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mRNA-type introns in U6 small nuclear RNA genes: implications for the catalysis in pre-mRNA splicing
Abstract:
U6 small nuclear RNA is one of the spliceosomal RNAs involved in pre-mRNA splicing. In the fission yeast Schizosaccharomyces pombe, the U6 RNA gene was found to have an intron similar to a nuclear pre-mRNA intron, and it was proposed that the U6 intron might be inserted erroneously during pre-mRNA splicing. Using the polymerase chain reaction, we analyzed the U6 RNA genes of 52 organisms. In addition to the five species of Schizosaccharomyces, we found that the yeast species Rhodotorula hasegawae and Rhodosporidium dacryoidum also have mRNA-type introns in their U6 genes; however, in all the other organisms tested, we found no intron within the region of the U6 gene examined. Four introns and one intron are present in the R. hasegawae and R. dacryoidum U6 genes, respectively; and these introns are located at sites differing from the location of the Schizosaccharomyces U6 intron. Most of the U6 introns locate within the conserved domain, which is strikingly similar in structure to the catalytic center of the negative strand of the satellite RNA of tobacco ring spot virus. The introns of the S. pombe and R. dacryoidum U6 genes are located immediately adjacent to the nucleotides that were shown to be essential for the second step of the splicing reaction. These results support the notion that U6 RNA has a catalytic role in pre-mRNA splicing and that U6 introns originated from insertion of an excised intron during pre-mRNA splicing.
Insights
The U6 small nuclear RNA gene contains introns in some yeasts, suggesting a catalytic role for U6 RNA in pre-mRNA splicing. These introns may have originated from excised introns during splicing.
Area of Science:
- Molecular Biology
- Genetics
- RNA Biology
Background:
- U6 small nuclear RNA (snRNA) is a critical component of the spliceosome, essential for pre-mRNA splicing.
- Introns, typically found in pre-mRNA, were unexpectedly discovered in the U6 RNA gene of Schizosaccharomyces pombe.
- It was hypothesized that these U6 introns might be artifacts of pre-mRNA splicing.
Purpose of the Study:
- To investigate the presence and distribution of introns within U6 RNA genes across diverse organisms.
- To explore the evolutionary origin and potential functional implications of U6 introns.
Main Methods:
- Polymerase chain reaction (PCR) was employed to analyze U6 RNA genes from 52 different organisms.
- Comparative sequence analysis was performed to identify and characterize introns within the U6 gene region.
Main Results:
- Introns were identified in the U6 genes of five Schizosaccharomyces species, Rhodotorula hasegawae, and Rhodosporidium dacryoidum.
- No introns were found in the U6 genes of the other 44 organisms examined within the studied region.
- The identified introns were located at various positions, with most situated within a conserved domain structurally similar to the catalytic center of tobacco ring spot virus satellite RNA.
- Introns in S. pombe and R. dacryoidum U6 genes were adjacent to nucleotides crucial for the second step of splicing.
Conclusions:
- The findings support the role of U6 RNA in catalysis during pre-mRNA splicing.
- The presence and location of U6 introns suggest they originated from the insertion of excised introns during the splicing process.