The compendium of Arabidopsis thaliana GLYCINE-RICH RNA-BINDING PROTEIN 8 in vivo targets determined by iCLIP
Abstract RNA-binding proteins impact RNA processing including splicing, translation and RNA decay to dictate the fate of RNAs. Thus, insights into RNA-protein interactions in the cell provide insights into regulatory networks regulating gene expression at the posttranscriptional level. In higher pla...
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Nature Portfolio
2025-08-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-05716-z |
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| author | Katja Meyer Martin Lewinski Tino Köster Dorothee Staiger |
| author_facet | Katja Meyer Martin Lewinski Tino Köster Dorothee Staiger |
| author_sort | Katja Meyer |
| collection | DOAJ |
| description | Abstract RNA-binding proteins impact RNA processing including splicing, translation and RNA decay to dictate the fate of RNAs. Thus, insights into RNA-protein interactions in the cell provide insights into regulatory networks regulating gene expression at the posttranscriptional level. In higher plants, only few RNA-binding proteins have their in vivo targets and binding sites determined, mostly due to technical challenges posed by plant tissue. We previously adapted individual nucleotide-resolution crosslinking and immunoprecipitation that relies on UV-light irradiation to stabilize RNA-protein interactions in the cell to Arabidopsis plants. Here, we profiled the in vivo binding landscape of the glycine-rich RNA-binding protein AtGRP8 by iCLIP. Transgenic plants expressing AtGRP8 fused to GREEN FLUORESCENT PROTEIN under the native promoter were subjected to UV-crosslinking. RNA-protein complexes were immunoprecipitated and bound RNAs were determined by RNA-seq. A bioinformatics pipeline tailor-made for Arabidopsis identified target RNAs, and delineated binding sites and binding motifs for AtGRP8. These data will aid in assembling a compendium of binding sites for plant RNA-binding proteins and contribute to unravel plant posttranscriptional networks. |
| format | Article |
| id | doaj-art-7e3e8d9fc8614480a13068daca2ea0eb |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
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| series | Scientific Data |
| spelling | doaj-art-7e3e8d9fc8614480a13068daca2ea0eb2025-08-20T04:01:47ZengNature PortfolioScientific Data2052-44632025-08-0112111110.1038/s41597-025-05716-zThe compendium of Arabidopsis thaliana GLYCINE-RICH RNA-BINDING PROTEIN 8 in vivo targets determined by iCLIPKatja Meyer0Martin Lewinski1Tino Köster2Dorothee Staiger3RNA Biology and Molecular Biology, Faculty of Biology, Bielefeld UniversityRNA Biology and Molecular Biology, Faculty of Biology, Bielefeld UniversityRNA Biology and Molecular Biology, Faculty of Biology, Bielefeld UniversityRNA Biology and Molecular Biology, Faculty of Biology, Bielefeld UniversityAbstract RNA-binding proteins impact RNA processing including splicing, translation and RNA decay to dictate the fate of RNAs. Thus, insights into RNA-protein interactions in the cell provide insights into regulatory networks regulating gene expression at the posttranscriptional level. In higher plants, only few RNA-binding proteins have their in vivo targets and binding sites determined, mostly due to technical challenges posed by plant tissue. We previously adapted individual nucleotide-resolution crosslinking and immunoprecipitation that relies on UV-light irradiation to stabilize RNA-protein interactions in the cell to Arabidopsis plants. Here, we profiled the in vivo binding landscape of the glycine-rich RNA-binding protein AtGRP8 by iCLIP. Transgenic plants expressing AtGRP8 fused to GREEN FLUORESCENT PROTEIN under the native promoter were subjected to UV-crosslinking. RNA-protein complexes were immunoprecipitated and bound RNAs were determined by RNA-seq. A bioinformatics pipeline tailor-made for Arabidopsis identified target RNAs, and delineated binding sites and binding motifs for AtGRP8. These data will aid in assembling a compendium of binding sites for plant RNA-binding proteins and contribute to unravel plant posttranscriptional networks.https://doi.org/10.1038/s41597-025-05716-z |
| spellingShingle | Katja Meyer Martin Lewinski Tino Köster Dorothee Staiger The compendium of Arabidopsis thaliana GLYCINE-RICH RNA-BINDING PROTEIN 8 in vivo targets determined by iCLIP Scientific Data |
| title | The compendium of Arabidopsis thaliana GLYCINE-RICH RNA-BINDING PROTEIN 8 in vivo targets determined by iCLIP |
| title_full | The compendium of Arabidopsis thaliana GLYCINE-RICH RNA-BINDING PROTEIN 8 in vivo targets determined by iCLIP |
| title_fullStr | The compendium of Arabidopsis thaliana GLYCINE-RICH RNA-BINDING PROTEIN 8 in vivo targets determined by iCLIP |
| title_full_unstemmed | The compendium of Arabidopsis thaliana GLYCINE-RICH RNA-BINDING PROTEIN 8 in vivo targets determined by iCLIP |
| title_short | The compendium of Arabidopsis thaliana GLYCINE-RICH RNA-BINDING PROTEIN 8 in vivo targets determined by iCLIP |
| title_sort | compendium of arabidopsis thaliana glycine rich rna binding protein 8 in vivo targets determined by iclip |
| url | https://doi.org/10.1038/s41597-025-05716-z |
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