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Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity.

Laver JD, Li X, Ancevicius K, Westwood JT, Smibert CA, Morris QD, Lipshitz HD - Nucleic Acids Res. (2013)

Bottom Line: We performed RNA co-immunoprecipitations followed by microarray analysis to identify Staufen-associated mRNAs in early Drosophila embryos.First, these Drosophila transcripts, as well as those human transcripts bound by human Staufen1 and 2, have 3' untranslated regions (UTRs) that are 3-4-fold longer than unbound transcripts.These structures map with high precision to previously identified Staufen-binding regions in Drosophila bicoid and human ARF1 3'UTRs.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8, Department of Cell & Systems Biology, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, Ontario, Canada L5L 1C6, Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, Ontario, Canada L5L 1C6, Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8 and Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, 160 College Street, Toronto, Ontario, Canada M5S 3E1.

ABSTRACT
Despite studies that have investigated the interactions of double-stranded RNA-binding proteins like Staufen with RNA in vitro, how they achieve target specificity in vivo remains uncertain. We performed RNA co-immunoprecipitations followed by microarray analysis to identify Staufen-associated mRNAs in early Drosophila embryos. Analysis of the localization and functions of these transcripts revealed a number of potentially novel roles for Staufen. Using computational methods, we identified two sequence features that distinguish Staufen's target transcripts from non-targets. First, these Drosophila transcripts, as well as those human transcripts bound by human Staufen1 and 2, have 3' untranslated regions (UTRs) that are 3-4-fold longer than unbound transcripts. Second, the 3'UTRs of Staufen-bound transcripts are highly enriched for three types of secondary structures. These structures map with high precision to previously identified Staufen-binding regions in Drosophila bicoid and human ARF1 3'UTRs. Our results provide the first systematic genome-wide analysis showing how a double-stranded RNA-binding protein achieves target specificity.

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Mapping of SRSs in the 3′UTRs of Staufen targets and non-targets. The three types of SRSs were mapped in the 3′UTRs of Staufen targets (A), length-matched non-targets (B) and a random subset of non-targets (C). The x-axis represents the 3′UTR in nucleotides, starting from the first nucleotide after the stop codon. Each 3′UTR is represented by a grey bar, within which the predicted SRS hits are represented by coloured bars (Type I: dark blue; Type II: light blue; Type III: red; Type III embedded in or overlapping with Type I: black; Type III embedded in or overlapping with Type II: magenta). For each SRS, the 5′-most nucleotide in the corresponding 15 of 19 or 10 of 12 motif is connected to the paired nucleotide in the partner arm by a line of the same colour as the SRS (Type I: dark blue, Type II: light blue, Type III: red).
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gkt702-F9: Mapping of SRSs in the 3′UTRs of Staufen targets and non-targets. The three types of SRSs were mapped in the 3′UTRs of Staufen targets (A), length-matched non-targets (B) and a random subset of non-targets (C). The x-axis represents the 3′UTR in nucleotides, starting from the first nucleotide after the stop codon. Each 3′UTR is represented by a grey bar, within which the predicted SRS hits are represented by coloured bars (Type I: dark blue; Type II: light blue; Type III: red; Type III embedded in or overlapping with Type I: black; Type III embedded in or overlapping with Type II: magenta). For each SRS, the 5′-most nucleotide in the corresponding 15 of 19 or 10 of 12 motif is connected to the paired nucleotide in the partner arm by a line of the same colour as the SRS (Type I: dark blue, Type II: light blue, Type III: red).

Mentions: We next mapped the locations of the three types of SRSs within the 3′UTRs of all Drosophila mRNAs (Supplementary Table S17). Figure 9 shows the locations of SRSs in the 3′UTRs of the Staufen target transcripts, length-matched non-target transcript 3′UTRs and a random subset of non-target 3′UTRs.Figure 9.


Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity.

Laver JD, Li X, Ancevicius K, Westwood JT, Smibert CA, Morris QD, Lipshitz HD - Nucleic Acids Res. (2013)

Mapping of SRSs in the 3′UTRs of Staufen targets and non-targets. The three types of SRSs were mapped in the 3′UTRs of Staufen targets (A), length-matched non-targets (B) and a random subset of non-targets (C). The x-axis represents the 3′UTR in nucleotides, starting from the first nucleotide after the stop codon. Each 3′UTR is represented by a grey bar, within which the predicted SRS hits are represented by coloured bars (Type I: dark blue; Type II: light blue; Type III: red; Type III embedded in or overlapping with Type I: black; Type III embedded in or overlapping with Type II: magenta). For each SRS, the 5′-most nucleotide in the corresponding 15 of 19 or 10 of 12 motif is connected to the paired nucleotide in the partner arm by a line of the same colour as the SRS (Type I: dark blue, Type II: light blue, Type III: red).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814352&req=5

gkt702-F9: Mapping of SRSs in the 3′UTRs of Staufen targets and non-targets. The three types of SRSs were mapped in the 3′UTRs of Staufen targets (A), length-matched non-targets (B) and a random subset of non-targets (C). The x-axis represents the 3′UTR in nucleotides, starting from the first nucleotide after the stop codon. Each 3′UTR is represented by a grey bar, within which the predicted SRS hits are represented by coloured bars (Type I: dark blue; Type II: light blue; Type III: red; Type III embedded in or overlapping with Type I: black; Type III embedded in or overlapping with Type II: magenta). For each SRS, the 5′-most nucleotide in the corresponding 15 of 19 or 10 of 12 motif is connected to the paired nucleotide in the partner arm by a line of the same colour as the SRS (Type I: dark blue, Type II: light blue, Type III: red).
Mentions: We next mapped the locations of the three types of SRSs within the 3′UTRs of all Drosophila mRNAs (Supplementary Table S17). Figure 9 shows the locations of SRSs in the 3′UTRs of the Staufen target transcripts, length-matched non-target transcript 3′UTRs and a random subset of non-target 3′UTRs.Figure 9.

Bottom Line: We performed RNA co-immunoprecipitations followed by microarray analysis to identify Staufen-associated mRNAs in early Drosophila embryos.First, these Drosophila transcripts, as well as those human transcripts bound by human Staufen1 and 2, have 3' untranslated regions (UTRs) that are 3-4-fold longer than unbound transcripts.These structures map with high precision to previously identified Staufen-binding regions in Drosophila bicoid and human ARF1 3'UTRs.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8, Department of Cell & Systems Biology, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, Ontario, Canada L5L 1C6, Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, Ontario, Canada L5L 1C6, Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8 and Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, 160 College Street, Toronto, Ontario, Canada M5S 3E1.

ABSTRACT
Despite studies that have investigated the interactions of double-stranded RNA-binding proteins like Staufen with RNA in vitro, how they achieve target specificity in vivo remains uncertain. We performed RNA co-immunoprecipitations followed by microarray analysis to identify Staufen-associated mRNAs in early Drosophila embryos. Analysis of the localization and functions of these transcripts revealed a number of potentially novel roles for Staufen. Using computational methods, we identified two sequence features that distinguish Staufen's target transcripts from non-targets. First, these Drosophila transcripts, as well as those human transcripts bound by human Staufen1 and 2, have 3' untranslated regions (UTRs) that are 3-4-fold longer than unbound transcripts. Second, the 3'UTRs of Staufen-bound transcripts are highly enriched for three types of secondary structures. These structures map with high precision to previously identified Staufen-binding regions in Drosophila bicoid and human ARF1 3'UTRs. Our results provide the first systematic genome-wide analysis showing how a double-stranded RNA-binding protein achieves target specificity.

Show MeSH
Related in: MedlinePlus