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Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs.

Foat BC, Stormo GD - Mol. Syst. Biol. (2009)

Bottom Line: In addition, we discovered six putative SCREs in flies and three in humans.We characterized the SCREs based on their condition-specific regulatory influences, the annotation of the transcripts that contain them, and their locations within transcripts.Overall, we show that modeling functional genomics data in terms of combined RNA structure and sequence motifs is an effective method for discovering the specificities and regulatory roles of RNA-binding proteins.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA.

ABSTRACT
Gene expression is regulated at each step from chromatin remodeling through translation and degradation. Several known RNA-binding regulatory proteins interact with specific RNA secondary structures in addition to specific nucleotides. To provide a more comprehensive understanding of the regulation of gene expression, we developed an integrative computational approach that leverages functional genomics data and nucleotide sequences to discover RNA secondary structure-defined cis-regulatory elements (SCREs). We applied our structural cis-regulatory element detector (StructRED) to microarray and mRNA sequence data from Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We recovered the known specificities of Vts1p in yeast and Smaug in flies. In addition, we discovered six putative SCREs in flies and three in humans. We characterized the SCREs based on their condition-specific regulatory influences, the annotation of the transcripts that contain them, and their locations within transcripts. Overall, we show that modeling functional genomics data in terms of combined RNA structure and sequence motifs is an effective method for discovering the specificities and regulatory roles of RNA-binding proteins.

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Explaining Smaug-independent mRNA degradation. Not all maternally deposited mRNAs degrade in a Smaug-dependent manner. (A) These are the logos of two single-stranded RNA motifs that had strong correlations with decreasing mRNA levels in early embryogenesis in Drosophila. The Dm7 motif likely represents the specificity of an unknown trans-factor. The Pum motif is likely the specificity of Pumilio. (B) Both of these motifs correlated with decreasing mRNA levels in Δsmg activated eggs.
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f6: Explaining Smaug-independent mRNA degradation. Not all maternally deposited mRNAs degrade in a Smaug-dependent manner. (A) These are the logos of two single-stranded RNA motifs that had strong correlations with decreasing mRNA levels in early embryogenesis in Drosophila. The Dm7 motif likely represents the specificity of an unknown trans-factor. The Pum motif is likely the specificity of Pumilio. (B) Both of these motifs correlated with decreasing mRNA levels in Δsmg activated eggs.

Mentions: Tadros et al (2007) investigated the role of Smaug in early Drosophila development by measuring genome-wide mRNA expression in both wild-type and Δsmg activated eggs. Thus, they identified maternally deposited transcripts that were degraded by both Smaug-dependent and independent mechanisms. The authors do not provide candidate regulators that affect the degradation of the Smaug-independent mRNAs. With the hopes of identifying the specificity of such a regulator, we looked for any of our SCREs that negatively correlated with mRNA levels in both the wild-type and Δsmg activated eggs. We found none. However, as part of the preprocessing steps before the SCRE search, we discovered all of the significantly explanatory single-stranded mRNA motifs. The intention of this step was to increase the likelihood that any discovered SCREs reflected real structural elements and not a structure-like reflection of an otherwise single-stranded regulatory element. Although we do not discuss most of those results here, inspecting them for any motifs that correlated with mRNA degradation in the Δsmg eggs revealed two such motifs (Figure 6). The Dm7 motif and activity profile may belong to a yet uncharacterized RBP in Drosophila. Dm7 has the correct TFAP for a Smaug-independent regulator of mRNA stability during early embryogenesis, having strong negative correlations with mRNA levels as time elapses to 4–6 h in both wild-type and Δsmg activated eggs. Dm7 is similar to the UUGUU motifs identified in maternal unstable transcripts by De Renzis et al (2007). Another motif that we label ‘Pum' is almost certainly the specificity of Pumilio, the founding member of the Puf family of RBPs (Zhang et al, 1997). We confirmed that the Pum motif is the Pumilio specificity by testing how well its sequence scores predicted genome-wide association of mRNAs with Pumilio, using the microarray data of (Gerber et al, 2006; P-value <10−25). Strangely, the Pum motif only correlates with the degradation of mRNAs in the Δsmg activated eggs. This observation suggests that there is a more complex relationship between the regulatory activities of Pumilio and Smaug that could benefit from future experimental characterization.


Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs.

