Recommended Readings: Mary Hynes, Ph.D., May 23

Monday Lecture Series
Monday, May 23, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Mary Hynes, Ph.D.
Research Associate Professor,
Laboratory of Neural Specification and Development,
The Rockefeller University

Widespread Differential Expression of 3’ UTR and Cognate Coding Region Sequences in Neurons and Other Tissues

Recommended Readings:

Heiman, M., Kulicke, R., Fenster, R. J., Greengard, P., & Heintz, N. (2014). Cell type–specific mRNA purification by translating ribosome affinity purification (TRAP). Nature Protocols, 9(6), 1282-1291. doi: 10.1038/nprot.2014.085.

Kocabas, A., Duarte, T., Kumar, S., & Hynes, M. A. (2015). Widespread differential expression of coding region and 3′ UTR sequences in neurons and other tissues. Neuron, 88(6), 1149-1156. doi: 10.1016/j.neuron.2015.10.048.

Recommended Readings: David Tollervey, Ph.D., April 10

Friday Lecture Series
Friday, April 10, 2015
3:45 p.m., Caspary Auditorium

David Tollervey, Ph.D.,
Wellcome Trust Centre for Cell Biology,
University of Edinburgh

Lighting Up RNA Interactions

Recommended Readings

Empirical Articles

Granneman, S., Kudla, G., Petfalski, E., & Tollervey, D. (2009). Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs. Proceedings of the National Academy of Sciences, 106(24), 9613-9618. doi:10.1073/pnas.0901997106

Helwak, A., Kudla, G., Dudnakova, T., & Tollervey, D. (2013). Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell, 153(3), 654-665. doi:10.1016/j.cell.2013.03.043

Helwak, A., & Tollervey, D. (2014). Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH). Nature Protocols, 9(3), 711-728. doi:10.1038/nprot.2014.043

Tuck, A. C., & Tollervey, D. (2013). A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs. Cell, 154(5), 996-1009. doi:10.1016/j.cell.2013.07.047

Review Papers

Schneider, C., & Tollervey, D. (2013). Threading the barrel of the RNA exosome. Trends in Biochemical Sciences, 38(10), 485-493. doi:10.1016/j.tibs.2013.06.013

Tuck, A. C., & Tollervey, D. (2011). RNA in pieces. Trends in Genetics, 27(10), 422-432. doi:10.1016/j.tig.2011.06.001

Recommended Readings: Rachel Green, Ph.D. December 10

Special Seminar Series
Wednesday, December 10, 2014
4:00 p.m., Carson Family Auditorium (CRC)

Rachel Green, Ph.D.
Department of Molecular Biology and Genetics,
Johns Hopkins University School of Medicine
Howard Hughes Medical Institute

Intimate Connections Between mRNA Decay and Translation

Recommended Readings

Empirical Articles

Djuranovic, S., Nahvi, A., & Green, R. (2012). miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science, 336(6078), 237–240. doi:10.1126/science.1215691

Koutmou, K. S., McDonald, M. E., Brunelle, J. L., & Green, R. (2014). RF3:GTP promotes rapid dissociation of the class 1 termination factor. RNA, 20(5), 609–620. doi:10.1261/rna.042523.113

Shoemaker, C. J., Eyler, D. E., & Green, R. (2010). Dom34:Hbs1 promotes subunit dissociation and peptidyl-tRNA drop-off to initiate no-go decay. Science, 330(6002), 369–372. doi:10.1126/science.1192430

Shoemaker, C. J., & Green, R. (2011). Kinetic analysis reveals the ordered coupling of translation termination and ribosome recycling in yeast. Proceedings of the National Academy of Sciences, 108(51), E1392–8. doi:10.1073/pnas.1113956108

Review Papers

Dever, T. E., & Green, R. (2012). The elongation, termination, and recycling phases of translation in eukaryotes. Cold Spring Harbor Perspectives in Biology, 4(7), a013706. doi:10.1101/cshperspect.a013706

Shoemaker, C. J., & Green, R. (2012). Translation drives mRNA quality control. Nature Structural & Molecular Biology, 19(6), 594–601. doi:10.1038/nsmb.2301

Recommended Readings: Amédée des Georges, Ph.D. October 20

Special Lecture Series
Monday, October 20, 2014
4:00 p.m., Carson Family Auditorium

Amédée des Georges, Ph.D.
Postdoctoral Associate,
Department of Biochemistry and Molecular Biophysics,
Columbia University

