Maize RNA Structures

Status: Published in Genome Research (2023) Funding: San Diego Supercomputer Center, Pittsburgh Supercomputing Center Collaborators: Galen T. Martin, Jeanelle Guardado-Mendez, Aline Muyle, Alexandros Bousios, Brandon S. Gaut

Overview

We discovered novel miRNA-like secondary structures in maize (Zea mays) genes and transposable elements that correlate with small RNA production, DNA methylation patterns, and gene expression levels. This breakthrough reveals previously unknown regulatory mechanisms in one of the world’s most important food crops.

Key Findings

• Diverse patterns of RNA secondary structures exist across genes and transposable elements
• These structures are strongly associated with siRNA production
• RNA structure explains up to 27% of variation in siRNA production across transposable element families
• Structures correlate with epigenetic silencing (DNA methylation)
• Discovered new class of tiny RNAs in maize genes with regulatory potential

Impact

Scientific: First comprehensive demonstration that RNA structure plays a functional role in triggering gene silencing in plants

Agricultural: Provides new targets for crop improvement through epigenetic engineering

Computational: Developed open-source pipelines for RNA structure analysis at genome scale

Media Coverage

• SDSC Press Release: “Supercomputing Simulations in Multiyear Study of Corn to Address Food Insecurity Reveal Surprising Molecular Results”
• ACCESS-CI: “An a-MAIZE-ingly Surprising Discovery”

Publication

Solares, E.A., Martin, G.T., Guardado-Mendez, J., Muyle, A., Bousios, A., & Gaut, B.S. (2023). “Diverse patterns of secondary structure across genes and transposable elements are associated with siRNA production and epigenetic fate.” Genome Research.