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Why eukaryotic cells use introns to enhance gene expression: splicing reduces transcription-associated mutagenesis by inhibiting topoisomerase I cutting activity.

Niu DK, Yang YF - Biol. Direct (2011)

Bottom Line: The costs and benefits of spliceosomal introns in eukaryotes have not been established.The cleavage and religation activity of DNA strands by DNA topoisomerase I was recently shown to account for transcription-associated mutagenesis.Experimentally test whether transcription-associated mutagenesis is lower in intron-containing genes than in intronless genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China. dengkeniu@hotmail.com

ABSTRACT

Background: The costs and benefits of spliceosomal introns in eukaryotes have not been established. One recognized effect of intron splicing is its known enhancement of gene expression. However, the mechanism regulating such splicing-mediated expression enhancement has not been defined. Previous studies have shown that intron splicing is a time-consuming process, indicating that splicing may not reduce the time required for transcription and processing of spliced pre-mRNA molecules; rather, it might facilitate the later rounds of transcription. Because the densities of active RNA polymerase II on most genes are less than one molecule per gene, direct interactions between the splicing apparatus and transcriptional complexes (from the later rounds of transcription) are infrequent, and thus unlikely to account for splicing-mediated gene expression enhancement.

Presentation of the hypothesis: The serine/arginine-rich protein SF2/ASF can inhibit the DNA topoisomerase I activity that removes negative supercoiling of DNA generated by transcription. Consequently, splicing could make genes more receptive to RNA polymerase II during the later rounds of transcription, and thus affect the frequency of gene transcription. Compared with the transcriptional enhancement mediated by strong promoters, intron-containing genes experience a lower frequency of cut-and-paste processes. The cleavage and religation activity of DNA strands by DNA topoisomerase I was recently shown to account for transcription-associated mutagenesis. Therefore, intron-mediated enhancement of gene expression could reduce transcription-associated genome instability.

Testing the hypothesis: Experimentally test whether transcription-associated mutagenesis is lower in intron-containing genes than in intronless genes. Use bioinformatic analysis to check whether exons flanking lost introns have higher frequencies of short deletions.

Implications of the hypothesis: The mechanism of intron-mediated enhancement proposed here may also explain the positive correlation observed between intron size and gene expression levels in unicellular organisms, and the greater number of intron containing genes in higher organisms.

Reviewers: This article was reviewed by Dr Arcady Mushegian, Dr Igor B Rogozin (nominated by Dr I King Jordan) and Dr Alexey S Kondrashov. For the full reviews, please go to the Reviewer's Reports section.

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Schematic illustration of the effect of splicing on DNA topology and accessibility to RNA polymerase II. (A) SR proteins inhibit the cleavage and religation activity of DNA topoisomerase I (Top1). Therefore, after one round of transcription, DNA becomes less twisted and more accessible to RNA polymerase II (RNAP II). (B) In an intronless gene, Top1 actively removes the negative supercoiling generated by transcription. Transcription does not change the topological status of an intronless gene. For simplicity, nucleosomes are not shown.
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Figure 1: Schematic illustration of the effect of splicing on DNA topology and accessibility to RNA polymerase II. (A) SR proteins inhibit the cleavage and religation activity of DNA topoisomerase I (Top1). Therefore, after one round of transcription, DNA becomes less twisted and more accessible to RNA polymerase II (RNAP II). (B) In an intronless gene, Top1 actively removes the negative supercoiling generated by transcription. Transcription does not change the topological status of an intronless gene. For simplicity, nucleosomes are not shown.

Mentions: In eukaryotic cells, topoisomerase I has another function; acting as a kinase to phosphorylate the serine/arginine-rich (SR) proteins like SF2/ASF [56,57]. When topoisomerase I is associated with hypophosphorylated SF2/ASF, its negative supercoiling removal activity is inhibited [58,59]. In addition, the substrate of SR protein phosphorylation, ATP, can also inhibit topoisomerase I mediated DNA cleavage [60]. Because phosphorylation of SR proteins is required for efficient splice-site recognition and the assembly of spliceosomes [61-63], we propose the following scenario; for intron splicing, SR proteins are phosphorylated by topoisomerase I, which inhibits its negative supercoiling removal activity. Because of intron splicing, the negative supercoiling generated during transcription is removed at a much lower efficiency. Consequently, intron splicing changes the transcribed gene into a less twisted state (Figure 1A). By contrast, in intronless genes, the negative supercoiling generated by transcription is removed efficiently by topoisomerase I, and so the gene reverts back to its original topological status after transcription (Figure 1B). The binding of proteins to less twisted DNA is thermodynamically favored, and thus the separation of two strands is facilitated [49,50,64,65].


