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Published on: July 28, 2017
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Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae
Kyle Palos1, Anna C Nelson Dittrich1, Li'ang Yu1
1The Boyce Thompson Institute, Cornell University, Ithaca, New York, USA.
The Plant Cell
|June 6, 2022
Summary
Researchers identified ~130,000 long intergenic noncoding RNAs (lincRNAs) in four Brassicaceae species using extensive RNA-sequencing data. Functional analyses revealed conserved lincRNAs crucial for germination and seed development.
Area of Science:
- Plant molecular biology
- Transcriptomics
- Genomics
Background:
- Long intergenic noncoding RNAs (lincRNAs) are a significant class of eukaryotic transcripts with largely unknown functions.
- Plant RNA-sequencing data offers a valuable resource for lincRNA identification and comparative analysis.
Purpose of the Study:
- To perform a harmonized identification and annotation of lincRNAs across four Brassicaceae species.
- To enable cross-species functional and genomic comparisons of lincRNAs.
- To prioritize functional lincRNA candidates for further study.
Main Methods:
- Processed over 24 Terabase pairs of RNA-sequencing data from >16,000 experiments.
- Utilized nanopore RNA-seq, transcriptome-wide structural, peptide, and epigenomic data for characterization.
- Employed comparative genomics, transcriptomics, and guilt-by-association analyses for functional prediction.
Main Results:
- Identified approximately 130,000 lincRNAs in Arabidopsis thaliana, Camelina sativa, Brassica rapa, and Eutrema salsugineum.
- Characterized lincRNAs, identifying conserved motifs and sequence/transcriptional conservation.
- Validated the functional importance of specific lincRNAs in germination and seed development through T-DNA insertion mutants.
Conclusions:
- This study provides a comprehensive catalog and annotation of lincRNAs in Brassicaceae.
- Identified conserved lincRNAs with potential roles in plant development and stress response.
- The findings facilitate future functional studies of lincRNAs in this important plant family.
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