), 109-111

Chen, G., Swem, L., Swem, D., Stauff, D., O’Loughlin, C., Jeffrey, P., . . . Hughson, F. (2011). A strategy for antagonizing quorum sensing. Molecular Cell, 42(2), 199-209

Stauff, D. L., & Bassler, B. L. (2011). Quorum sensing in chromobacterium violaceum: DNA recognition and gene regulation by the CviR receptor. Journal of Bacteriology, 193(15), 3871-3878

Swem, L. R., Swem, D. L., O’Loughlin, C. T., Gatmaitan, R., Zhao, B., Ulrich, S. M., & Bassler, B. L. (2009). A quorum-sensing antagonist targets both membrane-bound and cytoplasmic receptors and controls bacterial pathogenicity. Molecular Cell, 35(2), 143-153

Teng, S. -., Schaffer, J. N., Tu, K. C., Mehta, P., Lu, W., Ong, N. P., . . . Wingreen, N. S. (2011). Active regulation of receptor ratios controls integration of quorum-sensing signals in vibrio harveyi. Molecular Systems Biology, 7