Limits...
Correlation between the secondary structure of pre-mRNA introns and the efficiency of splicing in Saccharomyces cerevisiae.

Rogic S, Montpetit B, Hoos HH, Mackworth AK, Ouellette BF, Hieter P - BMC Genomics (2008)

Bottom Line: The nature of these base-pairing interactions and their effect on splicing efficiency were most extensively studied in ribosomal protein gene RPS17B (previously known as RP51B).We show that it is necessary to consider suboptimal structure predictions and to compute the structural branchpoint distances in order to explain previously published splicing efficiency results.Our findings provide further insights into the role of pre-mRNA secondary structure in gene splicing in yeast and also offer basis for improvement of computational methods for splice site identification and gene-finding.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, University of British Columbia, Vancouver, Canada. rogic@bioinformatics.ubc.ca

ABSTRACT

Background: Secondary structure interactions within introns have been shown to be essential for efficient splicing of several yeast genes. The nature of these base-pairing interactions and their effect on splicing efficiency were most extensively studied in ribosomal protein gene RPS17B (previously known as RP51B). It was determined that complementary pairing between two sequence segments located downstream of the 5' splice site and upstream of the branchpoint sequence promotes efficient splicing of the RPS17B pre-mRNA, presumably by shortening the branchpoint distance. However, no attempts were made to compute a shortened, 'structural' branchpoint distance and thus the functional relationship between this distance and the splicing efficiency remains unknown.

Results: In this paper we use computational RNA secondary structure prediction to analyze the secondary structure of the RPS17B intron. We show that it is necessary to consider suboptimal structure predictions and to compute the structural branchpoint distances in order to explain previously published splicing efficiency results. Our study reveals that there is a tight correlation between this distance and splicing efficiency levels of intron mutants described in the literature. We experimentally test this correlation on additional RPS17B mutants and intron mutants within two other yeast genes.

Conclusion: The proposed model of secondary structure requirements for efficient splicing is the first attempt to specify the functional relationship between pre-mRNA secondary structure and splicing. Our findings provide further insights into the role of pre-mRNA secondary structure in gene splicing in yeast and also offer basis for improvement of computational methods for splice site identification and gene-finding.

Show MeSH
Portions of the RPS17B, RPS6B and APE2 introns containing computationally identified zipper stems. The free energy values (ΔG) for the shaded zipper stem are given in parentheses. Stems conserved between Saccharomyces sensu stricto group are also labeled.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2536676&req=5

Figure 9: Portions of the RPS17B, RPS6B and APE2 introns containing computationally identified zipper stems. The free energy values (ΔG) for the shaded zipper stem are given in parentheses. Stems conserved between Saccharomyces sensu stricto group are also labeled.

Mentions: The splicing efficiency study of RPS17B, RPS6B and APE2 genes containing wildtype and mutant introns supports our hypothesis that short structural branchpoint distances are required for efficient splicing. Although these distances are computed in the context of the secondary structure of the entire intron, our hypothesis is still consistent with the original hypothesis [3] that attributes the shortening of a long branchpoint distance to a single stem. Such stems, which we will refer to as 'zipper' stems, since they 'zip' the intron, are probably essential for achieving a short structural branchpoint distance. If we analyze the computed secondary structures of the RPS17B, RPS6B and APE2 wildtype introns we can easily identify stable stems whose 3' and 5' constituents are close to the donor site and the branchpoint sequence (Figure 9). The zipper stem labeled in the RPS17B intron is the same as the one identified in [9] using experimental structure probing.


Correlation between the secondary structure of pre-mRNA introns and the efficiency of splicing in Saccharomyces cerevisiae.

Rogic S, Montpetit B, Hoos HH, Mackworth AK, Ouellette BF, Hieter P - BMC Genomics (2008)

Portions of the RPS17B, RPS6B and APE2 introns containing computationally identified zipper stems. The free energy values (ΔG) for the shaded zipper stem are given in parentheses. Stems conserved between Saccharomyces sensu stricto group are also labeled.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2536676&req=5

Figure 9: Portions of the RPS17B, RPS6B and APE2 introns containing computationally identified zipper stems. The free energy values (ΔG) for the shaded zipper stem are given in parentheses. Stems conserved between Saccharomyces sensu stricto group are also labeled.
Mentions: The splicing efficiency study of RPS17B, RPS6B and APE2 genes containing wildtype and mutant introns supports our hypothesis that short structural branchpoint distances are required for efficient splicing. Although these distances are computed in the context of the secondary structure of the entire intron, our hypothesis is still consistent with the original hypothesis [3] that attributes the shortening of a long branchpoint distance to a single stem. Such stems, which we will refer to as 'zipper' stems, since they 'zip' the intron, are probably essential for achieving a short structural branchpoint distance. If we analyze the computed secondary structures of the RPS17B, RPS6B and APE2 wildtype introns we can easily identify stable stems whose 3' and 5' constituents are close to the donor site and the branchpoint sequence (Figure 9). The zipper stem labeled in the RPS17B intron is the same as the one identified in [9] using experimental structure probing.

Bottom Line: The nature of these base-pairing interactions and their effect on splicing efficiency were most extensively studied in ribosomal protein gene RPS17B (previously known as RP51B).We show that it is necessary to consider suboptimal structure predictions and to compute the structural branchpoint distances in order to explain previously published splicing efficiency results.Our findings provide further insights into the role of pre-mRNA secondary structure in gene splicing in yeast and also offer basis for improvement of computational methods for splice site identification and gene-finding.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, University of British Columbia, Vancouver, Canada. rogic@bioinformatics.ubc.ca

ABSTRACT

Background: Secondary structure interactions within introns have been shown to be essential for efficient splicing of several yeast genes. The nature of these base-pairing interactions and their effect on splicing efficiency were most extensively studied in ribosomal protein gene RPS17B (previously known as RP51B). It was determined that complementary pairing between two sequence segments located downstream of the 5' splice site and upstream of the branchpoint sequence promotes efficient splicing of the RPS17B pre-mRNA, presumably by shortening the branchpoint distance. However, no attempts were made to compute a shortened, 'structural' branchpoint distance and thus the functional relationship between this distance and the splicing efficiency remains unknown.

Results: In this paper we use computational RNA secondary structure prediction to analyze the secondary structure of the RPS17B intron. We show that it is necessary to consider suboptimal structure predictions and to compute the structural branchpoint distances in order to explain previously published splicing efficiency results. Our study reveals that there is a tight correlation between this distance and splicing efficiency levels of intron mutants described in the literature. We experimentally test this correlation on additional RPS17B mutants and intron mutants within two other yeast genes.

Conclusion: The proposed model of secondary structure requirements for efficient splicing is the first attempt to specify the functional relationship between pre-mRNA secondary structure and splicing. Our findings provide further insights into the role of pre-mRNA secondary structure in gene splicing in yeast and also offer basis for improvement of computational methods for splice site identification and gene-finding.

Show MeSH