MicroRNAs (miRNA) are a class of small non-coding RNAs that involve in regulation of gene expression.
lin-4 was the first discovered miRNA by Ambros and colleagues in C. elegans(Caenorhabditis elegans). After 7 years of the discovery of lin-4, Reinhart et al. reported lin-7( another miRNA in C. elegans).
A unique characteristic of miRNAs is that one miRNA can regulate the expression of several genes, while one gene can be targeted by different miRNAs.
Nomenclature guidelines for miRNA :
1. Respect species-specific gene nomenclature conventions.
- MIR125a and Mir125 are orthologous miRNA genes present in human and mouse.
2. Conveniently, it is used, MIR(for human), Mir(for mouse), mir(for zebrafish). All are italicized and “r” remain in the lower case except in the case of human. “r” represents the gene locus or gene.
- The Italicized form “MIR” (MiR, miR) with a capitalized “R”, is representative for the intermediate transcripts.
- The non-italicized form “MIR” (MIR, MiR) with a capitalized “R”, is representative for the mature microRNAs.
3. In writing the official name for miRNA, the reference to the species is removed. For example,
- The “mmu-” should be removed for the mouse gene “mmu-Mir-125a” and kept only if the database covering multiple species. For not getting confused, the reference to the organism should be clearly stated in the text.
4.The hyphen is removed that separating”Mir” from the number designator. Hyphens are not used in the case of human, mouse, and zebrafish. For example,
- the gene “hsa-MIR-125a” becomes MIR125A,
- “mmu-Mir-125a” becomes “Mir125a”, and
- “dre-mir-125aa” becomes “mir125aa”.
5.Various forms are specified by unambiguous designators. Example, for the mouse –
- The gene “Mir125a” has “pri-MiR125a” as the primary miRNA transcript.
- The miRNA precursor is“pre-MiR125a”.
- The mature form, “MiR125a”.
Hyphenation of the “pri-MiR” and “pre-MiR” are retained in accordance with the common usage of the “pre-mRNA” symbol to refer to a precursor to a messenger RNA.
Guide or mature strand and Passenger or star strand: Two mature product of Mir gene
6. One of the two mature products of a Mir gene was called the “mature strand” or “guide strand”as it is more highly expressed, while the less expressed opposite strand was called the “passenger strand” or “star strand” (miR*). Alternative strands can be differentially expressed in different species, tissues, developmental stages, and pathological states, requiring inversion of the miR/miR* annotation to reflect expression variations if the miR* strand is functionally active. Now, the “miR/miR*” symbolism replaced with the unbiased “5p/3p” strand annotation to indicate the position of the strand in the pre-MiRNA hairpin independently of its expression status in any given dataset. For example, MIR140-5p is the most highly expressed strand in cartilage but MIR140-3p is the most highly expressed miRNA strand in mouse ovaries and testes.
Biogenesis and regulation of miRNA
- In the first step of biogenesis of miRNA the gene is transcribed into large primary transcript called pri-miRNA. The pri-miRNA is 5’ capped and 3’ polyadenylated in structure. The transcription of miRNA is typically mediated by RNA polymerase II, although some of the pre-miRNAs are also generated by the RNA polymerase III.
- Now, the pri-miRNAs are cleaved by a microprocessor complex. This microprocessor complex is composed of the RNA-Binding protein known as DGCR8 and type III RNase Drosha. The cleaved products are approx 85 nucleotide stem-loop structures known as precursor miRNA (Pre-miRNA).
- The Ran/FTP/Exportin 5 complex transport the pre-miRNA from the nucleus to the cytoplasm. In the cytoplasm, the pre-miRNAsare processeds by another RNase III enzyme Dicer into 20-22 nucleotide long miRNA/miRNA * duplex ( * represent the passenger strand and the other complementary strand is called as the guide or mature strand).
- When this duplex unwound, the mature miRNA is incorporated into a protein complex. This protein complex is termed as RNA-induced silencing complex (RISC). The mature miRNA guides RISC to target mRNA.
Commercial miRNA microarray platforms
Gene expression microarray technology is a very powerful high throughput tool capable of monitoring the expression of thousands of genes in an organism simultaneously.