Researchers in Madrid report that the Streptococcus pneuomoniae genome is "organized in topology-reacting gene clusters" that respond to DNA supercoiling in Nucleic Acids Research this week. The team writes that down-regulated genomic clusters are "flanked by 11-40 kb AT-rich zones that might have a putative structural function" and suggest that DNA supercoiling "controls gene expression superimposed on other kinds of more specific regulatory mechanisms."
Eric Miska at the University of Cambridge and colleagues report that "miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans." Using the first miR-124 mutant in any organism, the authors found that the microRNA expression "coincides with neuronal morphogeneis," and that its transcriptome contains many targets that are "coexpressed with, and actively repressed by, miR-124." They conclude that miR-124 "contributes to defining cell-type-specific gene activity by repressing a diverse set of co-expressed genes."
A trio of researchers in Germany detail their method for "GOing Bayesian," using model-based gene set analysis approaches. Because "knowledge bases such as the Gene Ontology (GO) contain hundreds or thousands of categories with very high overlap between categories," the authors have developed a method to analyze "all categories at once by embedding them in a Bayesian network, in which gene response is modeled as a function of the activation of biological categories." They use probabilistic inference to identify active categories, and, on simulated data, their approach achieved 95 percent precision in doing so. Further application of their approach to a yeast data set showed that the method "provides high-level, summarized views of core biological processes and correctly eliminates confounding associations," the team says.
Also in Nucleic Acids Research this week, a team of investigators at the University of Vienna in Austria report their application of Genomic SELEX, "a method to identify protein-binding RNAs encoded in the genome," to a search for additional regulatory RNAs in Escherichia coli. They subjected an enriched SELEX pool to deep sequencing, mapped 8,865 sequences to the E. coli genome, and found that "the motif 5'-AAYAAYAA-3' was enriched in the selected RNAs and confers low-nanomolar affinity to Hfq."