Noncanonical open reading frames from lncRNAs encode functional micropeptides that help shape agronomic traits in...

Area of Science:

• Plant molecular biology
• Genomics
• Functional genomics

Background:

• Long noncoding RNAs (lncRNAs) were traditionally considered non-coding, but recent studies suggest they can encode functional peptides.
• Identifying and detecting functional open reading frames (ORFs) within lncRNAs (lncORFs) in plants presents significant technical challenges.

Purpose of the Study:

• To comprehensively identify and characterize micropeptides encoded by lncORFs in the rice genome.
• To investigate the biological functions and agronomic relevance of these lncORF-derived micropeptides in rice (Oryza sativa).

Main Methods:

• Integrated analysis of 119 ribosome profiling sequencing (Ribo-seq) datasets across diverse rice tissues and developmental stages.
• Validation of identified lncORF micropeptides using 1,188 mass spectrometry datasets and experimental methods.
• Evolutionary, variant-association, and gain/loss-of-function analyses to assess functional impact.

Main Results:

• Identified 8,253 potential lncORFs in the rice genome.
• Confirmed the existence of 776 lncORF micropeptides through mass spectrometry and experimental validation.
• Demonstrated that specific micropeptides regulate grain yield by modulating the number of small vascular bundles.

Conclusions:

• This study expands the functional repertoire of lncRNAs by revealing their capacity to encode micropeptides.
• Identified lncORF micropeptides represent a valuable genetic resource for enhancing rice agronomic traits, particularly grain yield.
• Provides a robust framework for discovering lncORF-derived peptides in other plant species.