Foat BC, Stormo GD - Mol. Syst. Biol. (2009)

Explaining Smaug-independent mRNA degradation. Not all maternally deposited mRNAs degrade in a Smaug-dependent manner. (A) These are the logos of two single-stranded RNA motifs that had strong correlations with decreasing mRNA levels in early embryogenesis in Drosophila. The Dm7 motif likely represents the specificity of an unknown trans-factor. The Pum motif is likely the specificity of Pumilio. (B) Both of these motifs correlated with decreasing mRNA levels in Δsmg activated eggs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2683727&req=5

f6: Explaining Smaug-independent mRNA degradation. Not all maternally deposited mRNAs degrade in a Smaug-dependent manner. (A) These are the logos of two single-stranded RNA motifs that had strong correlations with decreasing mRNA levels in early embryogenesis in Drosophila. The Dm7 motif likely represents the specificity of an unknown trans-factor. The Pum motif is likely the specificity of Pumilio. (B) Both of these motifs correlated with decreasing mRNA levels in Δsmg activated eggs.
Mentions: Tadros et al (2007) investigated the role of Smaug in early Drosophila development by measuring genome-wide mRNA expression in both wild-type and Δsmg activated eggs. Thus, they identified maternally deposited transcripts that were degraded by both Smaug-dependent and independent mechanisms. The authors do not provide candidate regulators that affect the degradation of the Smaug-independent mRNAs. With the hopes of identifying the specificity of such a regulator, we looked for any of our SCREs that negatively correlated with mRNA levels in both the wild-type and Δsmg activated eggs. We found none. However, as part of the preprocessing steps before the SCRE search, we discovered all of the significantly explanatory single-stranded mRNA motifs. The intention of this step was to increase the likelihood that any discovered SCREs reflected real structural elements and not a structure-like reflection of an otherwise single-stranded regulatory element. Although we do not discuss most of those results here, inspecting them for any motifs that correlated with mRNA degradation in the Δsmg eggs revealed two such motifs (Figure 6). The Dm7 motif and activity profile may belong to a yet uncharacterized RBP in Drosophila. Dm7 has the correct TFAP for a Smaug-independent regulator of mRNA stability during early embryogenesis, having strong negative correlations with mRNA levels as time elapses to 4–6 h in both wild-type and Δsmg activated eggs. Dm7 is similar to the UUGUU motifs identified in maternal unstable transcripts by De Renzis et al (2007). Another motif that we label ‘Pum' is almost certainly the specificity of Pumilio, the founding member of the Puf family of RBPs (Zhang et al, 1997). We confirmed that the Pum motif is the Pumilio specificity by testing how well its sequence scores predicted genome-wide association of mRNAs with Pumilio, using the microarray data of (Gerber et al, 2006; P-value <10−25). Strangely, the Pum motif only correlates with the degradation of mRNAs in the Δsmg activated eggs. This observation suggests that there is a more complex relationship between the regulatory activities of Pumilio and Smaug that could benefit from future experimental characterization.

Bottom Line: In addition, we discovered six putative SCREs in flies and three in humans.We characterized the SCREs based on their condition-specific regulatory influences, the annotation of the transcripts that contain them, and their locations within transcripts.Overall, we show that modeling functional genomics data in terms of combined RNA structure and sequence motifs is an effective method for discovering the specificities and regulatory roles of RNA-binding proteins.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63108, USA.

ABSTRACT
Gene expression is regulated at each step from chromatin remodeling through translation and degradation. Several known RNA-binding regulatory proteins interact with specific RNA secondary structures in addition to specific nucleotides. To provide a more comprehensive understanding of the regulation of gene expression, we developed an integrative computational approach that leverages functional genomics data and nucleotide sequences to discover RNA secondary structure-defined cis-regulatory elements (SCREs). We applied our structural cis-regulatory element detector (StructRED) to microarray and mRNA sequence data from Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We recovered the known specificities of Vts1p in yeast and Smaug in flies. In addition, we discovered six putative SCREs in flies and three in humans. We characterized the SCREs based on their condition-specific regulatory influences, the annotation of the transcripts that contain them, and their locations within transcripts. Overall, we show that modeling functional genomics data in terms of combined RNA structure and sequence motifs is an effective method for discovering the specificities and regulatory roles of RNA-binding proteins.

Show MeSH