Structures of Eukaryotic Translation Initiation Complexes by Single-Particle Cryo-EM, a Powerful Tool for the Study of Heterogeneous Samples

Recommended Readings

Empirical Articles

Hashem, Y., des Georges, A., Dhote, V., Langlois, R., Liao, H. Y., Grassucci, R. a, … Frank, J. (2013). Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit. Nature, 503(7477), 539–543. doi:10.1038/nature12658

Hashem, Y., des Georges, A., Dhote, V., Langlois, R., Liao, H. Y., Grassucci, R. a, … Frank, J. (2013). Structure of the mammalian ribosomal 43S preinitiation complex bound to the scanning factor DHX29. Cell, 153(5), 1108–1119. doi:10.1016/j.cell.2013.04.036

Hashem, Y., des Georges, A., Fu, J., Buss, S. N., Jossinet, F., Jobe, A., … Frank, J. (2013). High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature, 494(7437), 385–389. doi:10.1038/nature11872

Review Papers

Jackson, R. J., Hellen, C. U. T., & Pestova, T. V. (2010). The mechanism of eukaryotic translation initiation and principles of its regulation. Nature Reviews Molecular Cell Biology, 11(2), 113–127. doi:10.1038/nrm2838

Recommended Readings: James E. Darnell, Jr., M.D. May 19

Monday Lecture Series
Monday, May 19, 2014
4:00 p.m., Carson Family Auditorium

James E. Darnell, Jr., M.D.
Vincent Astor Professor Emeritus 
Head, Laboratory of Molecular Cell Biology
The Rockefeller University

Then and now – making mRNA: an unbiased (?) look at pre-mRNA synthesis and processing

Recommended Readings:

Empirical Papers

Brenner, S., Jacob, F., & Meselson, M. (1961). An unstable intermediate carrying information from genes to ribosomes for protein synthesis. Nature, 180(4776), 576–581.

Gros, F., Hiatt, H., Gilbert, W., & Kurland, C. (1961). Unstable ribonucleic acid revealed by pulse labelling of Escherichia coli. Nature, 190(4776), 581–585.

Jacob, F., & Monod, J. (1961). Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology, 3, 318–356.

Scherrer, K., Latham, H., & Darnell, J. E. (1963). Demonstration of an unstable RNA and of a precursor to ribosomal RNA in HeLa cells. Proceedings of the National Academy of Sciences, 49(2), 240–248.

Review Articles

Darnell, J. E. (1968). Ribonucleic acids from animal cells. Bacteriological Reviews, 32(3), 262–290.

Darnell, J. E. (2013). Reflections on the history of pre-mRNA processing and highlights of current knowledge: a unified picture. RNA, 19(4), 443–60. doi:10.1261/rna.038596.113

Licatalosi, D. D., & Darnell, R. B. (2010). RNA processing and its regulation: global insights into biological networks. Nature Reviews Genetics, 11(1), 75–87. doi:10.1038/nrg2673

Recommended Readings: Kristin Tessmar-Raible Ph.D. February 3

Monday, February 3, 2014
4:00 p.m., Carson Family Auditorium

Kristin Tessmar-Raible, Ph.D.
Junior Group Leader
Max F. Perutz Laboratories
University of Vienna

The Impact of Light on Nervous System Function

Recommended Readings:

Empirical Papers

Backfisch, B., Veedin Rajan, V. B., Fischer, R. M., Lohs, C., Arboleda, E., Tessmar-Raible, K., & Raible, F. (2013). Stable transgenesis in the marine annelid Platynereis dumerilii sheds new light on photoreceptor evolution. Proceedings of the National Academy of Sciences of the United States of America, 110(1), 193–198. doi:10.1073/pnas.1209657109

Fischer, R. M., Fontinha, B. M., Kirchmaier, S., Steger, J., Bloch, S., Inoue, D., … Tessmar-Raible, K. (2013). Co-expression of VAL- and TMT-opsins uncovers ancient photosensory interneurons and motorneurons in the vertebrate brain. PLoS Biology, 11(6), e1001585. doi:10.1371/journal.pbio.1001585

Zantke, J., Ishikawa-Fujiwara, T., Arboleda, E., Lohs, C., Schipany, K., Hallay, N., … Tessmar-Raible, K. (2013). Circadian and circalunar clock interactions in a marine annelid. Cell Reports, 5(1), 99–113. doi:10.1016/j.celrep.2013.08.031

Review Articles

Roenneberg, T., & Merrow, M. (2005). Circadian clocks – the fall and rise of physiology. Nature Reviews Molecular Cell Biology, 6(12), 965–971. doi:10.1038/nrm1766

Tessmar-Raible, K., Raible, F., & Arboleda, E. (2011). Another place, another timer: Marine species and the rhythms of life. BioEssays, 33(3), 165–172. doi:10.1002/bies.201000096

Recommended Readings: Juleen R. Zierath, Ph.D.

