# Small RNA vs microRNA: Key Differences Explained

## Introduction to Small RNAs and microRNAs

The term "small RNA" describes a heterogeneous collection of non-coding RNA molecules, typically 18–31 nucleotides in length, that function in a wide range of cellular processes including gene regulation, defense against foreign nucleic acids, and maintenance of genome integrity. The category encompasses several distinct classes—microRNAs (miRNAs), small interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), and a growing list of less-characterized species such as tRNA-derived fragments and small nucleolar RNA-derived RNAs. What unites them is their size and their association with Argonaute-family proteins, which serve as the effector platforms for their regulatory functions.

MicroRNAs are a specific, well-defined subset of small RNAs. They are endogenously encoded, processed from longer hairpin-containing precursor transcripts, and loaded into Argonaute proteins to direct post-transcriptional repression of messenger RNAs (mRNAs) through base-pairing interactions, most commonly within the 3′ untranslated region (UTR) of target transcripts. The distinction matters: all microRNAs are small RNAs, but not all small RNAs are microRNAs. This relationship is analogous to the difference between "vertebrates" and "mammals"—one is a broad category, the other a specific lineage within it.

### What Are Small RNAs?

Small RNAs are operationally defined by size fractionation: they are the RNA species that migrate between approximately 18 and 31 nucleotides on a denaturing polyacrylamide gel, distinct from transfer RNAs (tRNAs, ~76 nucleotides) and ribosomal RNAs (rRNAs, 120–4700 nucleotides). Beyond size, they share a common mechanistic theme—sequence-specific guidance of protein complexes to complementary nucleic acid targets.

The major classes differ in their origins and functions:

- **MicroRNAs (miRNAs):** Endogenous, genome-encoded, processed from hairpin precursors, regulate mRNA stability and translation.
- **Small interfering RNAs (siRNAs):** Can be endogenous or exogenous (e.g., viral double-stranded RNA), processed from long double-stranded RNA, direct cleavage of complementary mRNAs.
- **Piwi-interacting RNAs (piRNAs):** 24–31 nucleotides, expressed predominantly in germline cells, associate with Piwi-clade Argonaute proteins, silence [transposable elements](/knowledge/molecular-biology/transposable-element).

Additional classes include [Small Nuclear RNA](/knowledge/molecular-biology/small-nuclear-rna)-derived fragments and [Small RNA Containing Particles](/knowledge/molecular-biology/small-rna-containing-particles), though these are less well understood. The common thread is that small RNAs function as specificity determinants—they provide the sequence information that guides effector complexes to their targets.

### What Are microRNAs?

MicroRNAs are the most intensively studied class of small RNAs. They are encoded in the genome, often within introns of protein-coding genes or in intergenic regions, and are transcribed by RNA polymerase II as long primary transcripts called pri-miRNAs. These transcripts fold into characteristic hairpin structures that are recognized and processed by the Microprocessor complex—comprising the RNase III enzyme Drosha and its cofactor DGCR8—to release a ~70-nucleotide precursor hairpin called pre-miRNA.

The pre-miRNA is exported to the cytoplasm by Exportin-5 in a Ran-GTP-dependent manner, where it is cleaved by the RNase III enzyme Dicer to produce a double-stranded duplex of ~22 nucleotides. One strand (the guide strand) is loaded into an Argonaute protein to form the RNA-induced silencing complex (RISC), while the passenger strand is typically degraded. The mature miRNA then guides RISC to complementary sequences in target mRNAs, leading to translational repression or mRNA destabilization.

The defining features of a microRNA are: (1) endogenous genomic origin, (2) processing through a defined hairpin intermediate, and (3) loading into an Argonaute protein for post-transcriptional regulation. These criteria distinguish miRNAs from other small RNA classes.

