Abstract
BACKGROUND: Long non-coding RNAs (lncRNAs) play key roles in regulating plant growth, development, and stress responses. Despite their increasing identification in plant transcriptomes, a systematic characterization of lncRNAs is still lacking, leaving a significant knowledge gap. To address this, we systematically identified and characterized Arabidopsis lncRNAs through integrative analysis of strand-specific RNA sequencing data and multi-omics datasets, revealing their genomic features, regulatory interactions, and evolutionary characteristics. RESULTS: Using a custom pipeline applied to hundreds of stranded RNA-seq datasets, we assembled a comprehensive catalog of 4,772 intergenic and antisense Arabidopsis lncRNAs. In comparing multiple key features of lncRNAs with those of protein-coding genes, we found that intergenic lncRNAs contain high transposable element-derived fragments and display broader TE diversity. Distinct DNA methylation and histone modification signatures further distinguished lncRNAs from protein-coding genes. We additionally uncovered R-loop connections and associations with sRNAs involved in post-transcriptional regulation and RNA-directed DNA methylation, with a minor subset classified as Pol V–transcribed. Of note, our results revealed lncRNAs mediating stress-responsive cis interactions and others linked to trait-associated loci. Probing further, an experimental evidence resource confirmed small peptide production from multiple lncRNA loci. Extending our investigation, comparative analyses across Brassicaceae species revealed syntenic lncRNAs enriched for shared sequence motifs despite substantial sequence divergence. CONCLUSIONS: This study provides a valuable and extensively annotated catalog of Arabidopsis lncRNAs, revealing their diverse genomic features, regulatory interactions, and evolutionary characteristics. Altogether, our work advocates for multi-omics integrative analysis as a potent strategy to efficiently enhance lncRNA annotation, providing insights into functionality and addressing annotation limitations. Our comprehensive bioinformatic analyses of Arabidopsis lncRNAs pave the way for future functional characterization of these transcripts.
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Claims 8
Claim · model-written summary
The pipeline assembled 4,772 intergenic and antisense Arabidopsis lncRNAs.
- Taxon
- Arabidopsis
Arabidopsise0 - Gene
- lncRNAse0
- Outcome
- cataloge0
- Value
- 4,772e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“we assembled a comprehensive catalog of 4,772 intergenic and antisense Arabidopsis lncRNAs”
Claim · model-written summary
Intergenic lncRNAs had high transposable element-derived fragments and broader TE diversity.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Gene
- intergenic lncRNAse0
- Outcome
- high transposable element-derived fragments and display broader TE diversitye0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“intergenic lncRNAs contain high transposable element-derived fragments and display broader TE diversity”
e1“Arabidopsis thaliana”
Claim · model-written summary
DNA methylation signatures distinguished lncRNAs from protein-coding genes.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Gene
- lncRNAse0
- Outcome
- DNA methylatione0
- Comparator
- protein-coding genese0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Distinct DNA methylation and histone modification signatures further distinguished lncRNAs from protein-coding genes”
e1“Arabidopsis thaliana”
Claim · model-written summary
Histone modification signatures distinguished lncRNAs from protein-coding genes.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Gene
- lncRNAse0
- Outcome
- histone modification signaturese0
- Comparator
- protein-coding genese0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Distinct DNA methylation and histone modification signatures further distinguished lncRNAs from protein-coding genes”
e1“Arabidopsis thaliana”
Claim · model-written summary
Analysis uncovered R-loop connections and associations with sRNAs involved in post-transcriptional regulation and RNA-directed DNA methylation.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Gene
- sRNAse0
- Outcome
- R-loop connections and associationse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We additionally uncovered R-loop connections and associations with sRNAs involved in post-transcriptional regulation and RNA-directed DNA methylation”
e1“Arabidopsis thaliana”
Claim · model-written summary
Some lncRNAs mediated stress-responsive cis interactions.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Gene
- lncRNAse0
- Outcome
- stress-responsive cis interactionse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“lncRNAs mediating stress-responsive cis interactions”
e1“Arabidopsis thaliana”
Claim · model-written summary
Experimental evidence confirmed small peptide production from multiple lncRNA loci.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae1
- Gene
- lncRNA locie0
- Outcome
- small peptide productione0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“an experimental evidence resource confirmed small peptide production from multiple lncRNA loci”
e1“Arabidopsis thaliana”
Claim · model-written summary
Syntenic lncRNAs across Brassicaceae were enriched for shared sequence motifs despite sequence divergence.
Verbatim
e0“comparative analyses across Brassicaceae species revealed syntenic lncRNAs enriched for shared sequence motifs despite substantial sequence divergence”