Although it may seem at first counterintuitive, the way a gene is packaged into chromatin can affect how the RNA transcript of that gene is ultimately spliced. Nucleosomes tend to be positioned over exons (which are, on average, close to the length of DNA in a nucleosome), and it has been proposed that these act as “speed bumps,” allowing the proteins responsible for exon definition to assemble on the RNA as it emerges from the polymerase. In addition, changes in chromatin structure are used to alter splicing patterns. There are two ways this can happen. First, because splicing and transcription are coupled, the rate at which RNA polymerase moves along DNA can affect RNA splicing. For example, if polymerase is moving slowly, exon skipping (see Figure 6–30A) is minimized: assembly of the initial spliceosome may be complete before an alternative choice of splice site even emerges from the RNA polymerase. The nucleosomes in condensed chromatin can cause polymerase to pause; the pattern of pauses in turn affects the extent of RNA exposed at any given time to the splicing machinery.
There is a second and more direct way that chromatin structure can affect RNA splicing. Although the details are not yet understood, specific histone modifications attract components of the spliceosome, and, because the chromatin being transcribed is in close association with the nascent RNA, these splicing components can easily be transferred to the emerging RNA. In this way, certain types of histone modifications can affect the final pattern of splicing.
We have seen that the choice of splice sites depends on such features of the premRNA transcript as the strength of the three signals on the RNA (the 5ʹand 3ʹ splice junctions and the branch point) for the splicing machinery, the co-transcriptional assembly of the spliceosome, chromatin structure, and the “bookkeeping” that underlies exon definition. We do not know exactly how accurate splicing normally is because, as we see later, there are several quality control systems that rapidly destroy mRNAs whose splicing goes awry. However, we do know that, compared with other steps in gene expression, splicing is unusually flexible.
Thus, for example, a mutation in a nucleotide sequence critical for splicing of a particular intron does not necessarily prevent splicing of that intron altogether. Instead, the mutation typically creates a new pattern of splicing (Figure 6–33). Most commonly, an exon is simply skipped (Figure 6–33B). In other cases, the mutation causes a cryptic splice junction to be efficiently used (Figure 6–33C). Apparently, the splicing machinery has evolved to pick out the best possible pattern of splice junctions, and if the optimal one is damaged by mutation, it will seek out the next best pattern, and so on. This inherent plasticity in the process of RNA splicing suggests that changes in splicing patterns caused by random mutations have been important in the evolution of genes and organisms. It also means that mutations that affect splicing can be severely detrimental to the organism: in addition to the β thalassemia, example presented in Figure 6–33, aberrant