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Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions (2012)

Scheibe, M., Butter, F., Hafner, M., Tuschl, T., Mann, M.

Oxford University Press

In: Nucleic Acids Research

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Publication Date: 2012-10-24

Description: Systematic analysis of the RNA-protein interactome requires robust and scalable methods. We here show the combination of two completely orthogonal, generic techniques to identify RNA-protein interactions: PAR-CLIP reveals a collection of RNAs bound to a protein whereas SILAC-based RNA pull-downs identify a group of proteins bound to an RNA. We investigated binding sites for five different proteins (IGF2BP1-3, QKI and PUM2) exhibiting different binding patterns. We report near perfect agreement between the two approaches. Nevertheless, they are non-redundant, and ideally complement each other to map the RNA-protein interaction network.

Keywords: RNA characterisation and manipulation

Print ISSN: 0305-1048

Electronic ISSN: 1362-4962

Topics: Biology

Published by Oxford University Press

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