A Genome-Wide Characterization of MicroRNA Genes in Maize

Michael D Mcmullen,Katherine Guill,Zhijie Liu,Christopher A Maher,Lifang Zhang,Sunita Kumari,Joshua C Stein,Jer-Ming Chia,Doreen Ware,Apurva Narechania

doi:10.1371/journal.pgen.1000716

Abstract

MicroRNAs (miRNAs) are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR–RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with ∼35% of ancestral sites retained as duplicate homoeologous miRNA genes. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes.

Highlights

The last decade has witnessed remarkable progress in our knowledge of the biogenesis and activity of diverse classes of small non-coding RNAs
MicroRNAs are non-coding RNAs that regulate gene expression post-transcriptionally and play roles in diverse pathways including those acting on development and responses to stress
The structures of unprocessed primary miRNA transcripts were determined by 59 RACE and 39

Summary

Introduction

The last decade has witnessed remarkable progress in our knowledge of the biogenesis and activity of diverse classes of small non-coding RNAs (sRNA). While the majority of plant sRNAs are transcribed from siRNA genes residing in repetitive and transposon-rich regions, and regulate chromatin silencing [4], a great deal of interest has been placed on miRNAs due to their ability to post-transcriptionally regulate gene expression [5] This is exemplified by the critical regulatory behavior of miRNAs at key positions in a variety of pathways, such as root [6,7], shoot [8], leaf [9,10,11] and flower [12,13] development and cell fate [14,15].

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