High-throughput sequencing of arabidopsis MicroRNAs: Evidence for frequent birth and death of MIRNA genes

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Abstract

MicroRNAs (miRNAs) are small single-stranded regulatory RNAs which function to suppress gene expression. Many miRNAs in the plant kingdom are ancient and are well conserved, while many are recently evolved. This investigation was undertaken to profile and study the evolution of miRNA of Arabidopsis thaliana. High-throughput sequencing enabled the investigators to profile miRNAs from wild-type and del and hen mutants; DCL proteins are necessary for maturation of most Arabidopsis miRNA precursors while HEN1 methylates the 3′ terminal residue of miRNAs, thereby increasing their stability. In addition, bioinformatics was employed to analyze the miRNA expression profiles including those in leaves infected by Pseudomonas syringae. The sequence-based profiling strategy revealed previously unknown miRNAs and a number of conserved and noncon- served miRNAs were detected. Sixteen new miRNAs were named but only eight were discussed in this article. Using the 5′ RACE assay, a comparison of the conserved and nonconserved miRNA revealed differences in the target genes; conserved miRNAs have targets with fewer functions, whereas nonconserved miRNA have targets wtih diverse functions (Fig. 1). In addition, conserved genes were found at multiple loci, whereas only three of 48 nonconserved miRNA were determined to be members of multigene families (i.e., most belonged to single-gene families). Most nonconserved miRNAs were also unaffected by mutation in DCL1 and HEN1, suggesting that the nonconserved miRNAs are not key components of regulatory networks. Foldback sequence analyses showed that more than 30% of the non- conserved miRNA were derived from specific genes and were formed by duplication events. The authors hypothesized that miRNAs continue to evolve, with some eventually losing their targets and subsequently their function, while others are stabilized with generated sequences that closely resemble the parental origin, and still others acquire new targeting specificities for new genes or new families which offered an evolutionary advantage. © 2008 Data Trace Publishing Company.

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Fahlgren, N., Howell, M., & Kasschau, K. (2008). High-throughput sequencing of arabidopsis MicroRNAs: Evidence for frequent birth and death of MIRNA genes. Chemtracts, 21(6), 220–221. https://doi.org/10.1371/journal.pone.0000219

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