MicroRNAs (miRNAs) are small, non-coding RNA molecules that play a significant role in regulating gene expression within cells. These tiny molecules, typically 19 to 25 nucleotides in length, do not code for proteins themselves. Instead, they operate at the post-transcriptional level, influencing whether and how much protein is made from a messenger RNA (mRNA) molecule. Understanding the precise structure of miRNAs is fundamental to grasping how they perform their diverse functions in biological processes.
From Gene to Mature MicroRNA
The journey of a microRNA begins in the cell’s nucleus, where miRNA genes are transcribed by RNA polymerase II into a long primary miRNA (pri-miRNA) transcript. This pri-miRNA is characterized by its distinctive hairpin-like structure, which serves as the initial template for miRNA production. These pri-miRNAs can be quite long, often exceeding 1000 nucleotides.
The pri-miRNA then undergoes processing by a complex known as the microprocessor, composed of the Drosha enzyme and its partner DGCR8. This complex cleaves the pri-miRNA, releasing a shorter precursor miRNA (pre-miRNA), typically around 60-100 nucleotides in length, that still retains a hairpin structure. The pre-miRNA is subsequently transported from the nucleus into the cytoplasm by Exportin-5.
In the cytoplasm, the pre-miRNA encounters another enzyme called Dicer. Dicer further processes the pre-miRNA by cleaving the loop of the hairpin, resulting in a short, double-stranded RNA duplex. One strand of this duplex, known as the mature miRNA, is then incorporated into the RNA-induced silencing complex (RISC), while the other strand is degraded.
Key Features of Mature MicroRNA Structure
The mature microRNA molecule, once processed and loaded into the RISC, is a single-stranded RNA. Specific regions within this short strand hold particular functional importance.
The most significant structural feature is the “seed region,” a short sequence of nucleotides located at the 5′ end of the mature miRNA. This region typically comprises 6-8 nucleotides, specifically positions 2 through 8 from the 5′ end. The seed region is highly conserved across species and is essential for recognizing and binding to target messenger RNA (mRNA) molecules.
While the seed region plays a dominant role, the less conserved 3′ region of the mature miRNA also contributes to its overall function. This 3′ end can influence the miRNA’s stability and participate in additional base-pairing interactions with target mRNAs, further refining the binding specificity.
How Structure Dictates Function
The unique structure of the mature miRNA directly enables its ability to regulate gene expression. Once the mature miRNA is formed, it is loaded into the RNA-induced silencing complex (RISC), where it acts as a guide molecule. The Argonaute (AGO) proteins within the RISC complex bind the mature miRNA and orient it for interaction with target mRNAs.
The seed region of the miRNA is particularly important for target recognition. This short sequence precisely base-pairs with complementary sequences, primarily found in the 3′ untranslated region (3′ UTR) of target mRNA molecules. This precise pairing initiates the gene silencing process, although perfect complementarity across the entire miRNA sequence is not always required.
Upon binding, the RISC complex, guided by the miRNA, can lead to either the degradation of the target mRNA or the inhibition of its translation into protein. The exact outcome often depends on the degree of complementarity between the miRNA and its target. For instance, a nearly perfect match can lead to mRNA cleavage, while partial complementarity more commonly results in translational repression or mRNA destabilization.
Variations and Modifications in MicroRNA Structure
MicroRNA structure, while generally consistent, is not entirely static and can exhibit subtle variations or modifications. One common type of structural variation involves “isomiRs,” which are miRNA isoforms that differ slightly from the canonical miRNA sequence in length or sequence. These variations can arise from imprecise cleavage by Drosha and Dicer during biogenesis, exonuclease-mediated shortening, or the addition of non-templated nucleotides.
IsomiRs, particularly those with shifts at their 5′ or 3′ ends, can have altered target specificities or binding affinities compared to their reference miRNAs. Even subtle changes in the seed region of an isomiR can lead to the targeting of entirely different mRNA molecules, thereby expanding the regulatory repertoire of miRNAs.
Beyond length and sequence variations, mature miRNA molecules can also undergo post-transcriptional chemical modifications. These modifications, such as nucleotide substitutions (miRNA editing) or the addition of nucleotides at the 3′ end, can influence miRNA stability, their loading into the RISC complex, or their interactions with target mRNAs.