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Updated: Jul 16, 2025
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A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
Published on: January 21, 2020
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Deciphering shared attributes of plant long non-coding RNAs through a comparative computational approach.
Vikash Kumar Yadav1,2, Siddhi Kashinath Jalmi3, Shalini Tiwari4
1School of Biological Sciences and Biotechnology, Goa University, Taleigao Plateau, Goa, 403206, India. vikash.yadav@nipgr.ac.in.
Scientific Reports
|September 12, 2023
Summary
Plant long non-coding RNAs (lncRNAs) show conserved genomic and epigenomic features across species. These lncRNAs, regulated by microRNAs (miRNAs), play crucial roles in plant growth and development.
Area of Science:
- Genomics and Epigenomics
- Plant Molecular Biology
- Non-coding RNA Research
Background:
- Long non-coding RNAs (lncRNAs) are emerging as critical regulators of genome function.
- Understanding lncRNA characteristics is essential for deciphering gene regulation in plants.
Purpose of the Study:
- To characterize the genomic and epigenomic features of lncRNAs in three key plant species: Arabidopsis thaliana, Oryza sativa, and Zea mays.
- To investigate the conservation of lncRNA features and their interactions with microRNAs (miRNAs) and transcription factors across these species.
Main Methods:
- Comparative analysis of 13,599 lncRNAs in A. thaliana, 11,565 in O. sativa, and 32,397 in Z. mays.
- Examination of lncRNA distribution, association with transposable elements, epigenetic marks (H3K9me2, cytosine methylation), and subcellular localization.
- Identification of conserved target mimic sites, potential miRNA targets, and transcription factor binding affinities.
Main Results:
- lncRNAs are distributed across chromosomes, with enrichment of Helitron elements and depletion of terminal inverted repeats in their transcription regions.
- lncRNA transcription regions exhibit weak epigenetic signals, except for H3K9me2 and cytosine methylation.
- Conserved miRNA-lncRNA interactions were identified, with targeted genes involved in diverse biological processes and lncRNAs showing affinity for conserved transcription factors like ERF and BBR-BPC.
Conclusions:
- Plant lncRNAs possess conserved genomic and epigenomic characteristics, suggesting conserved regulatory roles.
- miRNA-lncRNA interactions are a conserved mechanism influencing gene expression and biological processes in plants.
- lncRNAs likely play a significant, conserved role in governing plant growth and development across different species.
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