Quantification and transcriptome profiling reveal abundant, dynamic and translatable dephospho-CoA-capped RNAs

Area of Science:

• Molecular Biology
• RNA Biology
• Biochemistry

Background:

• Cellular metabolites are increasingly recognized as noncanonical RNA caps.
• Dephospho-CoA (dpCoA) RNA caps, though discovered early, remain poorly understood due to limited detection methods.

Purpose of the Study:

• To identify a specific enzyme for dpCoA-RNA decapping.
• To develop novel methods for quantifying and profiling dpCoA-RNA.
• To investigate the biological significance and characteristics of dpCoA-RNA.

Main Methods:

• Biochemical and structural analysis to identify Arabidopsis NUDT11 as a dpCoA-RNA decapping enzyme.
• Development of biochemical and transcriptomic assays for dpCoA-RNA quantification.
• Comparative analysis of dpCoA-RNA and m7G-RNA in Arabidopsis.

Main Results:

• Arabidopsis NUDT11 was identified as a specific dpCoA-RNA decapping enzyme.
• dpCoA-RNAs were detected across species and show tissue/condition-specific variations.
• In Arabidopsis, dpCoA-RNAs have unique transcription start sites, respond rapidly to high light, and are abundant (up to 15% of m7G-RNA).
• dpCoA-RNAs are associated with translating ribosomes and can be translated in human cells.

Conclusions:

• A specific decapping enzyme for dpCoA-RNA was identified, enabling new detection and profiling tools.
• dpCoA-RNA is a dynamic RNA cap present across species with potential roles in gene expression regulation.
• This study provides a toolkit for future research into dpCoA-RNA biology.