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| Item Type: | Article |
|---|---|
| Title: | Identification of proteins and miRNAs that specifically bind an mRNA in vivo |
| Creators Name: | Theil, K., Imami, K. and Rajewsky, N. |
| Abstract: | Understanding regulation of an mRNA requires knowledge of its regulators. However, methods for reliable de-novo identification of proteins binding to a particular RNA are scarce and were thus far only successfully applied to abundant noncoding RNAs in cell culture. Here, we present vIPR, an RNA-protein crosslink, RNA pulldown, and shotgun proteomics approach to identify proteins bound to selected mRNAs in C. elegans. Applying vIPR to the germline-specific transcript gld-1 led to enrichment of known and novel interactors. By comparing enrichment upon gld-1 and lin-41 pulldown, we demonstrate that vIPR recovers both common and specific RNA-binding proteins, and we validate DAZ-1 as a specific gld-1 regulator. Finally, combining vIPR with small RNA sequencing, we recover known and biologically important transcript-specific miRNA interactions, and we identify miR-84 as a specific interactor of the gld-1 transcript. We envision that vIPR will provide a platform for investigating RNA in vivo regulation in diverse biological systems. |
| Keywords: | Caenorhabditis elegans Proteins, Messenger RNA, MicroRNAs, Protein Binding, RNA-Binding Proteins, Transcription Factors, Animals, Caenorhabditis elegans |
| Source: | Nature Communications |
| ISSN: | 2041-1723 |
| Publisher: | Nature Publishing Group |
| Volume: | 10 |
| Number: | 1 |
| Page Range: | 4205 |
| Date: | 16 September 2019 |
| Official Publication: | https://doi.org/10.1038/s41467-019-12050-7 |
| PubMed: | View item in PubMed |
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