Parallel analysis of RNA ends reveals global microRNA-mediated target RNA cleavage in maize

Area of Science:

• Plant molecular biology
• Genomics
• Post-transcriptional gene regulation

Background:

• MicroRNAs (miRNAs) are crucial regulators of gene expression in eukaryotes.
• Previous miRNA target studies in maize were limited, lacking a global perspective.
• Understanding miRNA-target interactions is key to deciphering plant development and stress responses.

Purpose of the Study:

• To conduct a transcriptome-wide identification of miRNA targets in maize (Zea mays L.).
• To analyze the tissue-specific and developmental regulation of miRNA-mediated gene silencing.
• To discover and validate novel miRNA-target interactions, including those in seed germination.

Main Methods:

• Parallel Analysis of RNA Ends (PARE) sequencing was performed on nine different maize tissues across five developmental stages.
• Bioinformatic analysis was used to identify miRNA cleavage sites and predict miRNA targets.
• Experimental validation was employed for selected miRNA-target gene pairs.

Main Results:

• A comprehensive atlas of 246 miRNA targets for 60 maize miRNAs was generated.
• Tissue-preferential cleavage of target transcripts by specific miRNAs was observed.
• Negative-feedback regulation in miRNA biogenesis was identified for MIR159c and MIR169e.
• Several miRNA-target interactions crucial for seed germination were experimentally validated.

Conclusions:

• This study provides a valuable resource for maize miRNA research by establishing a wide and detailed miRNA-target interaction atlas.
• The findings enhance our understanding of post-transcriptional gene regulation in maize.
• The identified regulatory mechanisms offer insights into maize development, particularly seed germination.