Friday Lecture Series

Nicholson Lecture

Molecular Mechanisms for the Health-promoting Effects of Exercise: Why Muscle Matters!

Juleen R. Zierath, Ph.D., professor of physiology, department of molecular

medicine and surgery, Section for Integrative Physiology, Karolinska Institutet;

professor of integrative physiology and scientific director,

Novo Nordisk Foundation Center for Basic Metabolic Research,

Copenhagen University

October 25, 2013

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

Caspary Auditorium

Recommended Readings

Barrès, R., Yan, J., Egan, B., Treebak, J. T., Rasmussen, M., Fritz, T., . . . Zierath, J. R. (2012). Acute exercise remodels promoter methylation in human skeletal muscle. Cell Metabolism, 15(3), 405-411

Cantó, C., Jiang, L. Q., Deshmukh, A. S., Mataki, C., Coste, A., Lagouge, M., . . . Auwerx, J. (2010). Interdependence of AMPK and SIRT1 for metabolic adaptation to fasting and exercise in skeletal muscle. Cell Metabolism, 11(3), 213-219

Egan, B., Carson, B. P., Garcia-Roves, P. M., Chibalin, A. V., Sarsfield, F. M., Barron, N., . . . O’Gorman, D. J. (2010). Exercise intensity-dependent regulation of peroxisome proliferator-activated receptor γ coactivator-1α mRNA abundance is associated with differential activation of upstream signalling kinases in human skeletal muscle. Journal of Physiology, 588(10), 1779-1790

Egan, B., O’Connor, P. L., Zierath, J. R., & O’Gorman, D. J. (2013). Time course analysis reveals gene-specific transcript and protein kinetics of adaptation to short-term aerobic exercise training in human skeletal muscle. PLoS ONE, 8(9)

Egan, B., & Zierath, J. R. (2013). Exercise metabolism and the molecular regulation of skeletal muscle adaptation. Cell Metabolism, 17(2), 162-184

Russell, A. P., Lamon, S., Boon, H., Wada, S., Güller, I., Brown, E. L., . . . Akimoto, T. (2013). Regulation of miRNAs in human skeletal muscle following acute endurance exercise and short-term endurance training. Journal of Physiology, 591(18), 4637-4653

Szekeres, F., Chadt, A., Tom, R. Z., Deshmukh, A. S., Chibalin, A. V., Björnholm, M., . . . Zierath, J. R. (2012). The rab-GTPase-activating protein TBC1D1 regulates skeletal muscle glucose metabolism. American Journal of Physiology – Endocrinology and Metabolism, 303(4), E524-E533


Recommended Readings: Robert H. Singer, Ph.D.

Friday Lecture Series

Following Single mRNAs from Birth to Death

Robert H. Singer, Ph.D., professor and co-chair,

Department of Anatomy and Structural Biology, Albert Einstein College of Medicine

April 12, 2012

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

Caspary Auditorium

Recommended Readings

Ben-Ari, Y., Brody, Y., Kinor, N., Mor, A., Tsukamoto, T., Spector, D. L., . . . Shav-Tal, Y. (2010). The life of an mRNA in space and time. Journal of Cell Science, 123(10), 1761-1774

Darzacq, X., Yao, J., Larson, D. R., Causse, S. Z., Bosanac, L., De Turris, V., . . . Singer, R. H. (2009). Imaging transcription in living cells . Annual Review of Biophysics 38 (1) , pp. 173-196

Grünwald, D., & Singer, R. H. (2010). In vivo imaging of labelled endogenous Β-actin mRNA during nucleocytoplasmic transport. Nature, 467(7315), 604-607

Katz, Z. B., Wells, A. L., Park, H. Y., Wu, B., Shenoy, S. M., & Singer, R. H. (2012). β-Actin mRNA compartmentalization enhances focal adhesion stability and directs cell migration. Genes and Development, 26(17), 1885-1890

Lionnet, T., Czaplinski, K., Darzacq, X., Shav-Tal, Y., Wells, A. L., Chao, J. A., . . . Singer, R. H. (2011). A transgenic mouse for in vivo detection of endogenous labeled mRNA. Nature Methods, 8(2), 165-170

Park, H. Y., Buxbaum, A. R., & Singer, R. H. (2010). Single mRNA tracking in live cells. Methods in Enzymology, 472, 387-406

Trcek, T., Larson, D. R., Moldón, A., Query, C. C., & Singer, R. H. (2011). Single-molecule mRNA decay measurements reveal promoter-regulated mRNA stability in yeast. Cell, 147(7), 1484-1497


Recommended Readings: Andrew Grimson, Ph.D.

