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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
Published on: August 9, 2019
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A combined sequence and structure based method for discovering enriched motifs in RNA from in vivo binding data
Maya Polishchuk1, Inbal Paz2, Refael Kohen2
1Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel; Vavilov Institute of General Genetics, Russian Academy of Science, Moscow 11933, Russia.
Methods (San Diego, Calif.)
|March 10, 2017
Summary
SMARTIV is a new computational tool that identifies RNA binding protein (RBP) sequence and structure preferences from cellular data. This method enhances understanding of how RBPs bind to RNA targets.
Area of Science:
- Molecular Biology
- Bioinformatics
- Computational Biology
Background:
- RNA binding proteins (RBPs) are crucial regulators of cellular processes.
- RBPs recognize RNA targets through sequence and structural interactions.
- Existing methods like CLIP-seq identify binding sites but lack structural preference data.
Purpose of the Study:
- To develop a computational tool for discovering combined sequence and structure binding motifs of RBPs.
- To integrate sequence, binding scores, and predicted RNA secondary structure from in vivo data.
- To provide a unified and visually intuitive representation of RBP binding preferences.
Main Methods:
- SMARTIV, a novel computational tool, was developed.
- It analyzes in vivo RNA binding data, including target site sequences, binding scores, and predicted RNA secondary structures.
- The tool generates combined sequence and structure binding motifs.
Main Results:
- SMARTIV was tested on CLIP-seq data from various platforms and RBPs.
- The generated motifs were highly consistent with known RBP binding preferences.
- The tool successfully provided additional insights into the structural preferences of RBPs.
Conclusions:
- SMARTIV effectively discovers combined sequence and structure binding motifs from in vivo RBP binding data.
- This tool addresses the challenge of inferring both sequence and structural preferences of RBPs.
- SMARTIV offers a valuable approach for characterizing RBP-RNA interactions and enhancing visual perception of binding motifs.
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