Identification and characterization of new structured RNA classes in plants.

Area of Science:

• Plant genomics
• Molecular biology
• RNA biology

Background:

• Alternative splicing diversifies the transcriptome and protein function.
• RNA secondary structures (strucRNAs) can influence splicing in cis.
• Few cis-regulatory strucRNAs are known in plants.

Purpose of the Study:

• To identify cis-regulatory strucRNAs in plant genomes.
• To investigate the role of strucRNAs in alternative splicing and nonsense-mediated decay (NMD).

Main Methods:

• Comparative genomics approach applied to 130 plant genomes.
• Identification and analysis of structured RNA (strucRNA) candidates.
• Experimental validation of selected candidates.

Main Results:

• Identified 16 strucRNA candidates.
• Five candidates predicted to regulate alternative splicing and NMD.
• Two of the five cis-regulatory strucRNAs were experimentally validated.
• Modest levels of covariation observed in predicted strucRNA motifs.

Conclusions:

• Discovered novel cis-regulatory strucRNAs in plants, expanding known mechanisms of RNA regulation.
• Experimental validation supports the role of these strucRNAs in alternative splicing and NMD.
• Comparative genomics has limitations for identifying strucRNAs with low mutation rates; alternative approaches may be needed.