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mRNA Interactome Capture from Plant Protoplasts
Published on: July 28, 2017
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AtCircDB: a tissue-specific database for Arabidopsis circular RNAs.
Jiazhen Ye1, Lin Wang2, Shuzhang Li1
1Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong, China.
Briefings in Bioinformatics
|October 3, 2017
Summary
A new database, AtCircDB, identifies thousands of tissue-specific circular RNAs in Arabidopsis. This resource aids plant circular RNA research and reveals links to alternative splicing and chloroplasts.
Area of Science:
- Plant molecular biology
- Bioinformatics
- Genomics
Background:
- Circular RNAs (circRNAs) are prevalent in eukaryotes but lack a dedicated tissue-specific database for Arabidopsis.
- This absence hinders comprehensive studies of plant circRNAs and their functions.
Purpose of the Study:
- To develop a comprehensive, tissue-specific database for Arabidopsis circular RNAs.
- To systematically identify, store, retrieve, and analyze circRNAs and their interactions in plants.
Main Methods:
- Analyzed 622 Arabidopsis RNA sequencing datasets from 87 studies.
- Identified circRNAs by back-splicing sites and characterized tissue-specific circRNAs.
- Developed a detection score metric and defined super circular RNA regions.
Main Results:
- Characterized 84,685 circRNAs, including 30,648 tissue-specific circRNAs and 3,486 miRNA-circRNA interactions.
- Validated a detection score metric that enhances circRNA detection accuracy.
- Identified super circular RNA regions associated with alternative splicing and chloroplasts.
Conclusions:
- AtCircDB provides a valuable resource for storing, retrieving, and visualizing Arabidopsis circRNAs.
- The database facilitates deeper understanding of circRNA regulatory networks in plants.
- Findings highlight the importance of tissue-specific circRNAs in plant biology.
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