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Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome.

Riordan DP, Herschlag D, Brown PO - Nucleic Acids Res. (2010)

Bottom Line: We computationally analyzed the sequences of Saccharomyces cerevisiae mRNAs bound in vivo by 29 specific RBPs, identifying eight novel candidate motifs and confirming or extending six earlier reported recognition elements.Biochemical selections for RNA sequences selectively recognized by 12 yeast RBPs yielded novel motifs bound by Pin4, Nsr1, Hrb1, Gbp2, Sgn1 and Mrn1, and recovered the known recognition elements for Puf3, She2, Vts1 and Whi3.Most of the RNA elements we uncovered were associated with coherent mRNA expression changes and were significantly conserved in related yeasts, supporting their functional importance and suggesting that the corresponding RNA-protein interactions are evolutionarily conserved.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA. driordan@stanford.edu

ABSTRACT
Post-transcriptional regulation of gene expression, including mRNA localization, translation and decay, is ubiquitous yet still largely unexplored. How is the post-transcriptional regulatory program of each mRNA encoded in its sequence? Hundreds of specific RNA-binding proteins (RBPs) appear to play roles in mediating the post-transcriptional regulatory program, akin to the roles of specific DNA-binding proteins in transcription. As a step toward decoding the regulatory programs encoded in each mRNA, we focused on specific mRNA-protein interactions. We computationally analyzed the sequences of Saccharomyces cerevisiae mRNAs bound in vivo by 29 specific RBPs, identifying eight novel candidate motifs and confirming or extending six earlier reported recognition elements. Biochemical selections for RNA sequences selectively recognized by 12 yeast RBPs yielded novel motifs bound by Pin4, Nsr1, Hrb1, Gbp2, Sgn1 and Mrn1, and recovered the known recognition elements for Puf3, She2, Vts1 and Whi3. Most of the RNA elements we uncovered were associated with coherent mRNA expression changes and were significantly conserved in related yeasts, supporting their functional importance and suggesting that the corresponding RNA-protein interactions are evolutionarily conserved.

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Conservation of RNA elements in Saccharomyces. Phylogenetic conservation rates of all sites for each RNA motif were calculated between S. cerevisiae and each of six related Saccharomyces species (par, paradoxus; mik, mikatae; kud, kudriavzevii; bay, bayanus; cas, castellii; klu, kluyveri) based on multiple alignments of the indicated genomic regions. For ‘Overall Conservation', each cell is shaded according to the −log10 P-value measuring if the observed conservation rate of motif sites in that species is significantly greater than expected by chance based on randomized alignments. For ‘target conservation', the cell for each species is shaded to depict the −log10 P-value measuring if the conservation rate of motif sites present within sequences of target mRNAs bound by the cognate RBP is significantly greater than the conservation rate of motif sites from all other transcripts. All P-values were calculated based on the hyper-geometric distribution. Asterisks denote motifs that correspond to previously reported binding sites for the associated RBP. For exact data values and details see Supplementary Data S4.
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Figure 4: Conservation of RNA elements in Saccharomyces. Phylogenetic conservation rates of all sites for each RNA motif were calculated between S. cerevisiae and each of six related Saccharomyces species (par, paradoxus; mik, mikatae; kud, kudriavzevii; bay, bayanus; cas, castellii; klu, kluyveri) based on multiple alignments of the indicated genomic regions. For ‘Overall Conservation', each cell is shaded according to the −log10 P-value measuring if the observed conservation rate of motif sites in that species is significantly greater than expected by chance based on randomized alignments. For ‘target conservation', the cell for each species is shaded to depict the −log10 P-value measuring if the conservation rate of motif sites present within sequences of target mRNAs bound by the cognate RBP is significantly greater than the conservation rate of motif sites from all other transcripts. All P-values were calculated based on the hyper-geometric distribution. Asterisks denote motifs that correspond to previously reported binding sites for the associated RBP. For exact data values and details see Supplementary Data S4.

Mentions: Using these criteria, we found significant evidence of conservation for almost all of the RNA motifs we tested––including the new SELEX-derived recognition elements for Gbp2, Hrb1, Nsr1 and Pin4, and the novel predicted motifs for Ssd1 and Puf2––in at least one related species (P < 0.01) (Figure 4). Statistical significance of overall conservation rates was established based on a model using permuted versions of each alignment file that were carefully constrained to preserve the identical per-nucleotide conservation rates from the original alignments (‘Materials and Methods’ section). As an additional analysis, we also asked if the conservation rate for each RNA motif was significantly greater for the collection of sites present in the mRNA targets of its cognate RBP than for sites present in all other transcripts. We found significant evidence of this type of ‘target-specific’ preferential conservation for many putative RBP recognition elements––including the motifs for Puf3, Puf4, Puf5, Vts1, Puf2, Ssd1, Gbp2, Pin4 and Whi3 (P < 0.01) (Figure 4). Together, this evidence for purifying selection acting to preserve functional recognition elements during evolution suggests that the corresponding post-transcriptional regulatory networks specified by these elements have been conserved among Saccharomyces species as well.Figure 4.


Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome.

