Biogenesis, turnover, and mode of action of plant microRNAs

Abstract

MicroRNAs (miRNAs) are small RNAs that control gene expression through silencing of target mRNAs. Mature miRNAs are processed from primary miRNA transcripts by the endonuclease activity of the DICER-LIKE1 (DCL1) protein complex. Mechanisms exist that allow the DCL1 complex to precisely excise the miRNA from its precursor. Our understanding of miRNA biogenesis, particularly its intersection with transcription and other aspects of RNA metabolism such as splicing, is still evolving. Mature miRNAs are incorporated into an ARGONAUTE (AGO) effector complex competent for target gene silencing but are also subjected to turnover through a degradation mechanism that is beginning to be understood. The mechanisms of miRNA target silencing in plants are no longer limited to AGO-catalyzed slicing, and the contribution of translational inhibition is increasingly appreciated. Here, we review the mechanisms underlying the biogenesis, turnover, and activities of plant miRNAs.

Figure 1.

Summary of the Major Steps in miRNA Biogenesis and Turnover. Multiple transcription factors (TFs) control the transcription of MIR genes. The formation of the DCL1 complex and its recruitment to pri-miRNA are mediated by protein–protein interactions and structural features of the pri-miRNA. Some proteins may have dual roles in the recruitment of either the DCL1 complex or the spliceosome to pri-miRNA. As described in the text, protein phosphorylation status may affect the DCL1–DDL interaction and the enhancement of DCL1 processing accuracy by HYL1. Predicted protein phosphorylation (indicated by ℗) may affect distinct steps in pri-miRNA processing, but the role of phosphorylation in other steps (question marks) remains unknown. Functional RISC may include additional unknown AGO interacting proteins (dashed outline). Proteins are color coded according to known functions in MIR transcription (pink), splicing (orange), DCL processing (light blue), phospho-regulation (purple), RISC assembly (green), and miRNA stabilization and turnover (red).

Figure 2.

Overview of miRNA-Mediated Gene Silencing. Pri-miRNAs are processed in the nucleus and mature miRNAs are exported to the cytoplasm. miRNAs are incorporated into AGO proteins and mediate posttranscriptional gene silencing through slicing or translational inhibition. The cytoplasmic locations of RISC loading or miRNA target slicing are unknown in plants, but a recent study indicated that translational repression occurs on the ER. P-body components required for translational inhibition play additional but uncharacterized roles in this process, and their relationship to the ER is unknown. AGO import into the nucleus directs transcriptional silencing of target genes. Speculative molecular events, or locations of the events, are indicated by a question mark. Proteins are color coded as in Figure1 with additional classification according to known functions in target mRNA degradation (yellow) and non-AGO proteins implicated in translational repression (dark blue).