RNA Journal Club 6/18/09
A UPF3-mediated regulatory switch that maintains RNA surveillance
Wai-Kin Chan, Angela D Bhalla, Hervé Le Hir, Lam Son Nguyen, Lulu Huang, Jozef Gécz & Miles F Wilkinson
Nature Structural & Molecular Biology 16 (7): 747-53, July 2009.
doi:10.1038/nsmb.1612
Hummers sell paranoia
While walking through the MIT campus this evening I passed by a parked red Hummer truck emblazoned with the word “BioDefense.” The ostentatious and environmentally ruinous Hummer as a vehicle to protect life from harm? Ironic yes, but actually probably a travel vehicle, and advertisement, owned by a company named BioDefense corporation. They sell a device called the “MailDefender”, a chamber that converts your anthrax, smallpox, plague, E. coli, influenza, HIV, botulism, ricin, and bird flu laced mail into safe reading.
OK, I don’t mean to be facetious – I’m aware people have died from such bioterrorist mail – but I’m amused by any product advertised on the side of a Hummer.
Surely the long-range lights (see roof) stop anthrax in its tracks. And botulism is no match for that grill bar.
I drove a Hummer once and couldn’t stop laughing. It was a big, bright orange disaster, with enourmous tires so tall that they reached my belly. You know a street vehicle is ridiculous when you need to grab a handle to pull yourself in.
So I was sad when I read Chinese investors decided to buy the Hummer brand. Hummer is the one GM species I wanted to see go extinct.
Scott Valastyan teaches Bob Weinberg about microRNAs
Led by the sage Scott Valastyan, a graduate student in Bob Weinberg’s laboratory, a new study in the June 12 issue of Cell demonstrates miR-31’s role in inhibiting breast cancer metastasis. Cell’s website recognizes the paper with a video where Bob and Scott are a first-rate scientific tag team:
(Original video removed)
UPDATE APRIL 2015: The above referenced paper and two related papers by the same authors were recently retracted. Cell’s notice contains the most detailed description of the problem.
Retraction notices:
http://genesdev.cshlp.org/content/29/6/686.1.full
In Progress: Keystone Nice
It has been very slow going, but I have been updating the Keystone Nice post. As of tonight, I’ve gotten through the Monday morning session (for the speakers that had my attention), so there are notes from talks by:
Andrew Fire
David Bartel
V. Narry Kim
Gunter Meister
Qinghua Liu
Bruce Paterson
Erik Sontheimer
Dinshaw Patel
Jin-Biao Ma
Scott Kennedy
Craig Mello
David C. Baulcombe
Peter Sarnow
Yukihide Tomari
Eric C. Lai
More talk notes to come later. I do realize there is some futility to this, since by the time I get all the information up, it will almost all be published! However, the post has been getting the most views on the blog, so I intend to finish what I started.
RNA Journal Club 6/11/09
Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies
Chengjian Li, Vasily V. Vagin, Soohyun Lee, Jia Xu, Shengmei Ma, Hualin Xi, Hervé Seitz, Michael D. Horwich, Monika Syrzycka, Barry M. Honda, Ellen L.W. Kittler, Maria L. Zapp, Carla Klattenhoff, Nadine Schulz, William E. Theurkauf, Zhiping Weng and Phillip D. Zamore
Cell 137 (3): 509-521, April 2009.
doi:10.1016/j.cell.2009.04.027
RNA Journal Club 6/4/09
The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs
Michele Trabucchi, Paola Briata, MariaFlor Garcia-Mayoral, Astrid D. Haase, Witold Filipowicz, Andres Ramos, Roberto Gherzi & Michael G. Rosenfeld
Nature 459 (7249): 1010-1014, June 2009.
doi:10.1038/nature08025
RNA Journal Club 5/28/09
A MicroRNA Imparts Robustness against Environmental Fluctuation during Development
Xin Li, Justin J. Cassidy, Catherine A. Reinke, Stephen Fischboeck and Richard W. Carthew
Cell 137 (2): 273-282, April 2009.
doi:10.1016/j.cell.2009.01.058
Bob Weinberg’s Words of Wisdom
A few days ago I attended an informal talk by the cancer biologist Bob Weinberg, who discussed some of his family history, upbringing, and early career, peppering many chunks of wisdom onto the attentive audience throughout. While introducing him, a colleague mentioned that Bob has received 62 awards for his scientific pursuits. Among these are the National Medal of Science (1997), and the Wolf Prize in Medicine (2004). He has also written the reference textbook on cancer, The Biology of Cancer. So as a scientist and educator, this man is solid gold.
