What are the mechanisms of alternative splicing?

Alternative splicing arises through three primary mechanisms: exon shuffling, constitutively spliced exons, and exonization of transposable elements. Exon shuffling involves rearranging exons within a gene to create different mRNA transcripts.  This approach involves the creation of novel genes through the fusion of two or more exons from different genes or the duplication of individual exons. The process begins with the generation of DNA fragments compromising exons or a mix of exons from eukaryotic genes. These fragments are then mixed and amplified alongside synthetic chimeric oligonucleotides, leading to random splicing. The resulting spliced fragments are further organized into complete genes using overlap PCR, where each fragment serves as both a primer and template. Recombination takes place when the synthetic chimeric oligonucleotide connects one exon from one parent gene with another exon from a different parent gene. 

Constitutive splicing is the mechanism of removing introns and linking exons together in order they are found in genes. During alternative splicing however, specific exons may be skipped, leading to the production of different types of mature mRNA. Transposable elements are DNA sequences capable of relocating themselves within a genome. These elements become incorporated into genes and can serve as exons during alternative splicing, leading to the generation of novel mRNA transcripts. Alternative splicing is also influenced by various factors like the strength of splice sites, RNA structures, chromatin modifications, and the presence of splicing factors. Changes in the activity of these factors and resulting spliced variants can indicate disease progression, and thus they may serve as diagnostic biomarkers.