## Biogenesis and Processing Pathways

### microRNA Biogenesis

The canonical microRNA biogenesis pathway proceeds through a series of well-defined steps:

1. **Transcription:** The miRNA gene is transcribed by RNA polymerase II into a primary transcript (pri-miRNA) that can be several kilobases long. This transcript contains a local hairpin structure of ~33 base pairs with a terminal loop and flanking single-stranded regions. The pri-miRNA is capped and polyadenylated like a typical mRNA.

2. **Nuclear processing:** The Microprocessor complex—Drosha (an RNase III enzyme) and DGCR8 (a double-stranded RNA-binding protein)—recognizes the junction between the single-stranded flanking regions and the base of the hairpin. Drosha cleaves ~11 base pairs from the base of the stem, releasing a ~65–70 nucleotide hairpin called pre-miRNA. This cleavage defines the 5′ and 3′ ends of the mature miRNA.

3. **Nuclear export:** Exportin-5 recognizes the pre-miRNA in a Ran-GTP-dependent manner and transports it through the nuclear pore complex into the cytoplasm. The pre-miRNA has a characteristic 2-nucleotide 3′ overhang generated by Drosha cleavage, which is essential for Exportin-5 recognition.

4. **Cytoplasmic processing:** Dicer, another RNase III enzyme, recognizes the pre-miRNA and cleaves both strands near the terminal loop, removing the loop and generating a ~22-nucleotide duplex with 2-nucleotide 3′ overhangs on both ends. This duplex contains the mature miRNA guide strand and the passenger strand (miRNA*).

5. **RISC loading:** The duplex is loaded into an Argonaute (AGO) protein. The strand with lower thermodynamic stability at its 5′ end is preferentially retained as the guide strand (the "asymmetric rule"). The passenger strand is unwound and degraded. The mature RISC—containing AGO, the guide miRNA, and accessory proteins such as GW182—is now competent for target recognition.

6. **Target recognition and silencing:** The miRNA guides RISC to complementary sequences in target mRNAs, typically in the 3′ UTR. Nucleotides 2–8 of the miRNA (the "seed region") are the primary determinants of target specificity. Perfect or near-perfect complementarity in the seed region is sufficient for target recognition, though additional pairing at the 3′ end enhances binding affinity.

It is important to note that non-canonical pathways exist. Some miRNAs are generated from introns (mirtrons) without Drosha processing, using the splicing machinery instead. Others bypass Dicer through alternative cleavage mechanisms. However, the canonical pathway accounts for the majority of known miRNAs.

### Other Small RNA Biogenesis Pathways

**siRNA biogenesis** differs fundamentally from miRNA biogenesis. siRNAs are processed from long, perfectly complementary double-stranded RNA (dsRNA). This dsRNA can originate from:

- Exogenous sources: viral replication intermediates, experimentally introduced dsRNA
- Endogenous sources: bidirectional transcription of genomic loci, hairpin transcripts, or RNA-dependent RNA polymerase activity

The dsRNA is cleaved by Dicer into 21–23 nucleotide duplexes with 2-nucleotide 3′ overhangs. Unlike miRNA processing, there is no Drosha-dependent step—Dicer alone processes the long dsRNA into siRNAs. The resulting duplexes are loaded into AGO proteins, and one strand is selected as the guide. Because the dsRNA is perfectly complementary, siRNAs can direct AGO-mediated cleavage of fully complementary target RNAs.

**piRNA biogenesis** is distinct from both miRNA and siRNA pathways. piRNAs are 24–31 nucleotides long, are generated from single-stranded precursors in a Dicer-independent manner, and associate with Piwi-clade Argonaute proteins rather than AGO proteins. The biogenesis involves a "ping-pong" amplification loop: primary piRNAs guide Piwi proteins to cleave transposon transcripts, generating new piRNAs that in turn guide cleavage of complementary transcripts, amplifying the response. piRNAs are essential for silencing transposable elements in germline cells.

The key distinction is that miRNA biogenesis requires both Drosha and Dicer (canonical pathway), siRNA biogenesis requires only Dicer, and piRNA biogenesis requires neither.

