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: Sohail Tavazoie, Ph.D. October 6

Monday Lecture Series
Monday, October 6, 2014
3:45 p.m., Caspary Auditorium

Sohail Tavazoie, Ph.D.
Leon Hess Assistant Professor and Head,
Elizabeth and Vincent Meyer Laboratory of Systems Cancer Biology,
The Rockefeller University
Senior Attending Physician,
The Rockefeller University Hospital

Molecular Control of Cancer Metastasis

Recommended Readings

Empirical Articles

Pencheva, N., Tran, H., Buss, C., Huh, D., Drobnjak, M., Busam, K., & Tavazoie, S. F. (2012). Convergent multi-miRNA targeting of ApoE drives LRP1/LRP8-dependent melanoma metastasis and angiogenesis. Cell, 151(5), 1068–1082. doi:10.1016/j.cell.2012.10.028

Png, K. J., Halberg, N., Yoshida, M., & Tavazoie, S. F. (2012). A microRNA regulon that mediates endothelial recruitment and metastasis by cancer cells. Nature, 481(7380), 190–194. doi:10.1038/nature10661

Png, K. J., Yoshida, M., Zhang, X. H.-F., Shu, W., Lee, H., Rimner, A., … Tavazoie, S. F. (2011). MicroRNA-335 inhibits tumor reinitiation and is silenced through genetic and epigenetic mechanisms in human breast cancer. Genes & Development, 25(3), 226–231. doi:10.1101/gad.1974211

Tavazoie, S. F., Alarcón, C., Oskarsson, T., Padua, D., Wang, Q., Bos, P. D., … Massagué, J. (2008). Endogenous human microRNAs that suppress breast cancer metastasis. Nature, 451(7175), 147–52. doi:10.1038/nature06487

Review Papers

Pencheva, N., & Tavazoie, S. F. (2013). Control of metastatic progression by microRNA regulatory networks. Nature Cell Biology, 15(6), 546–54. doi:10.1038/ncb2769

NCI Awards $9.6M for Research into Therapy-Resistant Prostate Cancer

The National Cancer Institute has awarded a five-year, $9.6 million grant to a multidisciplinary team of researchers who will study the molecular underpinnings of prostate cancers that progress to a therapy-resistant state.

The funding is for three projects. One will be directed at determining how hypoxic signals affect gene expression. Another will create new transgenic mouse models to better understand how kinases cooperate “to drive tumorigenesis.” The third project will focus on how microRNAs regulate cell proliferation and prostate cancer progression.

Recommended Readings: Robert B. Darnell M.D., PhD March 14, 2011

Monday Lecture Series

Maps of the RNA World

Robert B. Darnell M.D. , PhD

Investigator, Howard Hughes Medical Institute

 Laboratory of  Molecular Neuro-oncology

March 14, 2011

4:00 p.m.-5:00 p.m. Caspary Auditorium

Recommended Readings

Brooks, A.N.; Yang, L.; Duff, M.O.  et al.  2011.  Conservation of an  RNA regulatory map between Drosophila and mammalsGenome Research.  21(2):193-101

Misquitta-Ali, C.M.; Cheng, E.; O’Hanlon, D. et al.  2011.  Global profiling and moelcualr characterization of alternative splicing events misregulated in lung cancerMolecular and Cellular Biology.   31(1):138-150

Licatalosi, D.D.; and R.B. Darnell.  2010.  Applications of next-generation sequencing RNA processing and its regulation: global insights into biological networks.   Nature Reviews Genetics.   11(1):75-87

Zhang, C.L.; Frias, M.A.; Mele, A. et al.  2010.  Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls.  Science.   329(5990):439-443

Yano, M.; Hayakawa-Yano, Y; Mele, A.  et al.  2010.  Nova2 regulates neuronal migration through an RNA switch in disabled-1 signaling.  Neuron.   66(6):848-858

Chi, S.W.; Sang, J.B.; Mele, A. et al.  2009.   Argonaute HITS-CLIP decodes microRNA-mRNA interactions mapsNATURE   460(7254):479-486

Lactalosi, D. D.; Mele A.; and J.J. Fak.  2008.  HITS-CLIP yields genome-wide insights into brain alternative RNA processing.  NATURE.   456(7221):464-U22

Darnell, R.B.  2006.  Developing global insight into RNA regulation.  Cold Spring Harbor Symposium on Quantitative Biology( May 31-June 5, 2006) Cold Spring, NY.   71:321-327.

