We begin our discussion with a group of short RNAs that carry out RNA interference or RNAi. Here, short single-stranded RNAs (20–30 nucleotides) serve as guide RNAs that selectively reorganize and bind—through base-pairing—other RNAs in the cell. When the target is a mature mRNA, the small noncoding RNAs can inhibit its translation or even catalyze its destruction. If the target RNA molecule is in the process of being transcribed, the small noncoding RNA can bind to it and direct the formation of certain types of repressive chromatin on its attached DNA template (Figure 7–74). Three classes of small noncoding RNAs work in this way—microRNAs (miRNAs), small interfering RNAs (siRNAs), and piwi-interacting RNAs (piRNAs)—and we discuss them in turn in the next sections. Although they differ in the way the short pieces of single-stranded RNA are generated, all three types of short RNAs locate their targets through RNA–RNA base-pairing, and they generally cause reductions in gene expression.
Over 1000 different microRNAs (miRNAs) are produced from the human genome, and these appear to regulate at least one-third of all human protein-coding genes. Once made, miRNAs base-pair with specific mRNAs and fine-tune their translation and stability. The miRNA precursors are synthesized by RNA polymerase II and are capped and polyadenylated. They then undergo a special type of processing, after which the miRNA (typically 23 nucleotides in length) is assembled with a set of proteins to form an RNA-induced silencing complex or RISC. Once formed, the RISC seeks out its target mRNAs by searching for complementary nucleotide translational repression formation of heterochromatin cleavage of of target RNA is being transcribed
Figure 7–74 RNA interference in eukaryotes. Single-stranded interfering rnAs are generated from double-stranded rnA. they locate target rnAs through base-pairing and, at this point, several fates are possible, as shown. As described in the text, there are several types of rnA interference; the way the double-stranded rnA is produced and processed and the ultimate fate of the target rnA depends on the particular system.
sequences (Figure 7–75). This search is greatly facilitated by the Argonaute protein, a component of RISC, which holds the 5ʹ region of the miRNA so that it is optimally positioned for base-pairing to another RNA molecule (Figure 7–76). In animals, the extent of base-pairing is typically at least seven nucleotide pairs, and this pairing most often occurs in the 3ʹ UTR of the target mRNA.
Once an mRNA has been bound by an miRNA, several outcomes are possible. If the base-pairing is extensive (which is unusual in humans but common in many plants), the mRNA is cleaved (sliced) by the Argonaute protein, effectively removing the mRNA’s poly-A tail and exposing it to exonucleases (see Figure 7–69). Following cleavage of the mRNA, the RISC with its associated miRNA is released, and it can seek out additional mRNAs (see Figure 7–75). Thus, a single miRNA can act catalytically to destroy many complementary mRNAs. These miRNAs can be thus thought of as guide sequences that bring destructive nucleases into contact with specific mRNAs.
If the base-pairing between the miRNA and the mRNA is less extensive (as observed for most human miRNAs), Argonaute does not slice the mRNA; rather, translation of the mRNA is repressed and the mRNA is shuttled to P-bodies (see Figure 7–73) where, sequestered from ribosomes, it eventually undergoes poly-A tail shortening, decapping, and degradation.