Riordan DP, Herschlag D, Brown PO - Nucleic Acids Res. (2010)

Conservation of RNA elements in Saccharomyces. Phylogenetic conservation rates of all sites for each RNA motif were calculated between S. cerevisiae and each of six related Saccharomyces species (par, paradoxus; mik, mikatae; kud, kudriavzevii; bay, bayanus; cas, castellii; klu, kluyveri) based on multiple alignments of the indicated genomic regions. For ‘Overall Conservation', each cell is shaded according to the −log10 P-value measuring if the observed conservation rate of motif sites in that species is significantly greater than expected by chance based on randomized alignments. For ‘target conservation', the cell for each species is shaded to depict the −log10 P-value measuring if the conservation rate of motif sites present within sequences of target mRNAs bound by the cognate RBP is significantly greater than the conservation rate of motif sites from all other transcripts. All P-values were calculated based on the hyper-geometric distribution. Asterisks denote motifs that correspond to previously reported binding sites for the associated RBP. For exact data values and details see Supplementary Data S4.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3045596&req=5

Figure 4: Conservation of RNA elements in Saccharomyces. Phylogenetic conservation rates of all sites for each RNA motif were calculated between S. cerevisiae and each of six related Saccharomyces species (par, paradoxus; mik, mikatae; kud, kudriavzevii; bay, bayanus; cas, castellii; klu, kluyveri) based on multiple alignments of the indicated genomic regions. For ‘Overall Conservation', each cell is shaded according to the −log10 P-value measuring if the observed conservation rate of motif sites in that species is significantly greater than expected by chance based on randomized alignments. For ‘target conservation', the cell for each species is shaded to depict the −log10 P-value measuring if the conservation rate of motif sites present within sequences of target mRNAs bound by the cognate RBP is significantly greater than the conservation rate of motif sites from all other transcripts. All P-values were calculated based on the hyper-geometric distribution. Asterisks denote motifs that correspond to previously reported binding sites for the associated RBP. For exact data values and details see Supplementary Data S4.
Mentions: Using these criteria, we found significant evidence of conservation for almost all of the RNA motifs we tested––including the new SELEX-derived recognition elements for Gbp2, Hrb1, Nsr1 and Pin4, and the novel predicted motifs for Ssd1 and Puf2––in at least one related species (P < 0.01) (Figure 4). Statistical significance of overall conservation rates was established based on a model using permuted versions of each alignment file that were carefully constrained to preserve the identical per-nucleotide conservation rates from the original alignments (‘Materials and Methods’ section). As an additional analysis, we also asked if the conservation rate for each RNA motif was significantly greater for the collection of sites present in the mRNA targets of its cognate RBP than for sites present in all other transcripts. We found significant evidence of this type of ‘target-specific’ preferential conservation for many putative RBP recognition elements––including the motifs for Puf3, Puf4, Puf5, Vts1, Puf2, Ssd1, Gbp2, Pin4 and Whi3 (P < 0.01) (Figure 4). Together, this evidence for purifying selection acting to preserve functional recognition elements during evolution suggests that the corresponding post-transcriptional regulatory networks specified by these elements have been conserved among Saccharomyces species as well.Figure 4.

Bottom Line: We computationally analyzed the sequences of Saccharomyces cerevisiae mRNAs bound in vivo by 29 specific RBPs, identifying eight novel candidate motifs and confirming or extending six earlier reported recognition elements.Biochemical selections for RNA sequences selectively recognized by 12 yeast RBPs yielded novel motifs bound by Pin4, Nsr1, Hrb1, Gbp2, Sgn1 and Mrn1, and recovered the known recognition elements for Puf3, She2, Vts1 and Whi3.Most of the RNA elements we uncovered were associated with coherent mRNA expression changes and were significantly conserved in related yeasts, supporting their functional importance and suggesting that the corresponding RNA-protein interactions are evolutionarily conserved.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA. driordan@stanford.edu

ABSTRACT
Post-transcriptional regulation of gene expression, including mRNA localization, translation and decay, is ubiquitous yet still largely unexplored. How is the post-transcriptional regulatory program of each mRNA encoded in its sequence? Hundreds of specific RNA-binding proteins (RBPs) appear to play roles in mediating the post-transcriptional regulatory program, akin to the roles of specific DNA-binding proteins in transcription. As a step toward decoding the regulatory programs encoded in each mRNA, we focused on specific mRNA-protein interactions. We computationally analyzed the sequences of Saccharomyces cerevisiae mRNAs bound in vivo by 29 specific RBPs, identifying eight novel candidate motifs and confirming or extending six earlier reported recognition elements. Biochemical selections for RNA sequences selectively recognized by 12 yeast RBPs yielded novel motifs bound by Pin4, Nsr1, Hrb1, Gbp2, Sgn1 and Mrn1, and recovered the known recognition elements for Puf3, She2, Vts1 and Whi3. Most of the RNA elements we uncovered were associated with coherent mRNA expression changes and were significantly conserved in related yeasts, supporting their functional importance and suggesting that the corresponding RNA-protein interactions are evolutionarily conserved.

Show MeSH
Related in: MedlinePlus