Limits...
Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species.

Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G - PLoS Genet. (2008)

Bottom Line: Despite the status of Saccharomyces cerevisiae as arguably the most well-studied model eukaryote, we still do not have a full catalog or understanding of all its genes.Of the 185 transcripts we identified as novel to our study, greater than 80 percent come from regions of the genome that have lower conservation scores amongst closely related yeast species than 85 percent of the verified ORFs in S. cerevisiae.Such regions of the genome have typically been less well-studied, and by definition transcripts from these regions will distinguish S. cerevisiae from these closely related species.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Stanford University, Stanford, CA, USA.

ABSTRACT
A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it functions and how its transcriptional networks are controlled, and may provide insights into the organism's evolution. Despite the status of Saccharomyces cerevisiae as arguably the most well-studied model eukaryote, we still do not have a full catalog or understanding of all its genes. In order to interrogate the transcriptome of S. cerevisiae for low abundance or rapidly turned over transcripts, we deleted elements of the RNA degradation machinery with the goal of preferentially increasing the relative abundance of such transcripts. We then used high-resolution tiling microarrays and ultra high-throughput sequencing (UHTS) to identify, map, and validate unannotated transcripts that are more abundant in the RNA degradation mutants relative to wild-type cells. We identified 365 currently unannotated transcripts, the majority presumably representing low abundance or short-lived RNAs, of which 185 are previously unknown and unique to this study. It is likely that many of these are cryptic unstable transcripts (CUTs), which are rapidly degraded and whose function(s) within the cell are still unclear, while others may be novel functional transcripts. Of the 185 transcripts we identified as novel to our study, greater than 80 percent come from regions of the genome that have lower conservation scores amongst closely related yeast species than 85 percent of the verified ORFs in S. cerevisiae. Such regions of the genome have typically been less well-studied, and by definition transcripts from these regions will distinguish S. cerevisiae from these closely related species.

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An unannotated transcript found in this study, also found in other studies.This one is in a region of high conservation. See the legend for Figure 5 for details.
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pgen-1000299-g010: An unannotated transcript found in this study, also found in other studies.This one is in a region of high conservation. See the legend for Figure 5 for details.

Mentions: For each of the potential novel transcripts, their immediate surrounding regions were plotted (e.g. see Figures 5 through 10 and Figures S5 and S6) along with a track of the current annotation from SGD [18], and data from David et al. [25], Miura et al. [26], and Nagalakshmi et al. [37]. Additional tracks representing nucleosome positioning [67] and the degree of conservation between Saccharomyces cerevisiae and other closely related yeast species [68] were also plotted. In addition, the transcript's chromosome and its strand of origin are shown at the bottom of each plot. Six examples of transcripts unannotated in SGD and identified in this study can be seen in Figures 5 through 10, all of which are located in regions currently described as intergenic. Plots for all 365 currently unannotated transcripts identified in this study can be found in Figures S5 and S6.


Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species.

Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G - PLoS Genet. (2008)

An unannotated transcript found in this study, also found in other studies.This one is in a region of high conservation. See the legend for Figure 5 for details.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2601015&req=5

pgen-1000299-g010: An unannotated transcript found in this study, also found in other studies.This one is in a region of high conservation. See the legend for Figure 5 for details.
Mentions: For each of the potential novel transcripts, their immediate surrounding regions were plotted (e.g. see Figures 5 through 10 and Figures S5 and S6) along with a track of the current annotation from SGD [18], and data from David et al. [25], Miura et al. [26], and Nagalakshmi et al. [37]. Additional tracks representing nucleosome positioning [67] and the degree of conservation between Saccharomyces cerevisiae and other closely related yeast species [68] were also plotted. In addition, the transcript's chromosome and its strand of origin are shown at the bottom of each plot. Six examples of transcripts unannotated in SGD and identified in this study can be seen in Figures 5 through 10, all of which are located in regions currently described as intergenic. Plots for all 365 currently unannotated transcripts identified in this study can be found in Figures S5 and S6.

Bottom Line: Despite the status of Saccharomyces cerevisiae as arguably the most well-studied model eukaryote, we still do not have a full catalog or understanding of all its genes.Of the 185 transcripts we identified as novel to our study, greater than 80 percent come from regions of the genome that have lower conservation scores amongst closely related yeast species than 85 percent of the verified ORFs in S. cerevisiae.Such regions of the genome have typically been less well-studied, and by definition transcripts from these regions will distinguish S. cerevisiae from these closely related species.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Stanford University, Stanford, CA, USA.

ABSTRACT
A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it functions and how its transcriptional networks are controlled, and may provide insights into the organism's evolution. Despite the status of Saccharomyces cerevisiae as arguably the most well-studied model eukaryote, we still do not have a full catalog or understanding of all its genes. In order to interrogate the transcriptome of S. cerevisiae for low abundance or rapidly turned over transcripts, we deleted elements of the RNA degradation machinery with the goal of preferentially increasing the relative abundance of such transcripts. We then used high-resolution tiling microarrays and ultra high-throughput sequencing (UHTS) to identify, map, and validate unannotated transcripts that are more abundant in the RNA degradation mutants relative to wild-type cells. We identified 365 currently unannotated transcripts, the majority presumably representing low abundance or short-lived RNAs, of which 185 are previously unknown and unique to this study. It is likely that many of these are cryptic unstable transcripts (CUTs), which are rapidly degraded and whose function(s) within the cell are still unclear, while others may be novel functional transcripts. Of the 185 transcripts we identified as novel to our study, greater than 80 percent come from regions of the genome that have lower conservation scores amongst closely related yeast species than 85 percent of the verified ORFs in S. cerevisiae. Such regions of the genome have typically been less well-studied, and by definition transcripts from these regions will distinguish S. cerevisiae from these closely related species.

Show MeSH
Related in: MedlinePlus