## Mechanisms of Gene Silencing

### RISC Loading and Target Recognition

The RNA-induced silencing complex is the central effector of small RNA function. The core component is an Argonaute protein, which contains:

- **PAZ domain:** Binds the 2-nucleotide 3′ overhang of the small RNA duplex
- **MID domain:** Anchors the 5′ phosphate of the guide strand
- **PIWI domain:** Provides the RNase H-like endonuclease activity (slicer activity) in AGO2, the only human AGO with catalytic competence

RISC loading is an ATP-dependent process facilitated by the chaperone machinery (Hsc70/Hsp90). The small RNA duplex is unwound, and the strand with the less stable 5′ end is retained. The guide strand is positioned such that its seed region (nucleotides 2–8) is pre-organized in an A-form helical conformation, ready for base-pairing with target mRNAs.

Target recognition is governed by seed complementarity. For miRNAs, pairing between nucleotides 2–8 of the miRNA and the target mRNA is the primary determinant of specificity. Additional pairing at nucleotides 13–16 can enhance binding, and 3′ supplementary pairing provides further stabilization. For siRNAs, full complementarity across the entire small RNA is typical.

### Translational Repression vs [mRNA Degradation](/knowledge/molecular-biology/mrna-degradation)

The outcome of RISC-target interaction depends on the degree of complementarity:

**Perfect complementarity (siRNA-like):** When the small RNA is fully complementary to its target, AGO2's PIWI domain cleaves the mRNA at a position opposite nucleotides 10–11 of the guide strand. This endonucleolytic cleavage generates mRNA fragments with a 5′ phosphate and 3′ hydroxyl, which are rapidly degraded by exonucleases. This mechanism is the basis of [RNA interference](/blog/guides/rna-interference-a-practical-guide-to-gene-silencing-mechanisms) (RNAi) and is the primary mode of action for siRNAs.

**Partial complementarity (miRNA-like):** Most animal miRNAs have only partial complementarity to their targets, with perfect seed pairing but mismatches elsewhere. In this case, AGO2 does not cleave the mRNA. Instead, the RISC recruits GW182 (TNRC6 in humans), a scaffolding protein that interacts with:

- The CCR4-NOT deadenylase complex, which shortens the poly(A) tail
- The PAN2-PAN3 deadenylase complex
- Decapping factors (DCP1/DCP2)
- The 5′-to-3′ exonuclease XRN1

The result is mRNA deadenylation, decapping, and degradation from the 5′ end. Additionally, GW182 can recruit translational repressors that inhibit cap-dependent translation initiation. The relative contribution of [mRNA degradation](/knowledge/molecular-biology/mrna-degradation) versus translational repression varies by context, but in most experimental systems, mRNA destabilization accounts for the majority of repression.

The distinction between cleavage and non-cleavage outcomes is not absolute. Some miRNAs with extensive complementarity can direct AGO2-mediated cleavage, and some siRNAs with mismatches can repress translation. The degree of complementarity is the primary determinant, but the specific AGO protein and cellular context also contribute.

## Functional Diversity of Small RNAs

### siRNAs and RNA Interference

Small interfering RNAs are the effectors of RNA interference, a conserved mechanism for silencing genes with complementary sequences. The pathway was first described in *Caenorhabditis elegans* by Fire and Mello in 1998, who showed that double-stranded RNA triggers potent and specific gene silencing. Subsequent work demonstrated that dsRNA is processed into siRNAs that guide sequence-specific mRNA cleavage.

The biological functions of siRNAs include:

- **Antiviral defense:** In plants, fungi, and invertebrates, siRNAs derived from viral dsRNA direct cleavage of viral RNAs, limiting viral replication. This is a major antiviral mechanism in plants, where RNAi can spread systemically through plasmodesmata.
- **Transposon silencing:** Endogenous siRNAs (endo-siRNAs) derived from [transposable element](/knowledge/molecular-biology/transposable-element) transcripts can silence these elements in somatic cells, complementing the piRNA pathway in germline cells.
- **Heterochromatin formation:** In fission yeast (*Schizosaccharomyces pombe*), siRNAs guide the RNA-induced transcriptional silencing (RITS) complex to centromeric repeats, promoting histone H3 lysine 9 methylation and heterochromatin assembly.
- **Experimental tool:** Synthetic siRNAs are widely used to knock down gene expression in cultured cells and animal models. The [Small Interfering RNA](/knowledge/molecular-biology/small-interfering-rna) pathway is also the basis for several FDA-approved therapeutics, including patisiran for hereditary transthyretin amyloidosis.

