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High-resolution transcription atlas of the mitotic cell cycle in budding yeast.

Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM - Genome Biol. (2010)

Bottom Line: Our dataset presents the most comprehensive resource to date on gene expression during the budding yeast cell cycle.It reveals periodic expression of both protein-coding and non-coding RNA and profiles the expression of non-annotated RNAs throughout the cell cycle for the first time.This data enables hypothesis-driven mechanistic studies concerning the functions of non-coding RNAs.

View Article: PubMed Central - HTML - PubMed

Affiliation: EMBL - European Molecular Biology Laboratory, Department of Genome Biology, Meyerhofstr, Heidelberg, Germany. mgranovsk@gmail.com

ABSTRACT

Background: Extensive transcription of non-coding RNAs has been detected in eukaryotic genomes and is thought to constitute an additional layer in the regulation of gene expression. Despite this role, their transcription through the cell cycle has not been studied; genome-wide approaches have only focused on protein-coding genes. To explore the complex transcriptome architecture underlying the budding yeast cell cycle, we used 8 bp tiling arrays to generate a 5 minute-resolution, strand-specific expression atlas of the whole genome.

Results: We discovered 523 antisense transcripts, of which 80 cycle or are located opposite periodically expressed mRNAs, 135 unannotated intergenic non-coding RNAs, of which 11 cycle, and 109 cell-cycle-regulated protein-coding genes that had not previously been shown to cycle. We detected periodic expression coupling of sense and antisense transcript pairs, including antisense transcripts opposite of key cell-cycle regulators, like FAR1 and TAF2.

Conclusions: Our dataset presents the most comprehensive resource to date on gene expression during the budding yeast cell cycle. It reveals periodic expression of both protein-coding and non-coding RNA and profiles the expression of non-annotated RNAs throughout the cell cycle for the first time. This data enables hypothesis-driven mechanistic studies concerning the functions of non-coding RNAs.

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Venn diagram displays the overlap of our list of identified cell cycle-regulated protein-coding genes with the lists determined by the previous studies of Gauthier et al. [37], Pramila et al. [29], and Spellman et al. [30]. The overlap shows that we find an additional 223 genes not identified by Gauthier et al., among which 109 are unique to our dataset and were not previously defined by the other studies.
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Figure 4: Venn diagram displays the overlap of our list of identified cell cycle-regulated protein-coding genes with the lists determined by the previous studies of Gauthier et al. [37], Pramila et al. [29], and Spellman et al. [30]. The overlap shows that we find an additional 223 genes not identified by Gauthier et al., among which 109 are unique to our dataset and were not previously defined by the other studies.

Mentions: Previous studies have identified a large number of annotated periodic transcripts. Compared to the integrated dataset of Gauthier et al. [37], our list contains 223 additional periodic protein-coding genes, of which 109 were also not identified by Pramila et al. [29] and Spellman et al. [30] (Figure 4; Additional file 14). Only 3 of the 109 have been shown to be periodically expressed in small scale experiments [47]. GOslim analysis [48] showed that the biological function is unknown for 35 of these 109 genes, whereas 41 perform functions directly or indirectly associated with the regulation of the cell cycle, such as organelle organization and biogenesis, cytoskeleton organization and biogenesis, ribosome biogenesis and assembly, and so on (Additional file 15).


High-resolution transcription atlas of the mitotic cell cycle in budding yeast.

Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM - Genome Biol. (2010)

Venn diagram displays the overlap of our list of identified cell cycle-regulated protein-coding genes with the lists determined by the previous studies of Gauthier et al. [37], Pramila et al. [29], and Spellman et al. [30]. The overlap shows that we find an additional 223 genes not identified by Gauthier et al., among which 109 are unique to our dataset and were not previously defined by the other studies.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2864564&req=5

Figure 4: Venn diagram displays the overlap of our list of identified cell cycle-regulated protein-coding genes with the lists determined by the previous studies of Gauthier et al. [37], Pramila et al. [29], and Spellman et al. [30]. The overlap shows that we find an additional 223 genes not identified by Gauthier et al., among which 109 are unique to our dataset and were not previously defined by the other studies.
Mentions: Previous studies have identified a large number of annotated periodic transcripts. Compared to the integrated dataset of Gauthier et al. [37], our list contains 223 additional periodic protein-coding genes, of which 109 were also not identified by Pramila et al. [29] and Spellman et al. [30] (Figure 4; Additional file 14). Only 3 of the 109 have been shown to be periodically expressed in small scale experiments [47]. GOslim analysis [48] showed that the biological function is unknown for 35 of these 109 genes, whereas 41 perform functions directly or indirectly associated with the regulation of the cell cycle, such as organelle organization and biogenesis, cytoskeleton organization and biogenesis, ribosome biogenesis and assembly, and so on (Additional file 15).

Bottom Line: Our dataset presents the most comprehensive resource to date on gene expression during the budding yeast cell cycle.It reveals periodic expression of both protein-coding and non-coding RNA and profiles the expression of non-annotated RNAs throughout the cell cycle for the first time.This data enables hypothesis-driven mechanistic studies concerning the functions of non-coding RNAs.

View Article: PubMed Central - HTML - PubMed

Affiliation: EMBL - European Molecular Biology Laboratory, Department of Genome Biology, Meyerhofstr, Heidelberg, Germany. mgranovsk@gmail.com

ABSTRACT

Background: Extensive transcription of non-coding RNAs has been detected in eukaryotic genomes and is thought to constitute an additional layer in the regulation of gene expression. Despite this role, their transcription through the cell cycle has not been studied; genome-wide approaches have only focused on protein-coding genes. To explore the complex transcriptome architecture underlying the budding yeast cell cycle, we used 8 bp tiling arrays to generate a 5 minute-resolution, strand-specific expression atlas of the whole genome.

Results: We discovered 523 antisense transcripts, of which 80 cycle or are located opposite periodically expressed mRNAs, 135 unannotated intergenic non-coding RNAs, of which 11 cycle, and 109 cell-cycle-regulated protein-coding genes that had not previously been shown to cycle. We detected periodic expression coupling of sense and antisense transcript pairs, including antisense transcripts opposite of key cell-cycle regulators, like FAR1 and TAF2.

Conclusions: Our dataset presents the most comprehensive resource to date on gene expression during the budding yeast cell cycle. It reveals periodic expression of both protein-coding and non-coding RNA and profiles the expression of non-annotated RNAs throughout the cell cycle for the first time. This data enables hypothesis-driven mechanistic studies concerning the functions of non-coding RNAs.

Show MeSH