Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize

Area of Science:

• Genomics
• Molecular Biology
• Plant Science

Background:

• Circular RNAs (circRNAs) are increasingly recognized for their regulatory roles.
• Transposable elements (TEs) are major drivers of genomic variation in plants like maize.
• The potential link between TEs, circRNAs, and phenotypic variation remains largely unexplored.

Purpose of the Study:

• To investigate the origin and characteristics of circRNAs in maize.
• To determine the role of transposons, particularly LINE1-like elements (LLEs), in maize circRNA formation.
• To explore the association between transposon-derived circRNAs and phenotypic variation in maize.

Main Methods:

• CircRNA sequencing (circRNA-Seq) was performed on B73 maize seedling leaves.
• Bioinformatic analyses were used to identify and characterize circRNAs and their genomic features.
• Statistical methods were employed to assess the enrichment of transposon-related sequences and their correlation with gene expression and phenotypic data.

Main Results:

• 2804 high-confidence maize circRNAs were identified, exhibiting unique genomic features.
• Sequences of LINE1-like elements (LLEs) and their Reverse Complementary Pairs (LLERCPs) were significantly enriched near circRNA loci.
• Increased LLERCPs correlated with altered circRNA accumulation and decreased linear transcript levels, particularly in genes linked to phenotypic variation.

Conclusions:

• Transposons, via LLERCPs, are implicated in the formation of maize circRNAs.
• These circRNAs may play a role in modulating transcriptomic and phenotypic variation in maize.
• The study reveals a novel pathway for transposon-mediated regulation of gene expression and plant traits.