Why eukaryotic cells use introns to enhance gene expression: splicing reduces transcription-associated mutagenesis by inhibiting topoisomerase I cutting activity.

Niu DK, Yang YF - Biol. Direct (2011)

Schematic illustration of the effect of splicing on DNA topology and accessibility to RNA polymerase II. (A) SR proteins inhibit the cleavage and religation activity of DNA topoisomerase I (Top1). Therefore, after one round of transcription, DNA becomes less twisted and more accessible to RNA polymerase II (RNAP II). (B) In an intronless gene, Top1 actively removes the negative supercoiling generated by transcription. Transcription does not change the topological status of an intronless gene. For simplicity, nucleosomes are not shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3118952&req=5

Figure 1: Schematic illustration of the effect of splicing on DNA topology and accessibility to RNA polymerase II. (A) SR proteins inhibit the cleavage and religation activity of DNA topoisomerase I (Top1). Therefore, after one round of transcription, DNA becomes less twisted and more accessible to RNA polymerase II (RNAP II). (B) In an intronless gene, Top1 actively removes the negative supercoiling generated by transcription. Transcription does not change the topological status of an intronless gene. For simplicity, nucleosomes are not shown.
Mentions: In eukaryotic cells, topoisomerase I has another function; acting as a kinase to phosphorylate the serine/arginine-rich (SR) proteins like SF2/ASF [56,57]. When topoisomerase I is associated with hypophosphorylated SF2/ASF, its negative supercoiling removal activity is inhibited [58,59]. In addition, the substrate of SR protein phosphorylation, ATP, can also inhibit topoisomerase I mediated DNA cleavage [60]. Because phosphorylation of SR proteins is required for efficient splice-site recognition and the assembly of spliceosomes [61-63], we propose the following scenario; for intron splicing, SR proteins are phosphorylated by topoisomerase I, which inhibits its negative supercoiling removal activity. Because of intron splicing, the negative supercoiling generated during transcription is removed at a much lower efficiency. Consequently, intron splicing changes the transcribed gene into a less twisted state (Figure 1A). By contrast, in intronless genes, the negative supercoiling generated by transcription is removed efficiently by topoisomerase I, and so the gene reverts back to its original topological status after transcription (Figure 1B). The binding of proteins to less twisted DNA is thermodynamically favored, and thus the separation of two strands is facilitated [49,50,64,65].

Bottom Line: The costs and benefits of spliceosomal introns in eukaryotes have not been established.The cleavage and religation activity of DNA strands by DNA topoisomerase I was recently shown to account for transcription-associated mutagenesis.Experimentally test whether transcription-associated mutagenesis is lower in intron-containing genes than in intronless genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China. dengkeniu@hotmail.com

ABSTRACT

Background: The costs and benefits of spliceosomal introns in eukaryotes have not been established. One recognized effect of intron splicing is its known enhancement of gene expression. However, the mechanism regulating such splicing-mediated expression enhancement has not been defined. Previous studies have shown that intron splicing is a time-consuming process, indicating that splicing may not reduce the time required for transcription and processing of spliced pre-mRNA molecules; rather, it might facilitate the later rounds of transcription. Because the densities of active RNA polymerase II on most genes are less than one molecule per gene, direct interactions between the splicing apparatus and transcriptional complexes (from the later rounds of transcription) are infrequent, and thus unlikely to account for splicing-mediated gene expression enhancement.

Presentation of the hypothesis: The serine/arginine-rich protein SF2/ASF can inhibit the DNA topoisomerase I activity that removes negative supercoiling of DNA generated by transcription. Consequently, splicing could make genes more receptive to RNA polymerase II during the later rounds of transcription, and thus affect the frequency of gene transcription. Compared with the transcriptional enhancement mediated by strong promoters, intron-containing genes experience a lower frequency of cut-and-paste processes. The cleavage and religation activity of DNA strands by DNA topoisomerase I was recently shown to account for transcription-associated mutagenesis. Therefore, intron-mediated enhancement of gene expression could reduce transcription-associated genome instability.

Testing the hypothesis: Experimentally test whether transcription-associated mutagenesis is lower in intron-containing genes than in intronless genes. Use bioinformatic analysis to check whether exons flanking lost introns have higher frequencies of short deletions.

Implications of the hypothesis: The mechanism of intron-mediated enhancement proposed here may also explain the positive correlation observed between intron size and gene expression levels in unicellular organisms, and the greater number of intron containing genes in higher organisms.

Reviewers: This article was reviewed by Dr Arcady Mushegian, Dr Igor B Rogozin (nominated by Dr I King Jordan) and Dr Alexey S Kondrashov. For the full reviews, please go to the Reviewer's Reports section.

Show MeSH