Comparative analysis of the Dicer-like gene family reveals loss of miR162 target site in SmDCL1 from Salvia miltiorrhiza.

Fenjuan Shao,Shanfa Lu,Deyou Qiu

doi:10.1038/srep09891

Abstract

DCL1, the core component for miRNA biogenesis, is itself regulated by miR162 in Arabidopsis. MiRNA-mediated feedback regulation of AtDCL1 is important to maintain the proper level of DCL1 transcripts. However, it is unknown whether the miRNA-mediated regulation of DCL1 is conserved among plants. We analyzed the SmDCL gene family in Salvia miltiorrhiza, an emerging model plant for Traditional Chinese Medicine (TCM) studies, using a comprehensive approach integrating genome-wide prediction, molecular cloning, gene expression profiling, and posttranscriptional regulation analysis. A total of five SmDCLs were identified. Comparative analysis of SmDCLs and AtDCLs showed an apparent enlargement of SmDCL introns in S. miltiorrhiza. The absence of miR162 in S. miltiorrhiza and the loss of miR162 target site in SmDCL1 were unexpectedly found. Further analysis showed that the miR162 target site was not present in DCL1 from ancient plants and was gained during plant evolution. The gained miR162 target site might be lost in a few modern plants through nucleotide mutations. Our results provide evidence for the gain and loss of miR162 and its target sites in Dicer-like genes during evolution. The data is useful for understanding the evolution of miRNA-mediated feedback regulation of DCLs in plants.

Highlights

DCL1, the core component for miRNA biogenesis, is itself regulated by miR162 in Arabidopsis
MiRNAs are produced from transcripts with internal stem-loop structures[3], whereas plant small interfering RNAs (siRNAs) are derived from inverted repeat sequences, dsRNAs copied from single-stranded RNAs, over-lapping regions of bidirectional transcripts, or dsRNAs formed by virus replication[4]
DCLs have been identified from various plant species, functional characterization of DCLs is limited to a few plants, such as Arabidopsis and rice[18−20]

Summary

Introduction

DCL1, the core component for miRNA biogenesis, is itself regulated by miR162 in Arabidopsis. MiRNA-mediated feedback regulation of AtDCL1 is important to maintain the proper level of DCL1 transcripts. AtDCL4 functions in the biogenesis of 21 nt phased siRNAs and ta-siRNAs18 It is involved in dicing integrated viruses or transgenes into 21 nt siRNAs, which initiate transgene silencing and virus resistance[16]. OsDCL4, the homolog of AtDCL4, is responsible for the biogenesis of 21 nt siRNAs associated with inverted repeat transgenes, ta-siRNAs and other 21 nt phased siRNAs, and has been found to play a broader role in rice development than AtDCL4 in Arabidopsis[21,22]. Excision of MIR838 precursor leads to the production of truncated, non-functional AtDCL1 transcripts It provides a regulatory feedback mechanism supplementing miR162-directed regulation to maintain the proper level of AtDCL1 mRNA24. MiRNA-mediated negative feedback loops in other plant DCLs remain to be elucidated

Methods

Results

Conclusion