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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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Related in: MedlinePlus

Gene expression profiles for all identified cell-cycle-regulated ncRNAs ordered by their expression peak times. Each column of the CDC28 and alpha-factor time-course panels represents a single experimental 5-minute time-point. The scales on the left display the relative duration and number of transcripts expressed in each phase. In each row, white and dark red represent the minimum and maximum expression levels, respectively, of the corresponding transcript. Intermediate values are shown by colors that scale linearly over the range.
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Figure 2: Gene expression profiles for all identified cell-cycle-regulated ncRNAs ordered by their expression peak times. Each column of the CDC28 and alpha-factor time-course panels represents a single experimental 5-minute time-point. The scales on the left display the relative duration and number of transcripts expressed in each phase. In each row, white and dark red represent the minimum and maximum expression levels, respectively, of the corresponding transcript. Intermediate values are shown by colors that scale linearly over the range.

Mentions: Altogether, 598 periodic mRNAs, 37 cycling antisense RNAs, and 11 cycling intergenic transcripts were identified and ranked according to their peak time of expression (Figure 1; Additional file 5). Non-coding periodic transcripts were expressed in all cell-cycle phases (Figure 2; see Additional file 6 for the determination of the boundaries of the cell cycle phases). Overall, the peak times of antisense periodic expression were consistent with the waves of expression of periodic protein-coding genes [38]. To characterize the newly discovered periodic ncRNAs, we overlapped them with regions of conserved RNA secondary structure [39]. Despite their cell-cycle-regulated expression, the unannotated intergenic and antisense ncRNAs had little secondary structure (Additional file 6). Conversely, infrastructural ncRNAs, comprising tRNAs, rRNAs, small nuclear and small nucleolar RNAs, were highly structured but were not periodically expressed.


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)

Gene expression profiles for all identified cell-cycle-regulated ncRNAs ordered by their expression peak times. Each column of the CDC28 and alpha-factor time-course panels represents a single experimental 5-minute time-point. The scales on the left display the relative duration and number of transcripts expressed in each phase. In each row, white and dark red represent the minimum and maximum expression levels, respectively, of the corresponding transcript. Intermediate values are shown by colors that scale linearly over the range.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Gene expression profiles for all identified cell-cycle-regulated ncRNAs ordered by their expression peak times. Each column of the CDC28 and alpha-factor time-course panels represents a single experimental 5-minute time-point. The scales on the left display the relative duration and number of transcripts expressed in each phase. In each row, white and dark red represent the minimum and maximum expression levels, respectively, of the corresponding transcript. Intermediate values are shown by colors that scale linearly over the range.
Mentions: Altogether, 598 periodic mRNAs, 37 cycling antisense RNAs, and 11 cycling intergenic transcripts were identified and ranked according to their peak time of expression (Figure 1; Additional file 5). Non-coding periodic transcripts were expressed in all cell-cycle phases (Figure 2; see Additional file 6 for the determination of the boundaries of the cell cycle phases). Overall, the peak times of antisense periodic expression were consistent with the waves of expression of periodic protein-coding genes [38]. To characterize the newly discovered periodic ncRNAs, we overlapped them with regions of conserved RNA secondary structure [39]. Despite their cell-cycle-regulated expression, the unannotated intergenic and antisense ncRNAs had little secondary structure (Additional file 6). Conversely, infrastructural ncRNAs, comprising tRNAs, rRNAs, small nuclear and small nucleolar RNAs, were highly structured but were not periodically expressed.

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
Related in: MedlinePlus