Identification of Novel miRNAs and miRNA Dependent Developmental Shifts of Gene Expression in Arabidopsis thaliana

Shuhua Zhan,Lewis Lukens,Timothy Ravasi

doi:10.1371/journal.pone.0010157

Abstract

microRNAs (miRNAs) are small, endogenous RNAs of 20∼25 nucleotides, processed from stem-loop regions of longer RNA precursors. Plant miRNAs act as negative regulators of target mRNAs predominately by slicing target transcripts, and a number of miRNAs play important roles in development. We analyzed a number of published datasets from Arabidopsis thaliana to characterize novel miRNAs, novel miRNA targets, and miRNA-regulated developmental changes in gene expression. These data include microarray profiling data and small RNA (sRNA) deep sequencing data derived from miRNA biogenesis/transport mutants, microarray profiling data of mRNAs in a developmental series, and computational predictions of conserved genomic stem-loop structures. Our conservative analyses identified five novel mature miRNAs and seven miRNA targets, including one novel target gene. Two complementary miRNAs that target distinct mRNAs were encoded by one gene. We found that genes targeted by known miRNAs, and genes up-regulated or down-regulated in miRNA mutant inflorescences, are highly expressed in the wild type inflorescence. In addition, transcripts upregulated within the mutant inflorescences were abundant in wild type leaves and shoot meristems and low in pollen and seed. Downregulated transcripts were abundant in wild type pollen and seed and low in shoot meristems, roots and leaves. Thus, disrupting miRNA function causes the inflorescence transcriptome to resemble the leaf and meristem and to differ from pollen and seed. Applications of our computational approach to other species and the use of more liberal criteria than reported here will further expand the number of identified miRNAs and miRNA targets. Our findings suggest that miRNAs have a global role in promoting vegetative to reproductive transitions in A. thaliana.

Highlights

Plant microRNAs are involved in multiple developmental and physiological processes and negatively regulate gene transcript abundance through post-transcriptional repression of mRNAs, primarily by target cleavage [1]
Differences and similarities of transcriptome changes between mutants were not explained by known miRNA targets, as the number of known miRNA targets shared between two mutants was not correlated with the number of upregulated genes shared between two mutants
Across canonical miRNA biogenesis/transport mutants, the number of misexpressed, known miRNA targets did not correlate with the number of transcripts that changed in abundance

Summary

Introduction

Plant microRNAs (miRNAs) are involved in multiple developmental and physiological processes and negatively regulate gene transcript abundance through post-transcriptional repression of mRNAs, primarily by target cleavage [1]. MiRNAs are generated from endogenous loci that produce transcripts with internal stem loop structures that are processed to 20,25nt small double stranded RNAs. Many proteins of the miRNA biogenesis pathway are known. Pri-miRNAs are converted to stem-loop pre-miRNAs by DICER-LIKE1 (DCL1) [3] which interacts with the double stranded RNA-binding protein HYPONASTIC LEAVES1 (HYL1) [4] and SERRATE (SE) [5]. Hypomorphic dcl mutants have undetectable or very low levels of mature miRNAs [10], and miRNA accumulation is undetectable or very weak in null hen and hyl mutants [11,12]. Some miRNAs accumulate to wild-type levels, others have reduced abundance, and others are not detectable [13]

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Conclusion