Monday Lecture Series

Animal microRNAs: their ancient origin and contemporary targets

Andrew Grimson, Ph.D.

Postdoctoral Fellow

Whitehead Institute for Biomedical Research and Howard Hughes Medical Institute

Monday, March 2, 2009

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Articles:

Glazov, E. A., S. McWilliam, W. C. Barris, and B. P. Dalrymple. 2008. Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals. Molecular Biology and Evolution. 25(5):939-948.

Farh, K. K. -H, A. Grimson, C. Jan, B. P. Lewis, W. K. Johnston, L. P. Lim, C. B. Burge, and D. P. Bartel. 2005. Biochemistry: The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science. 310(5755):1817-1821.

Grimson, A., K. K. -H Farh, W. K. Johnston, P. Garrett-Engele, L. P. Lim, and D. P. Bartel. 2007. MicroRNA targeting specificity in mammals: Determinants beyond seed pairing. Molecular Cell. 27(1):91-105.

Grimson, A., M. Srivastava, B. Fahey, B. J. Woodcroft, H. R. Chiang, N. King, B. M. Degnan, D. S. Rokhsar, and D. P. Bartel. 2008. Early origins and evolution of microRNAs and piwi-interacting RNAs in animals. Nature. 455(7217):1193-1197.

Piriyapongsa, J., L. Mariño-Ramírez, and I. K. Jordan. 2007. Origin and evolution of human microRNAs from transposable elements. Genetics. 176(2):1323-1337.

Recommended Readings: Thomas Tuschl Ph.D.

Monday Lectures

Small RNA Sequencing Resolves Posttranscriptional

Regulatory Networks

Thomas Tuschl  Ph.D.

Howard Hughes Medical Institute

The Rockefeller University

4 p.m.  (refreshments at 3:45)

Monday, December 15, 2008

Welch Hall Level Two

Related Articles:

Zhao, Yi; Shunmin  He,; et al.    2008.  MicroRNA regulation of messenger-like noncoding RNAs: a network of mutual microRNA control    Trends in Genetics 24(7): 323-327.


Orom, Ulf Andersson; Finn Cilius Nielsen.    2008.  MicroRNA-10a binds the 5 ‘ UTR of ribosomal protein mRNAs and enhances their translation.   Molecular Cell  30 (4):460-471.


Hudder, Alice; and Raymond F. Novak. 2008.   miRNAs: Effectors of environmental influences on gene expression and disease.   Toxicological Sciences 103(2): 228-240.


Hu Shi-Jun; Yang Zeng-Ming.  2008. Mechanisms on the regulation of miRNAs expression.  Progress in Biochemistry and Biophysics  35(5): 483-487.    Request article from Markus Library


Lee, Ji Young; Soonhag Kim; et al.   2008.    Development of a dual-luciferase reporter system for in vivo visualization of microRNA biogenesis and posttranscriptional regulation.   Journal of Nuclear Medicine 49(2):285-294.  Request article from Markus Library.


Ku, Gregory; and Michael T. McManus.  2008.    Behind the scenes of a small RNA gene-silencing pathway.  Human Gene Therapy  19(1):17-26.   Request article from Markus Library.


Diederichs, Sven; and Daniel A.Haber.  2007.   Dual role for argonautes in MicroRNA processing and Posttranscriptional regulation of MicroRNA expression.  Cell  131(6): 1097-1108.


Zeng Yan; Heidi H. Sankala  et al. 2008.   Phosphorylation of Argonaute 2 at serine-387 facilitates its localization to processing bodies.  Biochemical Journal   413(part 3): 429-436.  


Ronemus, Michael; Matthew W. Vaughn;  et al.   2006.   MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by Argonaute, Dicer, and RNA-dependent RNA polymerase in Arabidopsis.   Plant Cell  18(7): 1559-1574.


 Chen, Po Yu; and Gunter Meister.    2005.   microRNA-guided posttranscriptional gene regulation.  Biological Chemistry  386(12):1205-1218.   Request article from Markus Library.