### piRNAs and Genome Stability

Piwi-interacting RNAs are the largest class of small RNAs in mammals, with hundreds of thousands of distinct sequences, yet they are expressed almost exclusively in germline cells. Their primary function is to silence transposable elements, which would otherwise cause genomic instability and infertility.

The piRNA pathway operates through a feed-forward amplification loop:

1. Primary piRNAs are transcribed from piRNA clusters—genomic regions enriched in transposon fragments—and processed in a Dicer-independent manner.
2. Primary piRNAs load into Piwi proteins (PIWIL1, PIWIL2, PIWIL3, PIWIL4 in humans) and guide them to complementary transposon transcripts.
3. Piwi-mediated cleavage of transposon mRNAs generates new piRNAs (secondary piRNAs) with a defined 5′ end.
4. Secondary piRNAs load into a different Piwi protein and target the opposite strand, amplifying the response.

This ping-pong cycle produces a robust defense against transposon mobilization. In addition to post-transcriptional silencing, piRNAs guide Piwi proteins to transposon loci in the nucleus, where they recruit histone methyltransferases to establish repressive chromatin marks (H3K9me3) and DNA methylation.

The functional diversity of small RNAs extends beyond these three classes. [Non Coding RNA](/knowledge/molecular-biology/non-coding-rna) research has revealed additional species, including tRNA-derived fragments that regulate translation under stress conditions and small RNAs derived from [Small Nuclear RNA](/knowledge/molecular-biology/small-nuclear-rna) processing. The field continues to expand as deep sequencing reveals new small RNA species.

## Methods to Study Small RNAs and microRNAs

### High-Throughput Sequencing

Small RNA sequencing (sRNA-seq) is the most comprehensive method for profiling small RNA populations. The workflow involves:

1. **Size selection:** Total RNA is fractionated on a denaturing polyacrylamide gel, and the 18–31 nucleotide fraction is excised and purified. This step is critical—contamination with tRNA fragments or degradation products can confound results.

2. **Adapter ligation:** RNA adapters are ligated to the 5′ and 3′ ends of the small RNAs. This step is biased by RNA structure and sequence; the 3′ adapter ligation is particularly inefficient for RNAs with 2′-O-methyl modifications at their 3′ ends (a feature of plant miRNAs and animal piRNAs).

3. **Reverse transcription and PCR amplification:** The ligated products are reverse transcribed and PCR-amplified. The number of PCR cycles should be minimized (typically 12–15) to reduce amplification bias.

4. **Sequencing and bioinformatics:** The library is sequenced on a high-throughput platform (Illumina is standard). Reads are trimmed of adapters, mapped to the genome, and annotated against known small RNA databases (miRBase for miRNAs). Differential expression analysis identifies changes between conditions.

A key consideration is that sRNA-seq cannot distinguish between mature miRNAs and other small RNAs of similar size. Annotation relies on genomic context and the presence of hairpin precursors. Additionally, sequencing bias can arise from adapter ligation efficiency, GC content, and PCR amplification—all of which should be controlled for in data analysis.

### Quantitative PCR and Northern Blotting

**Quantitative PCR (qPCR)** for small RNAs requires specialized approaches because standard reverse transcription primers (oligo-dT or random hexamers) are too long for 22-nucleotide templates. The most common method is stem-loop RT-qPCR:

1. A stem-loop reverse transcription primer, which has a 6-nucleotide extension complementary to the 3′ end of the target miRNA, is annealed to the miRNA.
2. Reverse transcription extends the primer, generating a cDNA that is longer than the original miRNA.
3. The cDNA is amplified using a miRNA-specific forward primer and a universal reverse primer complementary to the stem-loop sequence.

