So far my understanding of alternative splicing is as follows:
Let A, B, C, ... stand for genes of a cell's genome. When a gene is transcribed to pre-mRNA, it will contain exons and introns:
- pre-mRNA for gene A: Exon1 | Intron1 | Exon2 | ... ... | Exon $n_a$
- pre-mRNA for gene B: Exon1 | Intron1 | Exon2 | ... ... | Exon $n_b$
- pre-mRNA for gene C: ...
A spliceosome will then come and cut introns as well as some of the exons out. Which exons to splice is controlled by the splicing factors in a process known as the alternative splicing. Splicing factors are proteins that bind to specific RNA motifs on the pre-mRNA molecule and attract the spliceosomal complex.
Now let's say that a protein SRSF1 (from the SR protein family) recognises a motif in Exon1 of gene A. If we increase the concentration of protein SRSF1, it will increase the Exon1 skipping in gene A and we will have more protein A isoforms lacking Exon1.
But: the same SRSF1 protein can bind to another exon of another gene and thus alter the splicing pattern of another gene.
My question is: what if the cell needs only to change the splicing pattern of gene A and leave other genes untouched. How will the splicing factors induce this change?