Abstract
An evolutionarily conserved feature of introns is their ability to enhance expression of genes that harbor them. Introns have been shown to regulate gene expression at the transcription and post-transcription level. The general perception is that a promoter-proximal intron is most efficient in enhancing gene expression and the effect diminishes with the increase in distance from the promoter. Here we show that the intron regains its positive influence on gene expression when in proximity to the terminator. We inserted ACT1 intron into different positions within IMD4 and INO1 genes. Transcription Run-On (TRO) analysis revealed that the transcription of both IMD4 and INO1 was maximal in constructs with a promoter-proximal intron and decreased with the increase in distance of the intron from the promoter. However, activation was partially restored when the intron was placed close to the terminator. We previously demonstrated that the promoter-proximal intron stimulates transcription by affecting promoter directionality through gene looping-mediated recruitment of termination factors in the vicinity of the promoter region. Here we show that the terminator-proximal intron also enhances promoter directionality and results in compact gene architecture with the promoter and terminator regions in close physical proximity. Furthermore, we show that both the promoter and terminator-proximal introns facilitate assembly or stabilization of the preinitiation complex (PIC) on the promoter. On the basis of these findings, we propose that proximity to both the promoter and the terminator regions affects the transcription regulatory potential of an intron, and the terminator-proximal intron enhances transcription by affecting both the assembly of preinitiation complex and promoter directionality.
Highlights
One of the conserved features of eukaryotic protein-coding genes that distinguishes them from their prokaryotic counterparts is the presence of non-coding intervening regions called introns
A small number of yeast genes carry an intron in the middle of the gene, and an even fewer number have them in the vicinity of the terminator region
The effect of a promoter-proximal intron on transcription has been conserved during evolution as it is exhibited by simple eukaryotes like budding yeast as well as the most complex mammalian systems
Summary
One of the conserved features of eukaryotic protein-coding genes that distinguishes them from their prokaryotic counterparts is the presence of non-coding intervening regions called introns. Introns substantially enhance the expression of genes that accommodate them (Brinster et al, 1988; Palmiter et al, 1991; Okkema et al, 1993; Duncker et al, 1997; Lugones et al, 1999; Comeron, 2004; Juneau et al, 2006; Charron et al, 2007; Rose, 2008; Shabalina et al, 2010; Gallegos and Rose, 2015; Laxa, 2017; Shaul, 2017; Baier et al, 2020). A number of eukaryotic genes are dependent on introns for their normal expression. The ability to enhance gene expression though is not a universal feature of introns
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