Unbiased RNA–protein interaction screen by quantitative proteomics

Abstract

Mass spectrometry (MS)-based quantitative interaction proteomics has successfully elucidated specific protein-protein, DNA-protein, and small molecule-protein interactions. Here, we developed a gelfree, sensitive, and scalable technology that addresses the important area of RNA-protein interactions. Using aptamer-tagged RNA as bait, we captured RNA-interacting proteins from stable isotope labeling by amino acids in cell culture (SILAC)-labeled mammalian cell extracts and analyzed them by high-resolution, quantitative MS. Binders specific to the RNA sequence were distinguished from background by their isotope ratios between bait and control. We demonstrated the approach by retrieving known and novel interaction partners for the HuR interaction motif, H4 stem loop, ''zipcode'' sequence, tRNA, and a bioinformatically-predicted RNA fold in DGCR-8/Pasha mRNA. In all experiments we unambiguously identified known interaction partners by a single affinity purification step. The 5 region of the mRNA of DGCR-8/Pasha, a component of the microprocessor complex, specifically interacts with components of the translational machinery, suggesting that it contains an internal ribosome entry site.quantitative mass spectrometry ͉ ribonucleoprotein ͉ RNA-binding proteins ͉ HuR ͉ internal ribosome entry site R ibonucleic acid (RNA) is increasingly recognized for its diversity of cellular functions ranging from its classical roles as structural component in complexes such as the ribosome and its role as the central intermediate in gene expression to recentlydiscovered, critical roles in gene regulation (1). Analysis of RNA can efficiently be performed by hybridization or sequencing-based methods; however, in the cellular environment RNA is associated with RNA-binding proteins (RBPs) forming functional ribonucleoprotein (RNP) complexes. These proteins are essential to the function of RNPs but have been studied much less.Mass spectrometry (MS)-based proteomics has become a widespread tool for studying complex mixtures of proteins at high sensitivity (2, 3). High-resolution and high-accuracy technologies have recently been introduced at a large scale (4), and entire proteomes can now be quantified (5). Quantitative proteomics has also emerged as a powerful tool for detecting specific binding of proteins to baits by an unbiased proteome-wide screen using peptides and proteins (reviewed in ref. 6) and DNA (7, 8) as baits. These screens have provided candidates that subsequently proved to be of physiological importance in vivo (7, 9, 10). However, application of this technique to detect RBPs has not been reported to our knowledge.In one technology of quantitative proteomics, stable isotope labeling of amino acids in cell culture (SILAC), 2 cell populations are metabolically encoded with either 13 C 6 (heavy) amino acids or 12 C 6 (light) amino acids (11,12). Background proteins occur equally in control and bait eluate, and the SILAC peptide pairs consequently have a 1:1 intensity ratio. Specific binders to the bait have heavy/light ratio si...

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