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

FROM DNA TO RNA
323
intron
exon ~200
intron
SR
proteins
10–10 5 nucleotides nucleotides 10–10 5 nucleotides SR
proteins
CBC
U1
U2
U1
U2
5′ 3′
hnRNP
Chromatin Structure Affects RNA Splicing
poly-Abinding
proteins
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), MBoC6 and m6.33/6.32 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.
Figure 6–32 The exon definition
hypothesis. According to this idea,
SR proteins bind to each exon sequence
in the pre-mRNA and thereby help to
guide the snRNPs to the proper intron/
exon boundaries. This demarcation of
exons by the SR proteins occurs cotranscriptionally,
beginning at the CBC
(cap-binding complex) at the 5ʹ end.
It has been proposed that a group of
proteins known as the heterogeneous
nuclear ribonucleoproteins (hnRNPs)
may preferentially associate with intron
sequences, further helping the spliceosome
distinguish introns from exons. (Adapted
from R. Reed, Curr. Opin. Cell Biol.
12:340–345, 2000. With permission from
Elsevier.)
RNA Splicing Shows Remarkable Plasticity
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 5ʹ and 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