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Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system.

Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO - PLoS Biol. (2008)

Bottom Line: These potential RNA-recognition elements were diverse in sequence, structure, and location: some were found predominantly in 3'-untranslated regions, others in 5'-untranslated regions, some in coding sequences, and many in two or more of these features.Although this study only examined a small fraction of the universe of yeast RBPs, 70% of the mRNA transcriptome had significant associations with at least one of these RBPs, and on average, each distinct yeast mRNA interacted with three of the RBPs, suggesting the potential for a rich, multidimensional network of regulation.These results strongly suggest that combinatorial binding of RBPs to specific recognition elements in mRNAs is a pervasive mechanism for multi-dimensional regulation of their post-transcriptional fate.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America.

ABSTRACT
RNA-binding proteins (RBPs) have roles in the regulation of many post-transcriptional steps in gene expression, but relatively few RBPs have been systematically studied. We searched for the RNA targets of 40 proteins in the yeast Saccharomyces cerevisiae: a selective sample of the approximately 600 annotated and predicted RBPs, as well as several proteins not annotated as RBPs. At least 33 of these 40 proteins, including three of the four proteins that were not previously known or predicted to be RBPs, were reproducibly associated with specific sets of a few to several hundred RNAs. Remarkably, many of the RBPs we studied bound mRNAs whose protein products share identifiable functional or cytotopic features. We identified specific sequences or predicted structures significantly enriched in target mRNAs of 16 RBPs. These potential RNA-recognition elements were diverse in sequence, structure, and location: some were found predominantly in 3'-untranslated regions, others in 5'-untranslated regions, some in coding sequences, and many in two or more of these features. Although this study only examined a small fraction of the universe of yeast RBPs, 70% of the mRNA transcriptome had significant associations with at least one of these RBPs, and on average, each distinct yeast mRNA interacted with three of the RBPs, suggesting the potential for a rich, multidimensional network of regulation. These results strongly suggest that combinatorial binding of RBPs to specific recognition elements in mRNAs is a pervasive mechanism for multi-dimensional regulation of their post-transcriptional fate.

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Diverse Binding Specificity among RNA-Binding Proteins(A) Estimated number of RNA species (y-axis) associated with each protein in this survey (x-axis) at a 1% FDR threshold. The proportions of bound RNAs in each of several classes are represented by colors: nuclear-encoded mRNAs (black), nuclear introns (red), mitochondrion-encoded mRNAs (green), C/D box snoRNAs (cyan), H/ACA box snoRNAs (magenta), and all other RNAs (grey), which includes ribosomal RNAs, LSR1, NME1, SCR1, SRG1, TLC1, mitochondrial introns, unannotated “intergenic” transcripts (named IGR* and IGX* in Datasets S1–S3), tRNAs, and splice junctions. An asterisk (*) denotes proteins whose targets were identified using DNA microarrays that did not contain probes designed to detect most non-nuclear-encoded mRNAs. Six proteins from our previously published work (Puf1–5 and She2) are also included (marked with a plus sign [+]).(B) Hierarchically clustered heat map representation of RBPs and their RNA targets. Rows correspond to specific RBPs and columns correspond to RNAs. The certainty that the RNA is a bona fide target of the specified RBP is represented by a continuous black (10% FDR or greater) to yellow (0% FDR) scale.(C) The distribution of the number of RBPs bound per mRNA at 1% FDR threshold is shown as a bar plot. The black bars represent the values for the 31 RBPs associated with at least ten mRNAs, and the grey bars represent the 22 RBPs associated with at least ten mRNAs, but fewer than 500 mRNAs.
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pbio-0060255-g001: Diverse Binding Specificity among RNA-Binding Proteins(A) Estimated number of RNA species (y-axis) associated with each protein in this survey (x-axis) at a 1% FDR threshold. The proportions of bound RNAs in each of several classes are represented by colors: nuclear-encoded mRNAs (black), nuclear introns (red), mitochondrion-encoded mRNAs (green), C/D box snoRNAs (cyan), H/ACA box snoRNAs (magenta), and all other RNAs (grey), which includes ribosomal RNAs, LSR1, NME1, SCR1, SRG1, TLC1, mitochondrial introns, unannotated “intergenic” transcripts (named IGR* and IGX* in Datasets S1–S3), tRNAs, and splice junctions. An asterisk (*) denotes proteins whose targets were identified using DNA microarrays that did not contain probes designed to detect most non-nuclear-encoded mRNAs. Six proteins from our previously published work (Puf1–5 and She2) are also included (marked with a plus sign [+]).(B) Hierarchically clustered heat map representation of RBPs and their RNA targets. Rows correspond to specific RBPs and columns correspond to RNAs. The certainty that the RNA is a bona fide target of the specified RBP is represented by a continuous black (10% FDR or greater) to yellow (0% FDR) scale.(C) The distribution of the number of RBPs bound per mRNA at 1% FDR threshold is shown as a bar plot. The black bars represent the values for the 31 RBPs associated with at least ten mRNAs, and the grey bars represent the 22 RBPs associated with at least ten mRNAs, but fewer than 500 mRNAs.

