You'd Prefer An Argonaute

RNA Journal Club 1/12/12

Posted in RNA Journal Club by YPAA on January 12, 2012

Adaptation to P Element Transposon Invasion in Drosophila melanogaster

Jaspreet S. Khurana, Jie Wang, Jia Xu, Birgit S. Koppetsch, Travis C. Thomson, Anetta Nowosielska, Chengjian Li, Phillip D. Zamore, Zhiping Weng, and William E. Theurkauf

Cell 147, 1551–1563, 23 December 2011.
DOI 10.1016/j.cell.2011.11.042

RNA Journal Club 1/5/12

Posted in RNA Journal Club by YPAA on January 5, 2012

Selective Ribosome Profiling Reveals the Cotranslational Chaperone Action of Trigger Factor In Vivo

Eugene Oh, Annemarie H. Becker, Arzu Sandikci, Damon Huber, Rachna Chaba, Felix Gloge, Robert J. Nichols, Athanasios Typas, Carol A. Gross, Günter Kramer, Jonathan S. Weissman, and Bernd Bukau

Cell 147, 1295–1308, 9 December 2011.
DOI 10.1016/j.cell.2011.10.044

Cell Club 12/23/11

Posted in Evolution, Media by YPAA on December 23, 2011

Cell made a paperflick about a new study uncovering mechanisms of silencing of new transposons by piRNAs, from Bill Theurkauf and colleagues.

More evidence of non-boring scientists

Posted in Media, MIT by YPAA on December 17, 2011

Dennis is a cool dude; it’s self-reinforcing in his staff.

Remember, no grant could ever fund this kind of lab environment!

Kim Lab, Department of Biology, MIT

RNA Journal Club 12/15/11

Posted in RNA Journal Club by YPAA on December 15, 2011

The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing

Yehuda Brody, Noa Neufeld, Nicole Bieberstein, Sebastien Z. Causse, Eva-Maria Böhnlein, Karla M. Neugebauer, Xavier Darzacq, Yaron Shav-Tal

PLoS Biology | Volume 9 | Issue 1 | e1000573 | January 2011
doi:10.1371/journal.pbio.1000573

RNA Journal Club 12/8/11

Posted in RNA Journal Club by YPAA on December 8, 2011

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

Diana Y. Vargas, Khyati Shah, Mona Batish, Michael Levandoski, Sourav Sinha, Salvatore A.E. Marras, Paul Schedl, and Sanjay Tyagi

Cell 147, 1054–1065, 23 November 2011.
DOI 10.1016/j.cell.2011.10.024

RNA Journal Club 12/1/11

Posted in RNA Journal Club by YPAA on December 1, 2011

Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila

Filippo M. Cernilogar, Maria Cristina Onorati, Greg O. Kothe, A. Maxwell Burroughs, Krishna Mohan Parsi, Achim Breiling, Federica Lo Sardo, Alka Saxena, Keita Miyoshi, Haruhiko Siomi, Mikiko C. Siomi, Piero Carninci, David S. Gilmour, Davide F. V. Corona & Valerio Orlando

Nature AOP, 6 November 2011.
doi:10.1038/nature10492

RNA Journal Club 11/17/11

Posted in RNA Journal Club by YPAA on November 17, 2011

Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs

Yvonne Tay, Lev Kats, Leonardo Salmena, Dror Weiss, Shen Mynn Tan, Ugo Ala, Florian Karreth, Laura Poliseno, Paolo Provero, Ferdinando Di Cunto, Judy Lieberman, Isidore Rigoutsos, and Pier Paolo Pandolfi

Cell 147, 344–357, 14 October 2011.
DOI 10.1016/j.cell.2011.09.029

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An Extensive MicroRNA-Mediated Networkof RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma

Pavel Sumazin, Xuerui Yang, Hua-Sheng Chiu, Wei-Jen Chung, Archana Iyer, David Llobet-Navas, Presha Rajbhandari, Mukesh Bansal, Paolo Guarnieri, Jose Silva, and Andrea Califano

Cell 147, 370–381, 14 October 2011.
DOI 10.1016/j.cell.2011.09.041

R.I.P., H. Gobind Khorana

Posted in Media, MIT by YPAA on November 14, 2011

RNA Journal Club 11/10/11

Posted in RNA Journal Club by YPAA on November 10, 2011

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

Nicholas T. Ingolia, Liana F. Lareau, and Jonathan S. Weissman

Cell 147, 1–14, 11 November 2011.
DOI 10.1016/j.cell.2011.10.002

RNA Journal Club 11/3/11

Posted in RNA Journal Club by YPAA on November 3, 2011

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

Ci Chu, Kun Qu, Franklin L. Zhong, Steven E. Artandi, and Howard Y. Chang

Molecular Cell 44, 1–12, 18 November 2011.
DOI 10.1016/j.molcel.2011.08.027

RNA Journal Club 10/20/11

Posted in RNA Journal Club by YPAA on October 20, 2011

RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II

Mikel Zaratiegui, Stephane E. Castel, Danielle V. Irvine, Anna Kloc, Jie Ren, Fei Li, Elisa de Castro, Laura Marín, An-Yun Chang, Derek Goto, W. Zacheus Cande, Francisco Antequera, Benoit Arcangioli & Robert A. Martienssen

Nature AOP, 16 October 2011.
doi:10.1038/nature10501

Oh No Journal Club 10/13/11

Posted in YPAA Journal Club by YPAA on October 13, 2011

Holy smokes–four back-to-back papers on candy RNAs in today’s Cell?!

(1) Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs

Yvonne Tay, Lev Kats, Leonardo Salmena, Dror Weiss, Shen Mynn Tan, Ugo Ala, Florian Karreth, Laura Poliseno, Paolo Provero, Ferdinando Di Cunto, Judy Lieberman, Isidore Rigoutsos, Pier Paolo Pandolfi

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(2) A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

Marcella Cesana, Davide Cacchiarelli, Ivano Legnini, Tiziana Santini, Olga Sthandier, Mauro Chinappi, Anna Tramontano, Irene Bozzoni

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(3) An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma

Pavel Sumazin, Xuerui Yang, Hua-Sheng Chiu, Wei-Jen Chung, Archana Iyer, David Llobet-Navas, Presha Rajbhandari, Mukesh Bansal, Paolo Guarnieri, Jose Silva, Andrea Califano

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(4) In Vivo Identification of Tumor- Suppressive PTEN ceRNAs in an Oncogenic BRAF-Induced Mouse Model of Melanoma

Florian A. Karreth, Yvonne Tay, Daniele Perna, Ugo Ala, Shen Mynn Tan, Alistair G. Rust, Gina DeNicola, Kaitlyn A. Webster, Dror Weiss, Pedro A. Perez-Mancera, Michael Krauthammer, Ruth Halaban, Paolo Provero, David J. Adams, David A. Tuveson, Pier Paolo Pandolfi