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This Week in Nucleic Acids Research: Aug 18, 2010

In an advance, online publication of Nucleic Acids Research this week, an international research team describes a novel role for miR-382, which they've uncovered using miRNA-target pairs in human renal epithelial cells treated with transforming growth factor β1. "Knockdown of miR-382, which was upregulated by TGFβ1, attenuated TGFβ1-induced loss of the epithelial marker E-cadherin," while "knockdown of miR-382 attenuated TGFβ1-induced downregulation of SOD2," the authors write. SOD2 overexpression "ameliorated TGFβ1-induced loss of the epithelial marker," the authors also found.

In another paper published online in advance, an international research team describes "a network of conserved co-occurring motifs for the regulation of alternative splicing." Specifically, by using comparative analysis of mammalian genome alignments, the team found "11 conserved sequence motifs that might be involved in the regulation of alternative splicing." The authors suggest that their "results indicate that even more alternative splicing events will be found with the progress of large-scale and high-throughput analyses for various tissue samples and developmental stages."

Researchers at the Open University of Israel, the Weizmann Institute of Science, and the Broad Institute this week report a method for the identification of rare alleles and their carriers using "compressed se(que)nsing," or sequencing based on a compressed sensing approach. Noam Shental et al. "show via computer simulations that it enables the recovery of rare alleles and their carriers in larger groups than were possible before. ... For example, when targeting a small enough genomic region (100 bp) and using only 10 sequencing lanes and 10 distinct barcodes per lane, one recovers the identity of four rare allele carriers out of a population of over 4,000 individuals."

And in the current issue of Nucleic Acids Research, investigators at Stanford University and the University of Iowa present SpliceMap, a tool to detect splice junctions from RNA-seq data. SpliceMap, the authors write, can handle long reads, exploits paired-read information for enhanced accuracy, and "does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions." In their paper, the authors applied SpliceMap to analyze 23 million paired 50-nt reads from human brain tissue, and show that, when "compared to current methods, SpliceMap can achieve 12 percent higher sensitivity without sacrificing specificity." Study co-author Wing Wong recently spoke with our sister publication Genome Technology about SpliceMap.