We still have much to learn about CRISPR-based immunity in bacteria and archaebacteria. The mechanism through which viral sequences are first identified and integrated into the host genome is poorly understood, as is the way that the crRNAs find their complementary sequences in double-stranded DNA. Moreover, in different species of bacteria and archaebacteria, crRNAs are processed in different ways, and in some cases, the crRNAs can attack viral RNAs as well as DNAs.
We shall see in the following chapter that bacterial CRISPR systems have already been artificially “moved” into plants and animals, where they have become very powerful experimental tools for manipulating genomes.
Figure 7–78 CRISPR-mediated immunity in bacteria and archaebacteria. After infection by a virus (left panel), a small bit of DnA from the viral genome is inserted into the CriSpr locus. for this to happen, a small fraction of infected cells must survive the initial viral infection. the surviving cells, or more generally their descendants, transcribe the CriSpr locus and process the transcript into crrnAs (middle panel). Upon reinfection with a virus that the population has already been “vaccinated” against, the incoming viral DnA is destroyed by a complementary crrnA (right panel). for a CriSpr system to be effective, the crrnAs must not destroy the CriSpr locus itself, even though the crrnAs are complementary in sequence to it. in many species, in order for crrnAs to attack an invading DnA molecule, there must be additional short nucleotide sequences that are carried by the target molecule. Because these sequences, known as pAMs (protospacer adjacent motifs), lie outside the crrnA sequences, the host CriSpr locus is spared (see figure 8–55).
long noncoding rnAs have Diverse functions in the Cell
In this and the preceding chapters, we have seen that noncoding RNA molecules have many functions in the cell. Yet, as is the case with proteins, there remain many noncoding RNAs whose function is still unknown. Many RNAs of unknown function belong to a group known as long noncoding RNA (lncRNA). These are arbitrarily defined as RNAs longer than 200 nucleotides that do not code for protein. As methods have improved for determining the nucleotide sequences of all the RNA molecules produced by a cell line or tissue, the sheer number of lncRNAs (an estimated 8000 for the human genome, for example) came as a surprise to scientists. Most lncRNAs are transcribed by RNA polymerase II and have 5ʹ caps and poly-A tails, and, in many cases, they are spliced. It has been difficult to annotate lncRNAs because low levels of RNA are now known to be made from 75% of the human genome. Most of these RNAs are thought to result from the background “noise” of transcription and RNA processing. According to this idea, such nonfunctional RNAs provide no fitness advantage or disadvantage to the organism and are a tolerated by-product of the complex patterns of gene expression that need to be produced in multicellular organisms. For these reasons, it is difficult to estimate the number of lncRNAs that are likely to have a function in the cell and to distinguish them from the background transcription.
We have already encountered a few lncRNAs, including the RNA in telomerase (see Figure 5–33), Xist RNA (see Figure 7–52), and an RNA involved in imprinting (see Figure 7–49). Other lncRNAs have been implicated in controlling the enzymatic activity of proteins, inactivating transcription regulators, affecting splicing patterns, and blocking translation of certain mRNAs.