Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens

Area of Science:

• Plant molecular biology
• Transcriptomics and proteomics
• Gene regulation

Background:

• Alternative splicing (AS) significantly influences eukaryotic cell transcriptome and proteome.
• Understanding AS in different life stages and cell types is crucial for deciphering gene expression complexity.

Purpose of the Study:

• To analyze alternative splicing (AS) in protonemata, gametophores, and protoplasts of Physcomitrella patens.
• To assess the contribution of AS to proteome diversity.
• To investigate the role of long non-coding RNAs (lncRNAs) and hormone treatments in AS regulation.

Main Methods:

• Transcriptome and proteome profiling
• Identification of alternatively spliced genes
• Analysis of lncRNA binding sites
• Hormone treatment experiments (abscisic acid and methyl jasmonic acid)

Main Results:

• 12,043 genes were identified as subject to alternative splicing.
• Alternative splicing has a limited impact on proteome diversity.
• Thousands of complementary binding sites for lncRNAs were found on mRNAs and pre-mRNAs.
• Abscisic acid and methyl jasmonic acid treatments induced isoform-specific responses in serine/arginine-rich (SR) genes.

Conclusions:

• AS contributes minimally to proteome diversity in Physcomitrella patens.
• lncRNAs represent a potential regulatory layer for gene expression and AS.
• Specific plant hormones (ABA and MeJA) differentially regulate AS and SR gene transcription in distinct cell types.