Alternative Splicing under Cold Stress in Paper Mulberry

Area of Science:

• Plant molecular biology
• Genomics
• Stress physiology

Background:

• Paper mulberry (Broussonetia papyrifera) is a widely cultivated woody plant.
• Understanding cold adaptation mechanisms in plants is crucial for agriculture and ecology.
• Alternative splicing (AS) is a key regulatory mechanism in gene expression.

Purpose of the Study:

• To investigate the role of alternative splicing (AS) in paper mulberry's response to cold stress.
• To identify genes and pathways affected by cold-induced AS.
• To explore the regulatory mechanisms of AS under cold conditions.

Main Methods:

• Cold treatment of paper mulberry seedlings.
• RNA sequencing to identify alternative splicing events.
• Bioinformatic analysis to detect differential AS and gene expression.
• Analysis of splicing factors and DNA methylation patterns.

Main Results:

• A substantial number of alternative splicing (AS) events were detected under cold treatment, with alternative 3' splice site (A3) being most frequent.
• Differentially spliced genes were enriched in starch and sucrose metabolism and circadian rhythm pathways.
• A significant proportion of differentially spliced genes also showed differential expression, indicating coordinated regulation.
• 41 serine/arginine-rich (SR) splicing factors were identified, with many showing differential expression or AS.
• Genes with AS exhibited higher DNA methylation levels under cold stress compared to non-AS genes.

Conclusions:

• Alternative splicing plays a significant role in paper mulberry's cold acclimation.
• Coordinated regulation of AS and gene expression is crucial for cold stress adaptation.
• DNA methylation may be involved in regulating AS under cold stress.
• This study provides insights into the molecular mechanisms of plant cold tolerance.