This method is highly sensitive and specific, capable of detecting as few as 10 copies of a miRNA. However, it requires prior knowledge of the miRNA sequence and cannot discover new miRNAs.

**Northern blotting** is the gold standard for validating small RNA size and expression. The procedure involves:

1. Denaturing polyacrylamide gel electrophoresis (15% acrylamide, 8 M urea) to separate small RNAs by size.
2. Electrotransfer to a nylon membrane.
3. Hybridization with a radiolabeled or digoxigenin-labeled DNA oligonucleotide probe complementary to the target small RNA.
4. Detection by autoradiography or chemiluminescence.

Northern blotting provides information about the size of the detected RNA, which can distinguish mature miRNAs (~22 nt) from precursor forms (~70 nt). However, it requires microgram quantities of RNA and is less sensitive than qPCR or sequencing.

### Bioinformatics Tools

Computational analysis is essential for small RNA research. Key tools include:

- **miRBase:** The primary repository for miRNA sequences and annotations. As of the latest release, it contains over 38,000 hairpin precursors and 48,000 mature miRNAs across 271 species.
- **Target prediction algorithms:** Tools such as TargetScan, miRanda, and RNAhybrid predict miRNA targets based on seed complementarity, evolutionary conservation, and thermodynamic stability. These predictions require experimental validation.
- **sRNA annotation pipelines:** Tools like miRDeep2 and ShortStack identify miRNAs from sequencing data by detecting hairpin structures and processing signatures (2-nucleotide 3′ overhangs, defined 5′ ends).
- **[RNA structure prediction](/knowledge/bioinformatics/rna-structure-prediction-algorithms):** Programs like RNAfold and mfold predict the secondary structure of pri-miRNA transcripts, which is useful for identifying candidate miRNA genes.

A critical caveat: computational predictions are just that—predictions. The false-positive rate for target prediction is high, and experimental validation (e.g., reporter assays, crosslinking immunoprecipitation) is essential.

## Common Misconceptions and Pitfalls

### Overgeneralizing Small RNA Functions

A frequent error among students is assuming that all small RNAs function identically. In reality, the mechanisms differ substantially:

- miRNAs primarily repress translation and destabilize mRNAs through partial complementarity.
- siRNAs direct endonucleolytic cleavage of fully complementary targets.
- piRNAs silence transposons through both post-transcriptional and transcriptional mechanisms.

Additionally, not all small RNAs are involved in gene silencing. Some tRNA-derived fragments regulate translation by displacing translation initiation factors, and some small RNAs function as signaling molecules. The assumption that "small RNA = gene silencer" is an oversimplification.

### Confusing siRNA and microRNA

The distinction between siRNAs and miRNAs is a common source of confusion. The key differences are:

| Feature | microRNA | siRNA |
|---------|----------|-------|
| Origin | Endogenous, genome-encoded | Exogenous (viral, experimental) or endogenous |
| Precursor | Single-stranded hairpin (pri-miRNA) | Long double-stranded RNA |
| Processing enzymes | Drosha and Dicer | Dicer only |
| Target complementarity | Partial (seed region) | Perfect or near-perfect |
| Mechanism | Translational repression, mRNA destabilization | Endonucleolytic cleavage |
| Evolutionary conservation | Highly conserved | Less conserved |
| Number of targets | Hundreds per miRNA | Typically one or few |

The [Microrna siRNA](/knowledge/molecular-biology/microrna-sirna) distinction is fundamental to understanding small RNA biology, yet many students conflate the two because both are ~22 nucleotides and both associate with Argonaute proteins.

