Evo Devo

Evolutionary development - at the biological interface between genetic regulatory mechanisms and biological evolution.

intron retention

Intron retention is defined by the presence of a transcript-confirmed intron within a transcript-confirmed exon. Intron retention occurs when introns are not spliced out of the RNA transcript, resulting in the intron(s) being retained within the mRNA as part of an exon. This lengthening mechanism the commonest form of alternative splicing in plants and lower multicellular organisms.

Intron retention is probably the earliest version of alternative splicing to have evolved. The splicing machinery of single-celled organisms, such as yeast, operates by recognizing introns, in contrast with the SR protein system of higher organisms, which defines exons for the basal machinery.

In unicellular organisms, the splicing machinery can recognize only short (less than 500 nt) to recognition of short exons in long intron segments.

The average human protein-coding gene, for example, is 28,000 nucleotides long, and has 8.8 exons separated by 7.8 introns. Human exons are relatively short, typically about 120 nucleotides, whereas the introns can range from 100 to 100,000 nucleotides in length. Humans have the highest number of introns per gene of any organism and much of the energy we consume is devoted to the DNA repair and maintenance of introns, transcription, pre-mRNA splicing (removal of introns), and breakdown of introns at the end of the splicing reaction. In addition to energy costs, breakdown of splicing regulation results in disease.

The advantage of alternative splicing expresses itself as the roughly 90,000 human proteins coded by a mere 25,000 genes. Yet a mouse possesses almost the same number of genes as a human. Although approximately 100 million years have passed since mice and men shared a common ancestor, 99 percent of both human and mouse genes derive from that ancestor. Most of these genes share the same intron and exon arrangement, and the nucleotide sequences within our exons are also conserved to a high degree. However, roughly one quarter of the alternatively spliced exons in both genomes are specific either to human or to mouse. Thus, these alternately spliced exons have the potential to create species-specific proteins that could be responsible for diversification between the species. In fact, one category of alternatively spliced exons is unique to primates (humans, apes and monkeys) and probably contributed to primates' divergence from other mammals.

These primate-specific exons derive from mobile genetic elements called Alu elements that belong to a larger class of elements known as retrotransposons, which are short sequences of DNA able to replicate themselves and then to reinsert those copies back into the genome at random positions. Retrotransposons are found in almost all genomes, and they have had a profound influence by contributing to the genomic expansion that accompanied the evolution of multicellular organisms. Almost half of the human genome is made up of transposable elements, Alus being the most abundant.

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