ArticleRNA (New York, N.Y.)1999
Finding the right RNA: identification of cellular mRNA substrates for RNA-binding proteins.
Article in RNA (New York, N.Y.), 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Role of the RNA-binding protein family in gynecologic cancers.American journal of cancer research · 2023Review
- The iron chaperone and nucleic acid-binding activities of poly(rC)-binding protein 1 are separable and independently essential.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Trans-acting translational regulatory RNA binding proteins.Wiley interdisciplinary reviews. RNA · 2018Review
- KRAS Oncoprotein Expression Is Regulated by a Self-Governing eIF5A-PEAK1 Feed-Forward Regulatory Loop.Cancer research · 2018Article
- Advances in the characterization of RNA-binding proteins.Wiley interdisciplinary reviews. RNA · 2016Review
- The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages.Genome biology · 2015Article
- Genome-wide mapping of cellular protein-RNA interactions enabled by chemical crosslinking.Genomics, proteomics & bioinformatics · 2014Review
- iCLIP: protein-RNA interactions at nucleotide resolution.Methods (San Diego, Calif.) · 2014Article
- Computational Methods for CLIP-seq Data Processing.Bioinformatics and biology insights · 2014Review
- Global protein-RNA interaction mapping at single nucleotide resolution by iCLIP-seq.Methods in molecular biology (Clifton, N.J.) · 2014Article
- Protein-RNA interactions: new genomic technologies and perspectives.Nature reviews. Genetics · 2012Review
- iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution.Journal of visualized experiments : JoVE · 2011Article
- The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Transcript-specific decapping and regulated stability by the human Dcp2 decapping protein.Molecular and cellular biology · 2008Article
- RNA-binding protein RBMS3 is expressed in activated hepatic stellate cells and liver fibrosis and increases expression of transcription factor Prx1.Journal of molecular biology · 2007Article
- Identification of a set of KSRP target transcripts upregulated by PI3K-AKT signaling.BMC molecular biology · 2007Article
- eIF4E is a central node of an RNA regulon that governs cellular proliferation.The Journal of cell biology · 2006Article
- eIF4E promotes nuclear export of cyclin D1 mRNAs via an element in the 3'UTR.The Journal of cell biology · 2005Article
- Identification of mRNA that binds to eukaryotic initiation factor 5A by affinity co-purification and differential display.The Biochemical journal · 2004Article
- Identification of mRNAs associated with alphaCP2-containing RNP complexes.Molecular and cellular biology · 2003Article
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Authors and funding
3 authors.
Funding
Abstract
Defects in RNA-binding proteins have been implicated in human genetic disorders. However, efforts in understanding the functions of these proteins have been hampered by the inability to obtain their mRNA substrates. To identify cognate cellular mRNAs associated with an RNA-binding protein, we devised a strategy termed isolation of specific nucleic acids associated with proteins (SNAAP). The SNAAP technique allows isolation and subsequent identification of these mRNAs. To assess the validity of this approach, we utilized cellular mRNA and protein from K562 cells and alphaCP1, a protein implicated in a-globin mRNA stability, as a model system. Immobilization of an RNA-binding protein with the glutathione-S-transferase (GST) domain enables isolation of mRNA within an mRNP context and the identity of the bound mRNAs is determined by the differential display assay. The specificity of protein-RNA interactions was considerably enhanced when the interactions were carried out in the presence of cellular extract rather than purified components. Two of the mRNAs specifically bound by alphaCP1 were mRNAs encoding the transmembrane receptor protein, TAPA-1, and the mitochondrial cytochrome c oxidase subunit II enzyme, coxII. A specific poly(C)-sensitive complex formed on the TAPA-1 and coxII 3' UTRs consistent with the binding of aCP1. Furthermore, direct binding of purified alphaCP proteins to these 3' UTRs was demonstrated and the binding sites determined. These results support the feasibility of the SNAAP technique and suggest a broad applicability for the approach in identifying mRNA targets for clinically relevant RNA-binding proteins that will provide insights into their possible functions.
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