MicroRNAs: expression, regulation, and biological functions

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).

Function

miRNAs have multiple known functions, and several recent studies indicate their roles may be even more varied than previously thought. Known functions include: regulation of developmental transition between the first and second, and fourth to adult larval stages in C. Elegans; "promotion of cell proliferation, regulation of fat metabolism, and suppression of apoptosis in the fruit fly D. Melanogaster"; and "promotion of haematopoietic differentiation" in the house mouse M. Musculus (He and Hannon). In some plants, miRNAs are necessary for the regulation of leaf morphogenesis, floral-organ identity and flowering time (He and Hannon).

In addition, some proposed functions of miRNAs involve: embryonic eye, tail, neuronal, and muscle development in mice; hematopoiesis of the brain, lung, bone marrow, spleen, and thymus in vertebrates and some mammals; neuronal differentiation in C. Elegans; and anterior and posterior patterning of the hox-mediated development pathway group in vertebrates and insects (Pasquinelli, Hunter and Bracht). Other hypothesized functions include regulation of "viral function and human cancer" (Miska).

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).