A potent enhancer element in the 5′-UTR intron is crucial for transcriptional regulation of the human ubiquitin C gene

Bianchi, Marzia; Crinelli, Rita; Giacomini, Elisa; Carloni, Elisa; Magnani, Mauro

doi:10.1016/j.gene.2009.08.013

Cited by 58 publications

(81 citation statements)

References 66 publications

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“…The use of multiple TSS is widely spread in the human genome (Liang et al, 2014) and ubiquitin genes are not an exception: multiple start sites have indeed been described for the RPS27A gene (Kirschner and Stratakis, 2000) and also for the chicken testis polyubiquitin gene UbI (Mezquita et al, 1997). However, as far as we know, afterwards the study of Nenoi in 1996(Nenoi et al, 1996, that sets the hallmarks of the UBC gene structure, including the TSS, and our recent molecular studies Bianchi et al, 2009;Radici et al, 2013) no other investigations aimed to define the boundary between the true promoter and the transcribed region of UBC gene were performed. Yet, the gene records for UBC available in the GenBank database, provide different information as to the primary transcript length, with the untranslated exon 1 ranging from 64 bp (GenBank: D63791.1; AB009010.1) to 455 bp (GenBank: NM_021009.6).…”

Section: Discussionmentioning

confidence: 97%

Dynamic transcription of ubiquitin genes under basal and stressful conditions and new insights into the multiple UBC transcript variants

Bianchi

Giacomini

Crinelli

et al. 2015

Gene

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Section: Discussionmentioning

confidence: 97%

Dynamic transcription of ubiquitin genes under basal and stressful conditions and new insights into the multiple UBC transcript variants

Bianchi

Giacomini

Crinelli

et al. 2015

Gene

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“…Many other studies identified specific intron-hosted DNA elements that regulate transcription initiation. These elements include enhancers (Tourmente et al, 1993; Scohy et al, 2000; Bianchi et al, 2009; Beaulieu et al, 2011), silencers (Tourmente et al, 1993; Gaunitz et al, 2004, 2005), or other elements that modulate the function of the main upstream promoter (Bornstein et al, 1988; Zhang et al, 2011). …”

Section: Functions Associated With the Genomic Intronmentioning

confidence: 99%

The Function of Introns

Chorev¹,

Carmel²

2012

Front. Gene.

307

252

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The intron–exon architecture of many eukaryotic genes raises the intriguing question of whether this unique organization serves any function, or is it simply a result of the spread of functionless introns in eukaryotic genomes. In this review, we show that introns in contemporary species fulfill a broad spectrum of functions, and are involved in virtually every step of mRNA processing. We propose that this great diversity of intronic functions supports the notion that introns were indeed selfish elements in early eukaryotes, but then independently gained numerous functions in different eukaryotic lineages. We suggest a novel criterion of evolutionary conservation, dubbed intron positional conservation, which can identify functional introns.

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“…Introns can often stimulate transcription because of the presence of an enhancer or a promoter element within their sequence (6). Such introns can influence transcription even if their orientation is reversed (19). In contrast, splicing-dependent regulation of transcription requires a functional, splicing-competent intron within the body of the gene.…”

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confidence: 99%

Role for gene looping in intron-mediated enhancement of transcription

Moabbi

Agarwal

Kaderi

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

103

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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...

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A potent enhancer element in the 5′-UTR intron is crucial for transcriptional regulation of the human ubiquitin C gene

Cited by 58 publications

References 66 publications

Dynamic transcription of ubiquitin genes under basal and stressful conditions and new insights into the multiple UBC transcript variants

Dynamic transcription of ubiquitin genes under basal and stressful conditions and new insights into the multiple UBC transcript variants

The Function of Introns

Role for gene looping in intron-mediated enhancement of transcription

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