MicroRNA biogenesis, function, and developmental regulation across species

MicroRNAs (miRNAs) belong to a newly-appreciated and diverse class of small, regulatory, 21-25 nucleotide RNAs (Ke and al). They are endogenous, exist across many species from bacteria to mammals, and perform various regulatory functions related to physiology and development (He and Hannon). Defects in miRNA processing at the embryonic level in mammals are often lethal (Pasquinelli, Hunter and Bracht).

Discovery

The first miRNAs, lin-4 and its opposing phenotype lin-14, were discovered in 1993 through a mutagenesis screening involving post-embryonic development in the roundworm C. Elegans (He and Hannon). C. Elegans go through four larval stages; mutations in lin-4 affect regulatory timing and cause certain "cell-division patterns" from the first larval stage to repeat in later stages (He and Hannon). This operation takes place as a result of "antagonistic genetic interactions" between lin-4 and lin-14.Since then hundreds of miRNAs have been discovered to be involved in processes using "antisense complementarity to inhibit expression of specific mRNAs (He and Hannon; Pasquinelli, Hunter and Bracht). Lin-4 is actually a small temporal RNA (stRNA), found to be a prototype of the abundant and varied miRNAs found across many species from plants to mammals (He and Hannon). It is already known that 2% of "known human genes encode microRNAs" (Miska).

Biogenesis

In vertebrates, several stepwise processes are involved in the biogenesis of miRNA. First, miRNAs are "coded in genomes and formed into hairpin RNAs" (Fang and James). The mature miRNA is then generally formed from "one arm of the precursor hairpin," and released from the primary transcript (priRNA) through "stepwise processing by two ribonuclease-III (RNase III) enzymes -- Drosha and Dicer (He and Hannon). In the second process involved in miRNA biogenesis, the enzyme Argonaute is involved in genetic and biochemical factors. Specifically, the "duplex miRNAs (pre-miRNAs) are transferred to pre-micro-ribonucleoprotein (pre-miRNP), a multi-protein -- RNA complex whose constituents include Argonaute and RNA helicase" (Ke and al). In a third stage, pre-miRNAs are unwound into single strands by cofactors, releasing miRNP. Finally, miRNAs within miRNPs locate their RNA targets (Ke and al).

Identification

Scientists Ke, Liu, Liu, and Liang (2003) have listed the identification markers for miRNAs. To be identified as miRNAs, RNAs must: be single-stranded and between 21 and 25 nucleotides; be "cleaved from one arm of a longer endogenous double-stranded hairpin precursor" by the enzyme Dicer; exactly match genomic regions for encoding double-stranded precursor RNAs; be phylogenetically conserved with their "predicted precursor secondary structures"; be able to be confirmed with their precursors by northern blots; and miRNA precursors must aggregate whenever Dicer is wiped out in its original form (Ke and al).

Role in Gene Expression

miRNAs are uniquely suited for gene regulation, even more so than traditional protein regulators (Ke and al). For example, miRNAs are matched with targets on an "exquisitely specific" level, they can be generated more or less rapidly depending on current requirements due to their tiny size (this feature "may facilitate the precise temporal regulation, especially in developmental transitions via miRNAs"), miRNA biogenesis and deterioration are highly efficient, the numbers of various miRNAs thought to exist and pair with multiple targets via "different base-pairing modes" are astounding, a simple step could potentially create a novel complementary miRNA out of a duplicated fragment of a target gene (in the appropriate context), and miRNAs are uniquely suited to regulate genes via simple steric interference (Ke and al).

miRNAs have the ability to regulate gene expression by interacting with RNA, DNA, and proteins in physiological and developmental pathways at multiple levels. Specific gene-regulating roles involve: cell division; organism physiology; "chromatin remodeling; gene transcription"; RNA processing, location, transport, and stability; "translation efficiency"; protein regulations, and even second center gene regulatory network processes (Ke and al).

Overall, miRNAs, possible complimentary proteins, and their targets are involved in highly sophisticated networks of gene regulation (Fang and James). The variation in functions is vast and still mostly theoretical. This complexity is partly to that fact that even a single miRNA from either an intergenic or intronic region "can bind to and regulate" multiple targets; moreover, various miRNAs can bind and control a single target (Fang and James).