Abstract
RNA molecules interact with proteins to perform a variety of functions in living cells. The binding partners of many RNAs, in particular the newly discovered class of long noncoding RNAs (lncRNAs), remain largely unknown. RNA antisense purification coupled with mass spectrometry (RAP-MS) is a method that enables the identification of direct and specific protein interaction partners of a specific RNA molecule. Because RAP-MS uses direct RNA–protein cross-linking methods coupled along with highly denaturing purification conditions, RAP-MS provides a short list of high confidence protein interactors.
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Acknowledgments
We thank Christine Surka, Alexander Shishkin, and Jesse Engreitz for their help in developing the RAP-MS method and Parham Peyda, Tony Szempruch, and Ward Walkup IV for their helpful comments on the manuscript. This work was supported by a Caltech Division of Biology and Biological Engineering Fellowship and a National Institute of General Medical Sciences of the National Institutes of Health Pathway to Independence Award (K99GM120494) to C.A.M., as well as the New York Stem Cell Foundation, an NIH Director’s Early Independence Award (DP5OD012190), the Edward Mallinckrodt Foundation, Sontag Foundation, Searle Scholars Program, Pew-Steward Scholars program, and funds from the California Institute of Technology to M.G.
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McHugh, C.A., Guttman, M. (2018). RAP-MS: A Method to Identify Proteins that Interact Directly with a Specific RNA Molecule in Cells. In: Gaspar, I. (eds) RNA Detection. Methods in Molecular Biology, vol 1649. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7213-5_31
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DOI: https://doi.org/10.1007/978-1-4939-7213-5_31
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7212-8
Online ISBN: 978-1-4939-7213-5
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