In PLoS One this week, investigators at Helicos BioSciences say that for RNA-seq analysis, "it is essential to understand how technical variation impacts the quality and interpretability of results, how potential errors could be introduced by the protocol, how the source of RNA affects transcript detection, and how all of these variations can impact the conclusions drawn." By running a variety of human RNA samples through fragmentation, fractionation, cDNA synthesis, and single- versus multiple-tag counting protocols, the Helicos team assessed the advantages and disadvantages of RNA-seq versus digital gene expression technologies.
A team led by investigators at Harvard Medical School's Brigham and Women's Hospital presents evidence in PLoS One this week that says elevated CD46 expression in the lungs is protective against emphysema in a former smoker. Using microarrays and qRT-PCR, among other approaches, the team found that "higher expression of CD46 in the lungs of ex-smoker protects them from emphysema and chronic obstructive pulmonary disease by clearing the inflammation impeding the proliferation of CD8+ T cells and necrosis … restraining the complement cascade favors apoptosis over necrosis, protecting them from autoimmunity and chronic inflammation."
Researchers at Japan's RIKEN and elsewhere report the results of their genome-wide association study for osteoporosis susceptibility in which they assessed more than 270,000 SNPs in 1,747 participants. By following its staged association studied with re-sequencing, the team identified an osteoporosis-associated SNP within a previously unknown gene, FONG, on chromosome 2q33.1. The team reports in PLoS One that "FONG is predicted to encode a 147 amino-acid protein with a formiminotransferase domain in its N-terminal and is ubiquitously expressed in various tissues including bone," and suggests that its "findings … give a new insight into osteoporosis etiology and pathogenesis."
Over in PLoS Computational Biology, a trio of researchers at the British Columbia Cancer Agency and the University of British Columbia show that in both human and mouse, the "distributions of transposable elements reveal hazardous zones in mammalian introns." The researchers also report "several factors that likely contribute to whether a particular TE can influence gene transcription," they write, adding that "TEs in extremely close proximity — less than 20 bp — to exons show a strong bias to be near splice-donor sites."