TY - JOUR
T1 - The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts
AU - Baltz, Alexander G.
AU - Munschauer, Mathias
AU - Schwanhäusser, Björn
AU - Vasile, Alexandra
AU - Murakawa, Yasuhiro
AU - Schueler, Markus
AU - Youngs, Noah
AU - Penfold-Brown, Duncan
AU - Drew, Kevin
AU - Milek, Miha
AU - Wyler, Emanuel
AU - Bonneau, Richard
AU - Selbach, Matthias
AU - Dieterich, Christoph
AU - Landthaler, Markus
N1 - Funding Information:
We would like to express our gratitude to Nikolaus Rajewsky (MDC) and members of his lab for sharing the PAR-CLIP computational analysis pipeline for this study as well as Claudia Langnick and Mirjam Feldkamp from the Wei Chen lab (MDC) for sequencing. We thank the volunteers participating in the Human Proteome Folding Project on IBM's World Community Grid. As part of the Berlin Institute for Medical Systems Biology at the MDC, the research group of M.L. is funded by the Federal Ministry for Education and Research (BMBF) and the Senate of Berlin, Berlin, Germany. A.B. and M.M. are funded by the MDC/NYU PhD program.
PY - 2012/6/8
Y1 - 2012/6/8
N2 - Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation, and translation. We developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteomics and to display the protein occupancy on mRNA transcripts by next-generation sequencing. Application to a human embryonic kidney cell line identified close to 800 proteins. To our knowledge, nearly one-third were not previously annotated as RNA binding, and about 15% were not predictable by computational methods to interact with RNA. Protein occupancy profiling provides a transcriptome-wide catalog of potential cis-regulatory regions on mammalian mRNAs and showed that large stretches in 3' UTRs can be contacted by the mRNA-bound proteome, with numerous putative binding sites in regions harboring disease-associated nucleotide polymorphisms. Our observations indicate the presence of a large number of mRNA binders with diverse molecular functions participating in combinatorial posttranscriptional gene-expression networks.
AB - Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation, and translation. We developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteomics and to display the protein occupancy on mRNA transcripts by next-generation sequencing. Application to a human embryonic kidney cell line identified close to 800 proteins. To our knowledge, nearly one-third were not previously annotated as RNA binding, and about 15% were not predictable by computational methods to interact with RNA. Protein occupancy profiling provides a transcriptome-wide catalog of potential cis-regulatory regions on mammalian mRNAs and showed that large stretches in 3' UTRs can be contacted by the mRNA-bound proteome, with numerous putative binding sites in regions harboring disease-associated nucleotide polymorphisms. Our observations indicate the presence of a large number of mRNA binders with diverse molecular functions participating in combinatorial posttranscriptional gene-expression networks.
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U2 - 10.1016/j.molcel.2012.05.021
DO - 10.1016/j.molcel.2012.05.021
M3 - Article
C2 - 22681889
AN - SCOPUS:84861997955
SN - 1097-2765
VL - 46
SP - 674
EP - 690
JO - Molecular Cell
JF - Molecular Cell
IS - 5
ER -