Weinberg recounted one story about how, in the early 70’s, he crossed paths with a fraud who had shared his intense interest in the mechanisms by which infection with DNA tumor viruses could lead to transformation of mammalian cells. Weinberg had thought of several experiments to address the question, only to find out soon after that another investigator in Toronto had beat him to it, becoming a minor celebrity while giving talks up and down the east coast. However, the unthinkable quantity of data this investigator had amassed would soon end his career. (This outcome is assumed as Bob did not provide a name.) The data was fabricated. The first hint resulted from a back of the envelope calculation by a journal editor showing that the number of petri dishes required to generate the data far exceeded the number available to all scientists in the Toronto area during the relevant period.
Hot fields are of course vulnerable to fraud. Recently there was Woo Suk Hwang in the stem cell field, and Luk Van Parijs ran a lab studying RNAi technologies and immunology. Back in the late 80’s/early 90’s there was the notorious Imanishi-Kari/Baltimore affair. I suppose it’s possible that immunology was hot back then. Stranger things happened.
So how ’bout the small RNA field? No big scandals I can recall, (although I’m fairly new to the field). A search for the terms “miRNA” and “retraction” in Pubmed yields 3 results: one Science paper and a couple Nature papers. However, retracted papers and scientific fraud are not one and the same.
The controversies in the small RNA field seem to encompass smaller battles, say a partially disputed and highly visible paper with data that is not totally rebuked by others, but where the authors make overly great leaps in their interpretations. And as a colleague of mine pointed out, the field is so new and moves so quickly that there hasn’t been enough time for researchers to confirm all previously published results.
A paper claiming miRNAs can up-regulate translation under certain cellular conditions generated a lot of controversy. A recent presentation of this work by Joan Steitz at the Keystone meeting in April, more than a year after its initial publication, was still met with some underlying skepticism in the questions that were asked.
Bob Weinberg himself published a miRNA paper that generated some discussion in journals (1), and at conferences (2). But these last two examples are really cases of a healthy scientific discourse, openly discussing results and interpretations.
While in the literature I regularly encounter dubious data, it’s more often the dubiousness of some of the interpretations that bothers me. For novel published data I think it is beneficial to temper skepticism with belief. Considering alternative explanations for what one may consider questionable data is a much better intellectual exercise than discounting an entire paper, and just ragging on it.
But hey, what do I know. Listen to a guy like Bob Weinberg. He said he doesn’t even read the literature. He just talks to people.
(1) http://www.nature.com/nature/journal/v455/n7216/full/nature07362.html; http://www.nature.com/nature/journal/v455/n7216/full/nature07363.html
(2) Witnessed at Keystone RNAi, MicroRNA, and Non-Coding RNA 2008 meeting
RNA Journal Club 5/21/09
DNA Damage Regulates Alternative Splicing through Inhibition of RNA Polymerase II Elongation
Manuel J. Muñoz, M. Soledad Pérez Santangelo, Maria P. Paronetto, Manuel de la Mata, Federico Pelisch, Stéphanie Boireau, Kira Glover-Cutter, Claudia Ben-Dov, Matías Blaustein, Juan J. Lozano, Gregory Bird, David Bentley, Edouard Bertrand and Alberto R. Kornblihtt
Cell 137 (4): 708-720, May 2009.
doi:10.1016/j.cell.2009.03.010
RNA in NYT
An article published Wednesday in the New York TImes highlights a new Letter in Nature that further bolsters the RNA World hypothesis.
Hmm… time it is to dust off the old organic chemistry textbook from college and make sense of phrases like, (from paper): “…intra-adduct attack of the glycolaldehyde-derived hydroxyl group on the cyanamide-derived nitrile carbon…” Indeed.
