In the most recent issue of Genome Biology, Marco Marra and his colleagues use massively parallel sequencing to "characterize an adenocarcinoma of the tongue, before and after treatment" with sunitinib, sorafenib, and sulindac. Marra's team found mutations and amplifications "consistent with therapeutic resistance arising through activation of the MAPK and AKT pathways." They write that their results "provide direct in vivo genomic evidence for mutational evolution within a tumor under drug selection," and suggest that complete genomic characterization may aid in clinical decision-making for rare tumors.
Researchers at Washington University in St. Louis and their colleagues suggest that "multiple distinct small RNAs originated from the same microRNA precursors." Using an Arabidopsis model, the team found 19 miRNA precursors that "can yield multiple distinct miRNA-like RNAs in addition to miRNAs and miRNA*s." In their subsequent examinations of publicly available small-RNA deep-sequencing data for four additional plant species and four animals, the team found that "miRNA-like RNAs exist broadly in eukaryotes." Consequently, the authors suggest that "the pool of miRNAs is larger than was previously recognized, and miRNA-mediated gene regulation may be broader and more complex than previously thought."
Columbia University's Shengdong Ke and Lawrence Chasin show that "intronic motif pairs cooperate across exons to promote pre-mRNA splicing." Ke and Chasin found strongly co-occuring motifs in four intronic regions surrounding human exons, most of which are limited to 100 nucelotides of the exon and are "preferentially associated with weaker exons." The duo writes that "exon-flanking sequence pairs … promote exon inclusion and may play a role in the exon definition step in pre-mRNA splicing."
A trio of investigators at Johns Hopkins Bloomberg School of Public Health this week presents Myrna, "a cloud-computing pipeline for calculating differential gene expression in large RNA-Seq datasets." Ben Langmead et al. demonstrate the applicability of Myrna using publicly available datasets in their paper, published in the most recent issue of Genome Biology.