Using Introns to Increase Gene Expression

It has been known for several decades that introns can increase gene expression in diverse eukaryotes, although the mechanism remains unclear. Many efficiently spliced introns have no effect on expression, demonstrating that splicing is insufficient and suggesting that the introns that boost expression must contain stimulating sequences. However, deletion analysis and homology searches have failed to identify stimulatory sequences because they are degenerate, redundant and dispersed. The lack of recognizable signals has made it difficult to find new expression-enhancing introns. This talk will cover several practical aspects of selecting and using introns to increase transgene expression in plants. Introns that boost expression can be found using the IMEter algorithm, which measures the similarity of any sequence to the genome-wide composition of promoter-proximal introns and whose output strongly correlates with an intron’s effect on expression. Software was recently developed that facilitates the rapid generation of IMEters from any sequenced genome. This will greatly expand the number of endogenous introns that can be used to boost transgene expression in crops. Introns only affect expression when they are relatively close to the promoter (less than 1 Kb away), and it may be convenient to insert the intron into the 5’-UTR of a transgene. However, the optimal intron location for maximally increasing expression may be 200 – 300 nt downstream of the transcription start site. Most Arabidopsis genes respond to the stimulating effects of introns, although introns can override some kinds of gene regulation such as tissue-specificity.