Keystone Nice
I attended the Keystone Symposia: The Biology of RNA Silencing meeting held in Victoria, British Columbia, Canada April 25-30th. The scientific organizers were Witold Filipowicz (who showcased his vigourous dance moves the last night of the conference), and Erik Sontheimer. I thought the meeting was very good, perhaps a bit better than last year’s. The format emphasis on having a greater number of shorter talks worked well generally, helping retain audience attention, although sometimes the quality of some of the workshop talks dipped a bit below my expectations. Below I will try to provide brief summaries of some of the scientific stories told in Victoria. (Sorry if details seem very disjointed, I’m going from notes far more than memory. And in general, I’m pretty careful taking notes, but mistakes happen, so I apologize if there are any errors.)
Numbers preceding speaker names correspond to abstract numbers.
It may will take me a few many weeks to get all the info up, so check back for updates.
Saturday
Keynote Session
001 Andrew Fire: “Adventures in the Small RNA-ome”
Fire opened the conference with the first keynote session. He started with a brief review of RNAi in C. elegans, noting that administering a pool of small RNAs that corresponds to only a few molecules per cell where they act is sufficient to completely knockdown a target mRNA that may be found at thousands of copies per cell. And that long dsRNAs can end up as small ~25nt RNAs. Of course this is through RdRP, of which C. elegans has 4 putative forms.
RNA Journal Club 5/14/09
Sarah E. Calvoa, David J. Pagliarinia and Vamsi K. Mootha
PNAS 106 (18): 7507-7512, May 2009.
doi: 10.1073/pnas.0810916106
This week’s incisive summary and analysis by Robin Friedman:
Upstream ORFs (uORFs) generally consist of an AUG codon with an in-frame stop codon preceding the end of the canonical coding sequence (CDS). The uORFs therefore can either be entirely upstream of the CDS or overlapping the start of the CDS. uORFs have been shown to decrease CDS expression in many anecdotal cases, although translation of the CDS can still occur by leaky scanning or re-initiation. Early analysis suggested that <10% of vertebrate mRNAs had upstream AUGs, but more recent computational predictions suggested that >40% of vertebrate genes have uORFs. This study is the first to experimentally address the extent of uORF impact on a genome-wide scale.
The authors constructed a 5′ UTR dataset from refgene annotations, finding that 49% of human and 44% of mouse transcripts have at least one uORF. They next examined high-throughput MS/MS datasets for steady-state protein quantification at a genome-wide level. In each of four datasets, genes that have uORFs have lower protein expression than genes with no uORFs, even after normalizing to mRNA expression. uAUG context, the distance from cap to uORF, uORF conservation, and the number of uORFs all affected this difference in protein expression, whereas uORF length and distance from uORF to CDS did not.
While the previous experiments show that uORF-containing genes have lower steady-state protein levels, they do not show a direct effect of uORFs on translation. To test directly whether the uORFs affect translation, the authors created reporters with the 5’UTRs from randomly selected genes containing uORFs fused to luciferase. Compared to a single-nucleotide-mutant that removes the uAUG, the luciferase activity was reduced ~50% in five randomly selected mouse genes, while the mRNA level, assayed by qPCR, was mostly unchanged. For 10 mouse genes with MS/MS and conservation support for functional uORFs, the luciferase reporters showed 50-80% repression at the protein level.
Asking whether the uORFs could be involved in human polymorphism and disease, the authors queried dbSNP and the human gene mutation database for mutations that create or destroy uORFs. There are 509 genes with polymorphic uORFs, and 14 with recorded mutations linked with disease. Five of the polymorphisms were tested by qPCR, and the uORF was found to repress protein levels by 30-60%, while five of the disease-causing uORF mutations were found to repress by 70-100%.
This paper convincingly argues that uORFs are widespread in humans and have a widespread impact on protein expression. Much of this impact is likely conserved and functional. In addition, they provide interesting experimental support for the fact that uORFs typically repress at the translational level as opposed to through NMD and that CDS translation downstream of uORFs likely proceeds from leaky scanning rather than from re-initiation. While the mechanism has not been elucidated on a genome-wide scale, this paper provides an refreshing look at an often-ignored but important contribution to translational control.
RNA Journal Club 5/7/09
Cell-cell contact globally activates microRNA biogenesis
Hun-Way Hwanga, Erik A. Wentzelb and Joshua T. Mendell
PNAS 106 (17): 7016-7021, April 2009.
doi: 10.1073/pnas.0811523106
You'd Prefer An Argonaute 
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