01.01.2011 | Gumy, Laura F.; Yeo, Giles S.H.; Tung, Yi-Chun Loraine; Zivraj, Krishna H.; Willis, Dianna; Coppola, Giovanni; Lam, ..., RNA, 2011

mRNAs are transported, localized, and translated in axons of sensory neurons. However, little is known about the full repertoire of transcripts present in embryonic and adult sensory axons and how this pool of mRNAs dynamically changes during development. Here, we used a compartmentalized ...

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01.01.2011 | Erion, Thanh V.; Strobel, Scott A., RNA, 2011

The glycine riboswitch has a tandem dual aptamer configuration, where each aptamer is a separate ligand-binding domain, but the aptamers function together to bind glycine cooperatively. We sought to understand the molecular basis of glycine riboswitch cooperativity by comparing sites of ...

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01.01.2011 | Anhlan, Darisuren; Grundmann, Norbert; Makalowski, Wojciech; Ludwig, Stephan; Scholtissek, Christoph, RNA, 2011

The pandemic of 1918 was caused by an H1N1 influenza A virus, which is a negative strand RNA virus; however, little is known about the nature of its direct ancestral strains. Here we applied a broad genetic and phylogenetic analysis of a wide range of influenza virus genes, in particular the ...

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01.01.2011 | Ameres, Stefan L.; Hung, Jui-Hung; Xu, Jia; Weng, Zhiping; Zamore, Phillip D., RNA, 2011

In flies, 22–23-nucleotide (nt) microRNA duplexes typically contain mismatches and begin with uridine, so they bind Argonaute1 (Ago1), whereas 21-nt siRNA duplexes are perfectly paired and begin with cytidine, promoting their loading into Ago2. A subset of Drosophila endogenous siRNAs—the ...

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01.01.2011 | Auxilien, Sylvie; Rasmussen, Anette; Rose, Simon; Brochier-Armanet, Céline; Husson, Clotilde; Fourmy, Dominique; Gro ..., RNA, 2011

Methyltransferase enzymes that use S-adenosylmethionine as a cofactor to catalyze 5-methyl uridine (m5U) formation in tRNAs and rRNAs are widespread in Bacteria and Eukaryota, but are restricted to the Thermococcales and Nanoarchaeota groups amongst the Archaea. The RNA m5U ...

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01.01.2011 | Schmidt, Marie-Joëlle; West, Steven; Norbury, Chris J., RNA, 2011

Inhibition of eukaryotic DNA replication leads to the rapid suppression of histone synthesis, via 3' uridylation of cytoplasmic histone mRNAs followed by their Lsm1–7-mediated decapping and degradation. Here we show that the human cytoplasmic RNA terminal U-transferase ZCCHC11, recently ...

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01.01.2011 | Sperschneider, Jana; Datta, Amitava; Wise, Michael J., RNA, 2011

Pseudoknots are an essential feature of RNA tertiary structures. Simple H-type pseudoknots have been studied extensively in terms of biological functions, computational prediction, and energy models. Intramolecular kissing hairpins are a more complex and biologically important type of ...

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01.01.2011 | Seehafer, Carsten; Kalweit, Anne; Steger, Gerhard; Gräf, Stefan; Hammann, Christian, RNA, 2011

The hammerhead ribozyme was originally discovered in subviral plant pathogens and was subsequently also found in a few other genomic locations. Using a secondary structure–based descriptor, we have searched publicly accessible sequence databases for new examples of type III hammerhead ...

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01.01.2011 | Pagano, John M.; Clingman, Carina C.; Ryder, Sean P., RNA, 2011

Sequence-specific recognition of nucleic acids by proteins is required for nearly every aspect of gene expression. Quantitative binding experiments are a useful tool to measure the ability of a protein to distinguish between multiple sequences. Here, we describe the use of ...

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01.01.2011 | Kiss, Daniel L.; Andrulis, Erik D., RNA, 2011

Exosome complexes are composed of 10 to 11 subunits and are involved in multiple facets of 3' -> 5' RNA processing and turnover. The current paradigm stipulates that a uniform, stoichiometric core exosome, composed of single copies of each subunit, carries out all RNA metabolic functions in ...

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