Alternative splicing in development and function of chordate endocrine systems: a focus on Pax genes

Genome sequencing has facilitated an understanding of gene networks but has also shown that they are only a small part of the answer to the question of how genes translate into a functional organism. Much of the answer lies in epigenetics-heritable traits not directly encoded by the genome. One such phenomenon is alternative splicing, which affects over 75% of protein coding genes and greatly amplifies the number of proteins. Although it was postulated that alternative splicing and gene duplication are inversely proportional and, therefore, have similar effects on the size of the proteome, for ancient duplications such as occurred in the Pax family of transcription factors, that is not necessarily so. The importance of alternative splicing in development and physiology is only just coming to light. However, several techniques for studying isoform functions both in vitro and in vivo have been recently developed. As examples of what is known and what is yet to be discovered, this review focuses on the evolution and roles of the Pax family of transcription factors in development and on alternative splicing of endocrine genes and the factors that regulate them.