Proving that great minds think alike, two independent research groups have used similar methods to examine the impact of individual miRNAs on the proteome.
In a Nature report by Steven Gygi, David Bartel, and co-workers at Harvard Medical School, the Whitehead Institute for Biomedical Research, and the Massachusetts Institute of Technology, researchers used a quantitative mass spectrometric method called ‘stable isotope labeling with amino acids in cell culture’ (SILAC) to monitor changes in protein levels in HeLa cells after the separate introduction of three miRNAs (miR-1, miR-124, and miR-181). To investigate the effects of miRNA deficiency, the team analyzed the proteome of mouse neutrophils lacking miR-223. Each miRNA decreased the expression levels of hundreds of proteins, although the change in protein level was usually modest (1.5-2-fold). Target sites of the miRNAs were typically 5-6-nucleotide, complementary ‘seed sequences’ in the 3’ untranslated regions of the mRNAs. Find all the details in Nature, October 2008, 455, 64-71.
In a separate study also published in Nature, Matthias Selbach, Nikolaus Rajewsky, and colleagues at the Max Delbrück Center for Molecular Medicine and the University of Glasgow used a variant of the SILAC method (pulsed SILAC) to analyze changes in levels of proteins in HeLa cells after the separate transfection of five miRNAs (miR-1, miR-16, miR-30a, miR-155, and let-7b) or the knockdown of endogenous let-7b. The results of this study were in agreement with the report by Gygi, Bartel, and colleagues: a single miRNA could fine-tune the expression of hundreds of proteins. Selbach, Rajewsky, and co-workers also investigated miRNA target motifs and mechanisms of protein down-regulation. Read all about this study in Nature, October 2008, 455, 58-63.