Role for gene looping in intron-mediated enhancement of transcription

Abstract

Intron-containing genes are often transcribed more efficiently than nonintronic genes. The effect of introns on transcription of genes is an evolutionarily conserved feature, being exhibited by such diverse organisms as yeast, plants, flies, and mammals. The mechanism of intron-mediated transcriptional activation, however, is not entirely clear. To address this issue, we inserted an intron in INO1, which is a nonintronic gene, and deleted the intron from ASC1, which contains a natural intron. We then compared transcription of INO1 and ASC1 genes in the presence and absence of an intron. Transcription of both genes was significantly stimulated by the intron. The introns have a direct role in enhancing transcription of INO1 and ASC1 because there was a marked increase in nascent transcripts from these genes in the presence of an intron. Intron-mediated enhancement of transcription required a splicing competent intron. Interestingly, both INO1 and ASC1 were in a looped configuration when their genes contained an intron. Intron-dependent gene looping involved a physical interaction of the promoter and the terminator regions. In addition, the promoter region interacted with the 5′ splice site and the terminator with the 3′ splice site. Intron-mediated enhancement of transcription was completely abolished in the looping defective sua7-1 strain. No effect on splicing, however, was observed in sua7-1 strain. On the basis of these results, we propose a role for gene looping in intron-mediated transcriptional activation of genes in yeast.chromosome conformation capture | RNA polymerase II T he protein encoding genes in eukaryotes differ from their prokaryotic counterparts in having noncoding intervening regions called introns, which are removed by splicing to generate mature mRNA. Since their discovery in 1977, there has been considerable debate regarding the functional role of introns in eukaryotes (1). It is widely believed that introns increase proteomic complexity by facilitating expression of multiple proteins from a single gene by alternative splicing (2). In budding yeast, where more than 95% of genes are without introns and there are very few instances of alternative splicing, introns do not contribute significantly to the proteomic diversity (3). The presence of introns in all eukaryotes, despite the high cost of maintaining them and the existence of the elaborate splicing machinery needed to remove them, suggest that introns are playing a more fundamental and evolutionarily conserved role in eukaryotic cells.One role of introns that has been remarkably conserved among diverse organisms, and which confers an additional advantage to eukaryotic genes, is their effect on efficiency of gene expression (4-6). Introns significantly enhance the transcriptional output of genes that harbor them. The expression level of intronless transgenes in mammalian cells is often 10-100 times lower than their intron-containing counterparts (5). The inclusion of just one intron near the 5′ end of the gene increases transcription of th...

Transcription factor Ikaros Represses Protein Phosphatase 2A (PP2A) Expression through an Intronic Binding Site

“…Nevertheless, there are countless studies exemplifying the instances where transcription factor binding to the introns can influence the expression of the gene, and intron-mediated enhancement of genes is a well studied branch of gene expression (16). A recent study by Hoffmann et al (17) describes an intronic enhancer that promotes the expression of the UCP3 gene by the binding of SP1/SP3 transcription factors.…”

Role of RNA splicing in mediating lineage-specific expression of the von Willebrand factor gene in the endothelium

“…However, introns are also required for optimal gene expression in many systems, including yeast, plants, insects, mammalian tissue culture cells, and transgenic mice. 13,[15][16][17][18][19][20][21][22][23][24][25][26][27][28] In some cases, intron-dependent gene expression is mediated by transcriptional control elements. For example, previous studies in transgenic mice have implicated a role for intronic enhancers in mediating the expression of vascular endothelial growth factor receptor 2, Tie2, GATA2, and endoglin.…”

The 5′UTR Intron of Arabidopsis GGT1 Aminotransferase Enhances Promoter Activity by Recruiting RNA Polymerase II

“…IME targeting the level of transcription has been poorly described in the literature, but include mammals, yeast, and plants (Furger et al, 2002;Moabbi et al, 2012;Samadder et al, 2008). IME on the transcriptional level is rather weak, leading to fold changes that did not exceed 3-fold (Furger et al, 2002;Samadder et al, 2008).…”

“…59 proximal introns of genes have been found to be associated with intron-mediated enhancement (Callis et al, 1987;Mascarenhas et al, 1990). Introns have been shown to be required for high expression of many genes in several organisms including plants (Callis et al, 1987), mammals (Furger et al, 2002), Saccharomyces cerevisiae (Moabbi et al, 2012), nematodes (Okkema et al, 1993), and insects (Jiang et al, 2015). Moreover, 79% of all Arabidopsis genes contain introns (Arabidopsis Genome Initiative, 2000).…”