RNAi-directed heterochromatin formation is an important cell defense mechanism that limits the spread of transposable elements in genomes by maintaining their DNA sequences in a transcriptionally silent form. However, this same mechanism is also used in some normal processes in the cell. For example, in many organisms, the RNA interference machinery maintains the heterochromatin formed around centromeres. Centromeric DNA sequences are transcribed in both directions, producing complementary RNA transcripts that can base-pair to form double-stranded RNA. This double-stranded RNA triggers the RNA
Figure 7–77 RNA interference directed by siRNAs. in many organisms, double-stranded rnA can trigger both the destruction of complementary mrnAs (left) and transcriptional silencing (right). the change in chromatin structure induced by the bound ritS (rnAinduced transcriptional silencing) complex resembles that in figure 7–45.
interference pathway and stimulates formation of the heterochromatin that surrounds centromeres, which is necessary for the centromeres to segregate chromosomes accurately during mitosis.
pirnAs protect the Germ line from transposable elements
A third system of RNA interference relies on piRNAs (piwi-interacting RNAs, named for Piwi, a class of proteins related to Argonaute). piRNAs are made specifically in the germ line, where they block the movement of transposable elements. Found in many organisms, including humans, genes coding for piRNAs consist largely of sequence fragments of transposable elements. These clusters of fragments are transcribed and broken up into short, single-stranded piRNAs. The processing differs from that for miRNAs and siRNAs (for one thing, the Dicer enzyme is not involved), and the resulting piRNAs are slightly longer than miRNAs and siRNAs; moreover, they are complexed with Piwi rather than Argonaute proteins. Once formed, the piRNAs seek out RNA targets by base-pairing and, much like siRNAs, transcriptionally silence intact transposon genes and destroy any RNA (including mRNAs) produced by them.
Many mysteries surround piRNAs. Over a million piRNA species are coded in the genomes of many mammals and expressed in the testes, yet only a small fraction seem to be directed against the transposons present in those genomes. Are the piRNAs remnants of past invaders? Do they cover so much “sequence space” that they are broadly protective for any foreign DNA? Another curious feature of piRNAs is that many of them (particularly if base-pairing does not have to be perfect) should, in principle, attack the normal mRNAs made by the organism, yet they do not. It has been proposed that these large numbers of piRNAs may form a system to distinguish “self” RNAs from “foreign” RNAs and attack only the latter. If this is the case, there must be a special way for the cell to spare its own RNAs. One idea is that RNAs produced in the previous generation of an organism are somehow registered and set aside from piRNA attack in subsequent generations. Whether or not this mechanism truly exists, and, if so, how it might work, are questions that demonstrate our incomplete understanding of the full implications of RNA interference.