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Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics - assessment and update.

Freyhult E, Edvardsson S, Tamas I, Moulton V, Poole AM - BMC Res Notes (2008)

Bottom Line: Our motivation for revisiting this work is to report on the status of the candidate snoRNAs described in 1, and secondly, to report that a modified version of Fisher together with the available multiple yeast genome sequences was able to correctly identify several H/ACA snoRNAs for modification sites not identified by the snoGPS program 3.The modified source code for Fisher is made available as supplementary material.Our results confirm the validity of using minimum free energy (MFE) secondary structure prediction to guide comparative genomic screening for RNA families with few sequence constraints.

View Article: PubMed Central - HTML - PubMed

Affiliation: Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, S-751, 24 Uppsala, Sweden; Department of Clinical Microbiology, Clinical Bacteriology, Umeå University, 901 85 Umeå, Sweden. Eva.Freyhult@climi.umu.se

ABSTRACT

Background: The H/ACA family of small nucleolar RNAs (snoRNAs) plays a central role in guiding the pseudouridylation of ribosomal RNA (rRNA). In an effort to systematically identify the complete set of rRNA-modifying H/ACA snoRNAs from the genome sequence of the budding yeast, Saccharomyces cerevisiae, we developed a program - Fisher - and previously presented several candidate snoRNAs based on our analysis 1.

Findings: In this report, we provide a brief update of this work, which was aborted after the publication of experimentally-identified snoRNAs 2 identical to candidates we had identified bioinformatically using Fisher. Our motivation for revisiting this work is to report on the status of the candidate snoRNAs described in 1, and secondly, to report that a modified version of Fisher together with the available multiple yeast genome sequences was able to correctly identify several H/ACA snoRNAs for modification sites not identified by the snoGPS program 3. While we are no longer developing Fisher, we briefly consider the merits of the Fisher algorithm relative to snoGPS, which may be of use for workers considering pursuing a similar search strategy for the identification of small RNAs. The modified source code for Fisher is made available as supplementary material.

Conclusion: Our results confirm the validity of using minimum free energy (MFE) secondary structure prediction to guide comparative genomic screening for RNA families with few sequence constraints.

No MeSH data available.


Secondary structure predictions showing 3' hairpin structures of the two top candidates identified by Fisher. 3' hairpin structures from H- to ACA-box for (a) candidate 7 from Table 1, corresponding to snR80, and (b) Candidate 11 from table 1, corresponding to snR86. Residues forming the H-box, ψ-pocket and ACA-box are capitalised and circled.
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Figure 3: Secondary structure predictions showing 3' hairpin structures of the two top candidates identified by Fisher. 3' hairpin structures from H- to ACA-box for (a) candidate 7 from Table 1, corresponding to snR80, and (b) Candidate 11 from table 1, corresponding to snR86. Residues forming the H-box, ψ-pocket and ACA-box are capitalised and circled.

Mentions: We subsequently performed Northern blots to probe for expression of these candidates, and found that candidates 2 and 11 were expressed in S. cerevisiae (IT & AMP, unpublished observations). Candidate 2 corresponds to snR80, which was determined by Torchet et al. [2] to guide pseudouridylation of SSU759 and LSU776, and candidate 11 is snR86, which Torchet et al. demonstrated was required for pseudouridylation of LSU2314. None of the candidates for position 14 (SSU1415) were detected on Northern blots, and we concluded that these are false positives. Torchet et al. demonstrated that this pseudouridylation was guided by snR83, which Fisher fails to detect. As is evident from Table 1, snR80, snR82 and snR86 are conserved in diverse yeast species. Both snR80 and snR86 both form hairpin structures (3' hairpins shown in Figure 3). Alignment of snR80 from S. cerevisiae with snR80 sequences from other yeasts, shows that the H-box, ACA-box and the ψ3 and ψ4 boxes forming the 3' pseudouridylation pocket are almost perfectly conserved, with overall sequence similarity being high among sensu stricto species (S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus) (see Figure S1, Additional file 3). In the case of snR86, only the sequence corresponding to the 3' hairpin is conserved (i.e. from just upstream from the H-box to the 3' end) (see Figure S2, Additional file 3). Based on a comparison between snR86 sequences from S. cerevisiae and C. glabrata, Torchet et al. proposed that the large 5' region of sn86 was structurally conserved. We examined snR86 sequences from 10 yeast species, and, given the low sequence similarity, uncertainty on the genomic position of the 5'-end for these sequences, and the consequent difficulty in reliably aligning these, we are only confident of the conservation of structure of the 3' region (Figure 3, Figure S2 in Additional file 3).


Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics - assessment and update.

Freyhult E, Edvardsson S, Tamas I, Moulton V, Poole AM - BMC Res Notes (2008)

Secondary structure predictions showing 3' hairpin structures of the two top candidates identified by Fisher. 3' hairpin structures from H- to ACA-box for (a) candidate 7 from Table 1, corresponding to snR80, and (b) Candidate 11 from table 1, corresponding to snR86. Residues forming the H-box, ψ-pocket and ACA-box are capitalised and circled.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2551606&req=5

Figure 3: Secondary structure predictions showing 3' hairpin structures of the two top candidates identified by Fisher. 3' hairpin structures from H- to ACA-box for (a) candidate 7 from Table 1, corresponding to snR80, and (b) Candidate 11 from table 1, corresponding to snR86. Residues forming the H-box, ψ-pocket and ACA-box are capitalised and circled.
Mentions: We subsequently performed Northern blots to probe for expression of these candidates, and found that candidates 2 and 11 were expressed in S. cerevisiae (IT & AMP, unpublished observations). Candidate 2 corresponds to snR80, which was determined by Torchet et al. [2] to guide pseudouridylation of SSU759 and LSU776, and candidate 11 is snR86, which Torchet et al. demonstrated was required for pseudouridylation of LSU2314. None of the candidates for position 14 (SSU1415) were detected on Northern blots, and we concluded that these are false positives. Torchet et al. demonstrated that this pseudouridylation was guided by snR83, which Fisher fails to detect. As is evident from Table 1, snR80, snR82 and snR86 are conserved in diverse yeast species. Both snR80 and snR86 both form hairpin structures (3' hairpins shown in Figure 3). Alignment of snR80 from S. cerevisiae with snR80 sequences from other yeasts, shows that the H-box, ACA-box and the ψ3 and ψ4 boxes forming the 3' pseudouridylation pocket are almost perfectly conserved, with overall sequence similarity being high among sensu stricto species (S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus) (see Figure S1, Additional file 3). In the case of snR86, only the sequence corresponding to the 3' hairpin is conserved (i.e. from just upstream from the H-box to the 3' end) (see Figure S2, Additional file 3). Based on a comparison between snR86 sequences from S. cerevisiae and C. glabrata, Torchet et al. proposed that the large 5' region of sn86 was structurally conserved. We examined snR86 sequences from 10 yeast species, and, given the low sequence similarity, uncertainty on the genomic position of the 5'-end for these sequences, and the consequent difficulty in reliably aligning these, we are only confident of the conservation of structure of the 3' region (Figure 3, Figure S2 in Additional file 3).

Bottom Line: Our motivation for revisiting this work is to report on the status of the candidate snoRNAs described in 1, and secondly, to report that a modified version of Fisher together with the available multiple yeast genome sequences was able to correctly identify several H/ACA snoRNAs for modification sites not identified by the snoGPS program 3.The modified source code for Fisher is made available as supplementary material.Our results confirm the validity of using minimum free energy (MFE) secondary structure prediction to guide comparative genomic screening for RNA families with few sequence constraints.

View Article: PubMed Central - HTML - PubMed

Affiliation: Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, S-751, 24 Uppsala, Sweden; Department of Clinical Microbiology, Clinical Bacteriology, Umeå University, 901 85 Umeå, Sweden. Eva.Freyhult@climi.umu.se

ABSTRACT

Background: The H/ACA family of small nucleolar RNAs (snoRNAs) plays a central role in guiding the pseudouridylation of ribosomal RNA (rRNA). In an effort to systematically identify the complete set of rRNA-modifying H/ACA snoRNAs from the genome sequence of the budding yeast, Saccharomyces cerevisiae, we developed a program - Fisher - and previously presented several candidate snoRNAs based on our analysis 1.

Findings: In this report, we provide a brief update of this work, which was aborted after the publication of experimentally-identified snoRNAs 2 identical to candidates we had identified bioinformatically using Fisher. Our motivation for revisiting this work is to report on the status of the candidate snoRNAs described in 1, and secondly, to report that a modified version of Fisher together with the available multiple yeast genome sequences was able to correctly identify several H/ACA snoRNAs for modification sites not identified by the snoGPS program 3. While we are no longer developing Fisher, we briefly consider the merits of the Fisher algorithm relative to snoGPS, which may be of use for workers considering pursuing a similar search strategy for the identification of small RNAs. The modified source code for Fisher is made available as supplementary material.

Conclusion: Our results confirm the validity of using minimum free energy (MFE) secondary structure prediction to guide comparative genomic screening for RNA families with few sequence constraints.

No MeSH data available.