Recommended Readings: Nicholas Ingolias, PH.D. Monday Jan 4, 2010

Faculty Candidate Seminar

Genome-wide Translational Profiling by Ribosome Footprinting

Nicholas Ingolia, PH.D. 

Postdoctoral Fellow, Dept. of Cellular and Molecular Pharmacology, University of California, San Francisco

January 4, 2010

4:00 p.m. Welch Hall, Level Two

Recommended Readings:

Morris DR.  2009.  Ribosomal footprints on a transcriptome landscape.   GENOME BIOLOGY  10(4):article Number: 215    

Bailey-Serres J., Sorenson R., Juntawong P.  2009.  Getting the message across: cytoplasmic ribonucleoprotein complexes.  TRENDS IN PLANT SCIENCE   14(8): 443-453    

Sanz E, Yang L, Su T, Morris DR, McKnight GS, Amieux PS.  2009.  Cell-type-specific isolation of ribosome-associated mRNA from complex tissues.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA     106(33): 13939-13944   

 Ingolia NT, Ghaemmaghami S, Newman JRS, et al.  2009.  Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling.   SCIENCE   324(5924): 218-223   

Baek D., Villen J, Shin C, Camargo FD, Gygi SP, Bartel DP.  2008.  The impact of microRNAs on protein output.   NATURE   455(7209): 64-70  

Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. 2008. Widespread changes in protein synthesis induced by microRNAs   NATURE     455(7209): 58-63    

Berezikov E., Cuppen E., Plasterk RHA.  2006.  Approaches to microRNA discovery.   NATURE GENETICS     38(suppl 6): S2-S7    

Arava Y, Boas FE, Brown PO, Herschlag D.  2005.  Dissecting eukaryotic translation and its control by ribosome density mappingNUCLEIC ACIDS RESEARCH  33(8): 2421-2432   

AIDS: Clues To Virus-cancer Link Uncovered

ScienceDaily (June 18, 2009) — In a series of recently-published articles, a research team from the University of North Carolina at Chapel Hill Lineberger Comprehensive Cancer Center has uncovered clues to the development of cancers in AIDS patients.  The first article published in April in PLoS Pathogens demonstrated that the Kaposi sarcoma associated herpesvirus (KSHV) is not only present in every tumor cell, but that the cells also transcribe microRNAs (miRNA) from the virus.   The second study was published June 4 in the journal Blood looked at the activity of several miRNAs known to suppress tumor activity.   Finding the mechanisms through which viruses take over cellular systems, resulting in cancer, is a promising strategy for cancer prevention and treatment, since it is much more feasible to block viral infection or develop specific inhibitors of the viral genes than try to inhibit all of the genetic changes within a cancer.

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. 


Related Readings – Sohail F. Tavazoie PhD

Special Seminar Series

Human microRNAs That Suppress Breast Cancer Metastasis

Monday June 14, 2008 Welch Hall Level 2 Refreshments 3:45 p.m. Lecture 4 p.m.

Review Article:

Tavazoie, SF; Alarcon, C; et al.  2008.  Endogenous human microRNAs that suppress breast cancer metastasis.  NATURE  451(7175):147-U3

Related Articles:

Tavazoie, SF; Alvarez, VA; et al.  2005. Regulation of neuronal morphology and function by the tumor suppressors Tsc1 and Tsc2.  Nature Neuroscience   8(12):1727-1734

Beer, SK; Tavazoie, S; and M. Grunstein.  2004. Mapping global histone acetylation patterns to gene expression.  Cell 117(2):721-733