Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs

Area of Science:

• Plant Molecular Biology
• Transcriptomics
• Gene Regulation

Background:

• Plants exhibit dynamic gene expression changes in response to environmental cues like cold.
• Alternative splicing (AS) and long non-coding RNAs (lncRNAs) play crucial roles in plant stress responses.
• Understanding these regulatory mechanisms is vital for improving plant stress resilience.

Purpose of the Study:

• To investigate the role of lncRNA gene expression and AS in the early response of *Arabidopsis thaliana* to cold stress.
• To identify specific lncRNAs and splicing events involved in cold acclimation and freezing tolerance.

Main Methods:

• Utilized high-resolution RNA-sequencing on a diel time-series of *Arabidopsis thaliana* rosettes under cold stress.
• Analyzed differential expression (DE) and differential alternative splicing (DAS) of lncRNAs.
• Employed experiments with varying temperatures and a high-resolution time-course to assess AS sensitivity.

Main Results:

• Identified 135 lncRNA genes with cold-dependent DE and/or DAS, including natural antisense RNAs, sORF lncRNAs, and miRNA/tasiRNA precursors.
• Observed massive and rapid waves of transcriptional and AS activity in protein-coding genes and lncRNAs.
• Demonstrated that AS of some lncRNAs is highly sensitive to minor temperature changes, indicating tight regulation.
• Found a specific splicing event in *TAS1a* that is cold-inducible and may enhance siRNA production.

Conclusions:

• lncRNAs are significantly involved in the plant's cold stress response through both differential expression and alternative splicing.
• Alternative splicing of lncRNAs, particularly *TAS1a*, represents a sensitive and potentially adaptive regulatory mechanism.
• These findings identify candidate lncRNAs crucial for acclimation and freezing tolerance, offering targets for crop improvement.