Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

REGULATION OF GENE EXPRESSION BY NONCODING RNAs
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nucleotides that
search out target RNA
5′
phosphate
3′ OH (end of RNA)
active site, showing
2 Mg 2+ atoms needed for “slicing”
microRNA
Figure 7–76 Human Argonaute protein
carrying an miRNA. The protein is folded
into four structural domains, each indicated
by a different color. The miRNA is held in an
extended form that is optimal for forming
RNA–RNA base pairs. The active site
of Argonaute that “slices” a target RNA,
when it is extensively base-paired with the
miRNA, is indicated in red. Many Argonaute
proteins (three out of the four human
proteins, for example) lack the catalytic site
and therefore bind target RNAs without
slicing them. (Adapted from C.D. Kuhn
and L. Joshua-Tor, Trends Biochem. Sci.
38:263–271, 2013. With permission from
Cell Press.)
space in the genome when compared with a protein. Indeed, their small size is
one reason that miRNAs were discovered only recently. Although we are only
beginning to appreciate the full impact of miRNAs, it is clear that they represent
an important part of the cell’s equipment for regulating the expression of genes.
We discuss specific examples MBoC6 of miRNAs m7.113/7.77 that have key roles in development in
Chapter 21.
RNA Interference Is Also Used as a Cell Defense Mechanism
Many of the proteins that participate in the miRNA regulatory mechanisms just
described also serve a second function as a defense mechanism: they orchestrate
the degradation of foreign RNA molecules, specifically those that occur in
double-stranded form. Many transposable elements and viruses produce double-stranded
RNA, at least transiently, in their life cycles, and RNA interference
helps to keep these potentially dangerous invaders in check. As we shall see, this
form of RNAi also provides scientists with a powerful experimental technique to
turn off the expression of individual genes.
The presence of double-stranded RNA in the cell triggers RNAi by attracting
a protein complex containing Dicer, the same nuclease that processes miR-
NAs (see Figure 7–75). This protein cleaves the double-stranded RNA into small
fragments (approximately 23 nucleotide pairs) called small interfering RNAs
(siRNAs). These double-stranded siRNAs are then bound by Argonaute and other
components of RISC. As we saw above for miRNAs, one strand of the duplex RNA
is then cleaved by Argonaute and discarded. The single-stranded siRNA molecule
that remains directs RISC back to complementary RNA molecules produced by
the virus or transposable element. Because the match is usually exact, Argonaute
cleaves these molecules, leading to their rapid destruction.
Each time RISC cleaves a new RNA molecule, the RISC is released; thus, as
we saw for miRNAs, a single RNA molecule can act catalytically to destroy many
complementary RNAs. Some organisms employ an additional mechanism that
amplifies the RNAi response even further. In these organisms, RNA-dependent
RNA polymerases use siRNAs as primers to produce additional copies of double-strand
RNAs which are then cleaved into siRNAs. This amplification ensures
that, once initiated, RNA interference can continue even after all the initiating
double-stranded RNA has been degraded or diluted out. For example, it permits
progeny cells to continue carrying out the specific RNA interference that was provoked
in the parent cells.
In some organisms, the RNA interference activity can be spread by the transfer
of RNA fragments from cell to cell. This is particularly important in plants (whose
cells are linked by fine connecting channels, as discussed in Chapter 19), because
it allows an entire plant to become resistant to an RNA virus after only a few of
its cells have been infected. In a broad sense, the RNAi response resembles certain
aspects of the animal immune system; in both, an invading organism elicits a
customized response, and—through amplification of the “attack” molecules—the
host becomes systemically protected.