Mentions: The 40 proteins in the survey (and also Puf1–5 and She2 from our previous work [26,32]) displayed diverse patterns of specificity with regard to the numbers and types of RNA targets and their enrichment profiles (Figures 1 and S1, and Text S3). The number of confidently identified RNA targets varied widely among the proteins surveyed, ranging from fewer than ten (Nce102, Nrp1, Idh1, Rib2, Nop13, Bud27, Rna15, Pbp2, Dhh1, Upf1, and Mex67) to more than a thousand (Pab1, Pub1, Scp160, Npl3, Nrd1, and Bfr1) (Figure 1A). The two “negative controls,” Nce102 and Bud27, were each associated with specific RNAs. Nce102 was associated with eight distinct RNAs, whereas Bud27 was associated with two putative mRNA targets; interestingly, one of these putative targets (RPA190) was reproducibly enriched more than 300-fold, and both targets were lost when immunopurifications were performed in the absence of Mg2+ (unpublished data). Because neither Nce102 nor Bud27 was known or expected to associate with RNA, the RNAs identified as their targets may be spurious, but we cannot exclude the possibility that the RNA interactions we found for these two proteins are real and significant. Regardless, they provide a benchmark estimate of the number of RNA targets falsely identified for other RBPs. Aconitase (Aco1) and glyceraldehyde-3 phosphate dehydrogenase (Tdh3), two metabolic enzymes whose human orthologs also function as RBPs [46,47], but which were not previously known to be RBPs in yeast, associated with 38 and 155 RNAs, respectively, at 1% FDR, indicating that these enzymes are also RBPs in yeast.


Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system.

Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO - PLoS Biol. (2008)

Diverse Binding Specificity among RNA-Binding Proteins(A) Estimated number of RNA species (y-axis) associated with each protein in this survey (x-axis) at a 1% FDR threshold. The proportions of bound RNAs in each of several classes are represented by colors: nuclear-encoded mRNAs (black), nuclear introns (red), mitochondrion-encoded mRNAs (green), C/D box snoRNAs (cyan), H/ACA box snoRNAs (magenta), and all other RNAs (grey), which includes ribosomal RNAs, LSR1, NME1, SCR1, SRG1, TLC1, mitochondrial introns, unannotated “intergenic” transcripts (named IGR* and IGX* in Datasets S1–S3), tRNAs, and splice junctions. An asterisk (*) denotes proteins whose targets were identified using DNA microarrays that did not contain probes designed to detect most non-nuclear-encoded mRNAs. Six proteins from our previously published work (Puf1–5 and She2) are also included (marked with a plus sign [+]).(B) Hierarchically clustered heat map representation of RBPs and their RNA targets. Rows correspond to specific RBPs and columns correspond to RNAs. The certainty that the RNA is a bona fide target of the specified RBP is represented by a continuous black (10% FDR or greater) to yellow (0% FDR) scale.(C) The distribution of the number of RBPs bound per mRNA at 1% FDR threshold is shown as a bar plot. The black bars represent the values for the 31 RBPs associated with at least ten mRNAs, and the grey bars represent the 22 RBPs associated with at least ten mRNAs, but fewer than 500 mRNAs.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2573929&req=5

