Baek D, Villén J, Shin C, Camargo FD, Gygi SP, Bartel DP.
The impact of microRNAs on protein output.
Nature. 2008 Sep 4;455(7209):64-71.
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MicroRNA and Proteome Change
In this study, Baek et al. used a quantitative proteomics approach (i.e., “conventional” SILAC method) to analyze the proteome changes induced by the overexpression and knockout of several miRNAs. Interestingly, authors happened to choose the “brain”-specific miR-124 (furthermore the most abundant miRNA in the brain) to investigate the effects of miRNA ectopic expression in HeLa cells. Since the data presented in the article were not interpreted from the neuroscience perspective, further analyses of supplementary data might provide some insight to neuroscientists interested in the role of miR-124 in the brain. (None of the top 20 hits appears to be previously linked with Alzheimer disease.)
To complement the overexpression experiments, authors also studied the role of endogenous miRNA by using specific mir gene knockout mice. Since the effects of knockout of endogenous mir gene on proteome were basically the reciprocal of those obtained by the ectopic overexpression, these data suggest that the miRNA overexpression experiments may be physiologically relevant and an easy pilot study from which to get preliminary data.
From a technical point of view, it is of interest to know that TargetScan and PicTar performed the best, among several miRNA target prediction algorithms. This study is an exemplar of collaboration between proteomics lab (Dr. Gygi, the inventor of ICAT method) and microRNA lab (Dr. Bartel).
In a separate study by Selbach (Selbach et al., 2008), authors provided essentially similar data demonstrating that a single miRNA can regulate protein synthesis of hundreds or thousands of genes. The "variant" of the SILAC method described by authors (“Pulsed” SILAC) may be useful to apply to neurons, given the potential limitation of the conventional SILAC method to non-dividing cells (Spellman et al., 2008).
Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N.
Widespread changes in protein synthesis induced by microRNAs.
Nature. 2008 Sep 4;455(7209):58-63.
Spellman DS, Deinhardt K, Darie CC, Chao MV, Neubert TA.
Stable isotopic labeling by amino acids in cultured primary neurons: application to brain-derived neurotrophic factor-dependent phosphotyrosine-associated signaling.
Mol Cell Proteomics. 2008 Jun;7(6):1067-76.