### Technical Pitfalls in Detection

Experimental artifacts are common in small RNA research:

- **RNA degradation:** Small RNAs are relatively stable, but the larger precursors are not. Improper handling can generate degradation products that appear as small RNAs in sequencing data. Always assess RNA integrity before proceeding.
- **Adapter contamination:** In sRNA-seq, adapter dimers (ligated adapters without insert) can dominate the library. Size selection after adapter ligation is essential to remove these artifacts.
- **PCR bias:** Over-amplification can skew representation of small RNAs with different GC contents. Minimize PCR cycles and consider using unique molecular identifiers.
- **Genomic DNA contamination:** DNase treatment is essential; genomic DNA can generate spurious small RNA reads.
- **Annotation errors:** Many small RNA sequences map to multiple genomic loci. Misannotation can lead to incorrect conclusions about miRNA expression.

A practical recommendation: always validate key findings with an orthogonal method. If sequencing identifies a differentially expressed miRNA, confirm with stem-loop RT-qPCR. If a target is predicted computationally, validate with a [luciferase reporter assay](/knowledge/diagnostics/molecular/luciferase-reporter-assay).

## Practical Summary and Study Tips

### Key Takeaways

- **Small RNA is a broad category; microRNA is a specific subtype.** All microRNAs are small RNAs, but not all small RNAs are microRNAs.
- **Biogenesis differs:** miRNAs require Drosha and Dicer; siRNAs require only Dicer; piRNAs require neither.
- **Mechanism differs:** miRNAs typically repress translation and destabilize mRNAs; siRNAs direct mRNA cleavage; piRNAs silence transposons.
- **Function differs:** miRNAs regulate gene expression programs; siRNAs defend against viruses and transposons; piRNAs maintain genome integrity in germline cells.
- **Detection requires specialized methods:** Stem-loop RT-qPCR, Northern blotting, and small RNA sequencing each have distinct advantages and limitations.
- **Computational tools are essential but require validation:** Target predictions and miRNA annotations must be confirmed experimentally.

### Exam-Style Questions to Test Yourself

1. **Compare and contrast the biogenesis of microRNAs and siRNAs.** Include the enzymes involved, the precursor structures, and the subcellular locations of each step.

2. **A researcher identifies a 22-nucleotide RNA that is upregulated upon viral infection and is complementary to a viral mRNA.** Is this RNA likely a microRNA or an siRNA? Justify your answer.

3. **Explain why a microRNA with perfect complementarity to its target would be expected to cause mRNA cleavage, while a microRNA with only seed-region complementarity causes translational repression.**

4. **You are asked to design an experiment to identify novel microRNAs in a plant species.** What approach would you take, and what bioinformatics criteria would you use to distinguish genuine miRNAs from other small RNAs?

5. **A student claims that "all small RNAs are microRNAs."** Provide a counterargument using specific examples of non-miRNA small RNAs and their functions.

6. **Describe the role of the seed region in microRNA target recognition.** Why is this region so important, and what are the exceptions to seed-based targeting?

7. **Compare the mechanisms by which piRNAs and siRNAs silence transposable elements.** How do their biogenesis pathways differ, and why are piRNAs particularly important in germline cells?

## Frequently Asked Questions

### Is microRNA a type of small RNA?

Yes. MicroRNAs are a specific class of small RNAs, defined by their endogenous origin, hairpin precursor structure, and processing by Drosha and Dicer. The term "small RNA" encompasses microRNAs, siRNAs, piRNAs, and other classes. All microRNAs are small RNAs, but the reverse is not true.

### What is the main difference between small RNA and microRNA?

The main difference is scope. "Small RNA" is a broad category defined by size (18–31 nucleotides) and includes multiple classes with distinct biogenesis pathways and functions. "MicroRNA" is a specific class within this category, characterized by endogenous genomic origin, processing through a hairpin intermediate, and regulation of mRNA stability and translation. The distinction is analogous to "mammal" versus "human"—one is a general category, the other a specific member.