pbio-0060255-g001: Diverse Binding Specificity among RNA-Binding Proteins(A) Estimated number of RNA species (y-axis) associated with each protein in this survey (x-axis) at a 1% FDR threshold. The proportions of bound RNAs in each of several classes are represented by colors: nuclear-encoded mRNAs (black), nuclear introns (red), mitochondrion-encoded mRNAs (green), C/D box snoRNAs (cyan), H/ACA box snoRNAs (magenta), and all other RNAs (grey), which includes ribosomal RNAs, LSR1, NME1, SCR1, SRG1, TLC1, mitochondrial introns, unannotated “intergenic” transcripts (named IGR* and IGX* in Datasets S1–S3), tRNAs, and splice junctions. An asterisk (*) denotes proteins whose targets were identified using DNA microarrays that did not contain probes designed to detect most non-nuclear-encoded mRNAs. Six proteins from our previously published work (Puf1–5 and She2) are also included (marked with a plus sign [+]).(B) Hierarchically clustered heat map representation of RBPs and their RNA targets. Rows correspond to specific RBPs and columns correspond to RNAs. The certainty that the RNA is a bona fide target of the specified RBP is represented by a continuous black (10% FDR or greater) to yellow (0% FDR) scale.(C) The distribution of the number of RBPs bound per mRNA at 1% FDR threshold is shown as a bar plot. The black bars represent the values for the 31 RBPs associated with at least ten mRNAs, and the grey bars represent the 22 RBPs associated with at least ten mRNAs, but fewer than 500 mRNAs.
Mentions: The 40 proteins in the survey (and also Puf1–5 and She2 from our previous work [26,32]) displayed diverse patterns of specificity with regard to the numbers and types of RNA targets and their enrichment profiles (Figures 1 and S1, and Text S3). The number of confidently identified RNA targets varied widely among the proteins surveyed, ranging from fewer than ten (Nce102, Nrp1, Idh1, Rib2, Nop13, Bud27, Rna15, Pbp2, Dhh1, Upf1, and Mex67) to more than a thousand (Pab1, Pub1, Scp160, Npl3, Nrd1, and Bfr1) (Figure 1A). The two “negative controls,” Nce102 and Bud27, were each associated with specific RNAs. Nce102 was associated with eight distinct RNAs, whereas Bud27 was associated with two putative mRNA targets; interestingly, one of these putative targets (RPA190) was reproducibly enriched more than 300-fold, and both targets were lost when immunopurifications were performed in the absence of Mg2+ (unpublished data). Because neither Nce102 nor Bud27 was known or expected to associate with RNA, the RNAs identified as their targets may be spurious, but we cannot exclude the possibility that the RNA interactions we found for these two proteins are real and significant. Regardless, they provide a benchmark estimate of the number of RNA targets falsely identified for other RBPs. Aconitase (Aco1) and glyceraldehyde-3 phosphate dehydrogenase (Tdh3), two metabolic enzymes whose human orthologs also function as RBPs [46,47], but which were not previously known to be RBPs in yeast, associated with 38 and 155 RNAs, respectively, at 1% FDR, indicating that these enzymes are also RBPs in yeast.

Bottom Line: These potential RNA-recognition elements were diverse in sequence, structure, and location: some were found predominantly in 3'-untranslated regions, others in 5'-untranslated regions, some in coding sequences, and many in two or more of these features.Although this study only examined a small fraction of the universe of yeast RBPs, 70% of the mRNA transcriptome had significant associations with at least one of these RBPs, and on average, each distinct yeast mRNA interacted with three of the RBPs, suggesting the potential for a rich, multidimensional network of regulation.These results strongly suggest that combinatorial binding of RBPs to specific recognition elements in mRNAs is a pervasive mechanism for multi-dimensional regulation of their post-transcriptional fate.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America.

ABSTRACT
RNA-binding proteins (RBPs) have roles in the regulation of many post-transcriptional steps in gene expression, but relatively few RBPs have been systematically studied. We searched for the RNA targets of 40 proteins in the yeast Saccharomyces cerevisiae: a selective sample of the approximately 600 annotated and predicted RBPs, as well as several proteins not annotated as RBPs. At least 33 of these 40 proteins, including three of the four proteins that were not previously known or predicted to be RBPs, were reproducibly associated with specific sets of a few to several hundred RNAs. Remarkably, many of the RBPs we studied bound mRNAs whose protein products share identifiable functional or cytotopic features. We identified specific sequences or predicted structures significantly enriched in target mRNAs of 16 RBPs. These potential RNA-recognition elements were diverse in sequence, structure, and location: some were found predominantly in 3'-untranslated regions, others in 5'-untranslated regions, some in coding sequences, and many in two or more of these features. Although this study only examined a small fraction of the universe of yeast RBPs, 70% of the mRNA transcriptome had significant associations with at least one of these RBPs, and on average, each distinct yeast mRNA interacted with three of the RBPs, suggesting the potential for a rich, multidimensional network of regulation. These results strongly suggest that combinatorial binding of RBPs to specific recognition elements in mRNAs is a pervasive mechanism for multi-dimensional regulation of their post-transcriptional fate.

Show MeSH
Related in: MedlinePlus