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The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [RNA-seq]

ABSTRACT: 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. Close to one third of these proteins, were neither previously annotated nor could be functionally predicted to bind 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 unexpected mRNA-binders with novel molecular functions participating in combinatorial post-transcriptional gene-expression networks.

ORGANISM(S): Homo sapiens

PROVIDER: GSE38356 | GEO | 2012/06/01

SECONDARY ACCESSION(S): PRJNA167851

REPOSITORIES: GEO

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The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [protein occupancy profiling]

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