### Are all small RNAs involved in gene silencing?

No. While many small RNAs do function in gene silencing, this is not universal. Some small RNAs, such as certain tRNA-derived fragments, regulate translation without silencing genes. Others may function in signaling or in the regulation of RNA modifications. Additionally, the mechanisms of silencing differ: miRNAs repress translation and destabilize mRNAs, siRNAs direct mRNA cleavage, and piRNAs silence transposons at both transcriptional and post-transcriptional levels.

### How do microRNAs differ from siRNAs?

MicroRNAs and siRNAs differ in origin, biogenesis, and mechanism. MicroRNAs are endogenously encoded and processed from hairpin precursors by Drosha and Dicer. They typically have partial complementarity to their targets and repress translation or destabilize mRNAs. SiRNAs are processed from long double-stranded RNA by Dicer alone, have perfect complementarity to their targets, and direct endonucleolytic cleavage. SiRNAs can be exogenous (e.g., from viruses) or endogenous (e.g., from transposons).

### What techniques are used to detect microRNAs?

Common techniques include: (1) stem-loop RT-qPCR, which is sensitive and specific but requires known sequences; (2) Northern blotting, which provides size information but requires microgram quantities of RNA; (3) small RNA sequencing, which is comprehensive and can discover new miRNAs but is subject to biases; and (4) [in situ hybridization](/knowledge/molecular-biology/in-situ-hybridization), which provides spatial information. Each method has advantages and limitations, and validation with multiple methods is recommended.

### Can a small RNA be both a microRNA and a siRNA?

No. The classification of a small RNA as a microRNA or siRNA depends on its biogenesis pathway and structural features, not just its sequence. A microRNA is defined by its processing from a hairpin precursor by Drosha and Dicer. An siRNA is defined by its processing from long double-stranded RNA by Dicer alone. A single RNA molecule cannot have both origins. However, a microRNA with perfect complementarity to a target can direct mRNA cleavage, a mechanism typically associated with siRNAs.

### Why do students confuse small RNA and microRNA?

The confusion arises because the terms are often used loosely in the literature and in teaching materials. Additionally, both small RNAs and microRNAs are ~22 nucleotides, associate with Argonaute proteins, and regulate gene expression. The distinction becomes clearer when one focuses on biogenesis: microRNAs have a unique processing pathway involving Drosha and a hairpin intermediate, which distinguishes them from other small RNAs. Understanding the biogenesis pathways is the key to keeping the classes separate.

## Further Reading

- Kathirvel K et al. *Small RNA Sequencing Reveals a Distinct MicroRNA Signature between Glucocorticoid Responder and Glucocorticoid Non-Responder Primary Human Trabecular Meshwork Cells after Dexamethasone Treatment*. Genes. 2023. [PubMed 38002955](https://doi.org/10.3390/genes14112012)
- Zhang XX et al. *Long non-coding RNA small nucleolar RNA host gene 6 aggravates pancreatic cancer through upregulation of far upstream element binding protein 1 by sponging microRNA-26a-5p*. Chinese medical journal. 2020. [PubMed 32433053](https://doi.org/10.1097/CM9.0000000000000758)
- Qiu L et al. *Integrated mRNA and small RNA sequencing reveals microRNA regulatory network associated with internode elongation in sugarcane (Saccharum officinarum L.)*. BMC genomics. 2019. [PubMed 31699032](https://doi.org/10.1186/s12864-019-6201-4)
- Litwiniuk-Kosmala M et al. *Small RNA Deep Sequencing Uncovers microRNAs Associated with Hearing Loss in Vestibular Schwannoma*. The Laryngoscope. 2024. [PubMed 38459949](https://doi.org/10.1002/lary.31385)

## Related Clinical & Scientific Guides

* [MAPK Pathway: Mechanism, Function, and Clinical Relevance](/knowledge/molecular-biology/mapk-pathway)
* [Mammalian Cell Culture Bioreactors: A Practical Guide](/knowledge/molecular-biology/mammalian-cell-culture-bioreactor)
* [Nucleotide Formation: Biosynthesis and Assembly of DNA/RNA Building Blocks](/knowledge/molecular-biology/nucleotide-formation)