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This Week in PNAS: Apr 16, 2013

Eric Kandel and colleagues from Columbia University and elsewhere outline a method for cataloging sets of RNA transcripts shuttled to the synapse during learning. The enrichment-based approach takes advantage of interactions between these mRNAs and the transport protein kinesin, study authors say. For instance, in experiments on Aplysia sea slugs — a model organism for neuron research owing to its large brain cell size — the researchers unearthed almost 5,700 coding and non-coding sequences in the so-called synaptic transcriptome. "[W]e have succeeded in obtaining a comprehensive collection of RNAs targeted to Aplysia [central nervous system] synapses," they write. "We further show that myosin heavy chain mRNA, a cargo of kinesin, is localized to sensory neuron processes and is required specifically for the induction of long-term facilitation at sensory and motor neuron synapses."

Ohio State University's Carlo Croce and Stefano Volinia, from the University of Ferrara, look at the RNA and methylation profiles coinciding with survival patterns in individuals with a form of breast cancer called invasive ductal carcinoma. The duo brought together microRNA, messenger RNA, and DNA methylation data on hundreds of invasive ductal carcinoma patients assessed through the Cancer Genome Atlas — a search that uncovered 30 mRNAs and seven miRNAs showing promise as a prognostic signature, particularly for individuals with early stage tumors. The investigators subsequently verified the signature's ties to survival using data on almost 2,400 individuals with breast cancer from eight patient cohorts.

Biological interactions can offer important information for interpreting genome-wide screens, Columbia University researchers say in another study in the early, online edition of the Proceedings of the National Academy of Sciences. The team came up with a computational scheme called "cutoff linked to interaction knowledge," or CLIK, to take such interactions into account. In addition to describing the rationale for this approach, the investigators used data from five yeast gene disruption screens to highlight the potential benefits of the CLIK software and biological information it can provide.