Academic Journal
Systematic identification of post-transcriptional regulatory modules
| العنوان: | Systematic identification of post-transcriptional regulatory modules |
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| المؤلفون: | Matvei Khoroshkin, Andrey Buyan, Martin Dodel, Albertas Navickas, Johnny Yu, Fathima Trejo, Anthony Doty, Rithvik Baratam, Shaopu Zhou, Sean B. Lee, Tanvi Joshi, Kristle Garcia, Benedict Choi, Sohit Miglani, Vishvak Subramanyam, Hailey Modi, Christopher Carpenter, Daniel Markett, M. Ryan Corces, Faraz K. Mardakheh, Ivan V. Kulakovskiy, Hani Goodarzi |
| المصدر: | Nature Communications, Vol 15, Iss 1, Pp 1-21 (2024) |
| بيانات النشر: | Nature Portfolio |
| سنة النشر: | 2024 |
| المجموعة: | Directory of Open Access Journals: DOAJ Articles |
| مصطلحات موضوعية: | Science |
| الوصف: | In our cells, a limited number of RNA binding proteins (RBPs) are responsible for all aspects of RNA metabolism across the entire transcriptome. To accomplish this, RBPs form regulatory units that act on specific target regulons. However, the landscape of RBP combinatorial interactions remains poorly explored. Here, we perform a systematic annotation of RBP combinatorial interactions via multimodal data integration. We build a large-scale map of RBP protein neighborhoods by generating in vivo proximity-dependent biotinylation datasets of 50 human RBPs. In parallel, we use CRISPR interference with single-cell readout to capture transcriptomic changes upon RBP knockdowns. By combining these physical and functional interaction readouts, along with the atlas of RBP mRNA targets from eCLIP assays, we generate an integrated map of functional RBP interactions. We then use this map to match RBPs to their context-specific functions and validate the predicted functions biochemically for four RBPs. This study provides a detailed map of RBP interactions and deconvolves them into distinct regulatory modules with annotated functions and target regulons. This multimodal and integrative framework provides a principled approach for studying post-transcriptional regulatory processes and enriches our understanding of their underlying mechanisms. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| Relation: | https://doi.org/10.1038/s41467-024-52215-7; https://doaj.org/toc/2041-1723; https://doaj.org/article/e0a9c0d9b7a0471c8ee72df7e5f560df |
| DOI: | 10.1038/s41467-024-52215-7 |
| الاتاحة: | https://doi.org/10.1038/s41467-024-52215-7 https://doaj.org/article/e0a9c0d9b7a0471c8ee72df7e5f560df |
| رقم الانضمام: | edsbas.5E9D901F |
| قاعدة البيانات: | BASE |
| DOI: | 10.1038/s41467-024-52215-7 |
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