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

MPS-Authors
http://pubman.mpdl.mpg.de/cone/persons/resource/persons78974

Scheibe,  Marion
Mann, Matthias / Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons77831

Butter,  Falk
Mann, Matthias / Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons15941

Tuschl,  Thomas
Research Group of Combinatorical Biochemistry, MPI for biophysical chemistry, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons78356

Mann,  Matthias
Mann, Matthias / Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Max Planck Society;

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9897.full.pdf
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Citation

Scheibe, M., Butter, F., Hafner, M., Tuschl, T., & Mann, M. (2012). Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions. NUCLEIC ACIDS RESEARCH, 40(19), 9897-9902. doi:10.1093/nar/gks746.


Cite as: http://hdl.handle.net/11858/00-001M-0000-000E-776B-1
Abstract
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.