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.
Figure 7–58 Negative and positive control of alternative RNA splicing.
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).
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.
Until then, a gene had been defined operationally as a region of the genome that segregates as a single unit during meiosis and gives rise to a definable phenotypic trait, such as a red or a white eye in Drosophila or a round or wrinkled seed in peas. The work on Neurospora showed that most genes correspond to a region of the genome that directs the synthesis of a single enzyme. This led to the hypothesis that one gene encodes one polypeptide chain. The hypothesis proved fruitful for subsequent research; as more was learned about the mechanism of gene expression in the 1960s, a gene became identified as that stretch of DNA that was transcribed into the RNA coding for a single polypeptide chain (or a single structural RNA such as a tRNA or an rRNA molecule). The discovery of split genes and introns in the late 1970s could be readily accommodated by the original definition of a gene, provided that a single polypeptide chain was specified by the RNA transcribed from any one DNA sequence. But it is now clear that many DNA sequences in higher eukaryotic cells can produce a set of distinct (but related) proteins by means of alternative RNA splicing. How, then, is a gene to be defined?
In those relatively rare cases in which a single transcription unit produces two very different eukaryotic proteins, the two proteins are considered to be produced by distinct genes that overlap on the chromosome. It seems unnecessarily complex, however, to consider most of the protein variants produced by alternative RNA splicing as being derived from overlapping genes. A more sensible alternative is to modify the original definition to count a DNA sequence that is transcribed as a single unit and encodes one set of closely related polypeptide chains (protein isoforms) as a single protein-coding gene. This definition also accommodates those DNA sequences that encode protein variants produced by post-transcriptional processes other than RNA splicing, such as transcript cleavage and RNA editing (discussed below).
A Change in the Site of rnA transcript Cleavage and poly-A Addition Can Change the C-terminus of a protein