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Target recognition and binding mechanism

miRNAs often recognize target mRNAs through imperfect base pairing, particularly in the 3’ untranslated region (3’ UTR) of the mRNA. The “seed region” (nucleotides 2-8) at the 5’ end of the miRNA plays a crucial role in target recognition. Due to the imperfect base pairing, a single miRNA can regulate many target genes.

miRNAs generally have near-perfect or perfect complementarity to their target mRNAs, usually within the coding region. This leads to direct cleavage and degradation of the target mRNA. Plant miRNAs often have a one-to-one relationship with their targets.

Biogenesis and processing pathways

The primary miRNA (pri-miRNA) is processed in the nucleus by the Drosha-DGCR8 complex into a pre-miRNA. The pre-miRNA is then exported to the cytoplasm, where it is further processed by the enzyme Dicer to produce the mature miRNA.

Both the processing of pri-miRNAs into mature miRNAs and the loading into RISC take place mainly in the nucleus. The enzyme Dicer-like 1 (DCL1) is responsible for cleaving the pri-miRNA and pre-miRNA in a single-step process.

RISC Composition and Argonaute Proteins

The RISC is typically composed of an Argonaute protein (AGO1 being the most common) and the miRNA. There are multiple AGO proteins with diverse functions.

While AGO1 is the predominant Argonaute protein in plant miRNAs, some plants have additional AGO proteins with specialized roles, such as AGO2 and AGO7.

Function and Location of Target Sites

miRNAs usually target the 3’ UTR of mRNAs, leading to translational repression or, less commonly, mRNA degradation. Rarely, they can target the 5’ UTR or coding regions.

miRNAs predominantly target the coding regions or the 5’ UTRs of mRNAs, which often results in mRNA cleavage.

Length and Structure of Precursor miRNAs

Precursor miRNAs are typically 70-100 nucleotides long and have a characteristic hairpin structure.

Precursor miRNAs tend to be longer, ranging from 70 to 200 nucleotides, and the hairpin structures are often more variable.

Evolutionary Conservation

miRNAs are highly conserved across species, reflecting their critical roles in regulating fundamental biological processes.

While many miRNAs are conserved among closely related plant species, there is generally less conservation at broader taxonomic levels.