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

416 Chapter 7: Control of Gene Expression
but very common in flies. Budding yeast has ≈6200 genes, only about 300 of which
are subject to splicing, and nearly all of these have only a single intron. To say that
flies have only 2–3 times as many genes as yeasts greatly underestimates the difference
in complexity of these two genomes.
In some cases, alternative RNA splicing occurs because there is an intron
sequence ambiguity: the standard spliceosome mechanism for removing intron
sequences (discussed in Chapter 6) is unable to distinguish clearly between two
or more alternative pairings of 5ʹ and 3ʹ splice sites, so that different choices are
made by chance on different individual transcripts. Where such constitutive alternative
splicing occurs, several versions of the protein encoded by the gene are
made in all cells in which the gene is expressed.
In many cases, however, alternative RNA splicing is regulated. In the simplest
examples, regulated splicing is used to switch from the production of a nonfunctional
protein to the production of a functional one (or the other way around).
The transposase that catalyzes the transposition of the Drosophila P element,
for example, is produced in a functional form in germ cells and a nonfunctional
form in somatic cells of the fly, allowing the P element to spread throughout the
genome of the fly without causing damage in somatic cells (see Figure 5–61). The
difference in transposon activity has been traced to the presence of an intron
sequence in the transposase RNA that is removed only in germ cells.
In addition to enabling switching from the production of a functional protein
to the production of a nonfunctional one (or vice versa), the regulation of RNA
splicing can generate different versions of a protein in different cell types, according
to the needs of the cell. Tropomyosin, for example, is produced in specialized
forms in different types of cells (see Figure 6–26). Cell-type-specific forms of many
other proteins are produced in the same way.
RNA splicing can be regulated either negatively, by a regulatory molecule that
prevents the splicing machinery from gaining access to a particular splice site
on the RNA, or positively, by a regulatory molecule that helps direct the splicing
machinery to an otherwise overlooked splice site (Figure 7–58).
Because of the plasticity of RNA splicing, the blocking of a “strong” splicing
site will often expose a “weak” site and result in a different pattern of splicing.
Thus, the splicing of a pre-mRNA molecule can be thought of as a delicate balance
between competing splice sites—a balance that can easily be tipped by effects on
splicing of regulatory proteins.
The Definition of a Gene Has Been Modified Since the Discovery
of Alternative RNA Splicing
The discovery that eukaryotic genes usually contain introns and that their coding
sequences can be assembled in more than one way raised new questions about
the definition of a gene. A gene was first clearly defined in molecular terms in
the early 1940s from work on the biochemical genetics of the fungus Neurospora.
(A) NEGATIVE
CONTROL
(B) POSITIVE
CONTROL
pre-mRNA transcript
SPLICING
pre-mRNA transcript
NO SPLICING
mRNA
mRNA
repressor
R
NO SPLICING
activator
A
SPLICING
mRNA
mRNA
Figure 7–58 Negative and positive
control of alternative RNA splicing.
(A) In negative control, a repressor protein
binds to a specific sequence in the premRNA
transcript and blocks access of
the splicing machinery to a splice junction.
This often results in the use of a secondary
splice site, thereby producing an altered
pattern of splicing (see Figure 7–56).
(B) In positive control, the splicing
machinery is unable to remove a particular
intron sequence efficiently without
assistance from an activator protein.
Because RNA is flexible, the nucleotide
sequences that bind these activators can
be located many nucleotide pairs from
the splice junctions they control, and they
are often called splicing enhancers, by
analogy with the transcriptional enhancers
mentioned earlier in this chapter.