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Global coordination of transcriptional control and mRNA decay during cellular differentiation.

Amorim MJ, Cotobal C, Duncan C, Mata J - Mol. Syst. Biol. (2010)

Bottom Line: Their levels and half-lives were reduced in meu5 mutants, demonstrating that Meu5p stabilizes its targets.In the absence of meu5, all Mei4p targets were expressed with similar kinetics, indicating that Meu5p alters the global features of the gene expression program.Our data provide insight into the topology of regulatory networks integrating transcriptional and posttranscriptional controls.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.

ABSTRACT
The function of transcription in dynamic gene expression programs has been extensively studied, but little is known about how it is integrated with RNA turnover at the genome-wide level. We investigated these questions using the meiotic gene expression program of Schizosaccharomyces pombe. We identified over 80 transcripts that co-purify with the meiotic-specific Meu5p RNA-binding protein. Their levels and half-lives were reduced in meu5 mutants, demonstrating that Meu5p stabilizes its targets. Most Meu5p-bound RNAs were also targets of the Mei4p transcription factor, which induces the transient expression of approximately 500 meiotic genes. Although many Mei4p targets showed sharp expression peaks, Meu5p targets had broad expression profiles. In the absence of meu5, all Mei4p targets were expressed with similar kinetics, indicating that Meu5p alters the global features of the gene expression program. As Mei4p activates meu5 transcription, Mei4p, Meu5p and their common targets form a feed-forward loop, a motif common in transcriptional networks but not studied in the context of mRNA decay. Our data provide insight into the topology of regulatory networks integrating transcriptional and posttranscriptional controls.

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Related in: MedlinePlus

Meu5p associates with transcripts encoded by middle genes and regulates their expression. (A) Meu5p targets are expressed at low levels in meu5Δ cells. Comparison of expression levels between wild-type and meu5Δ pat1-synchronized meiotic cells (data as in Figure 1B). Meu5p-associated transcripts identified by RIp-chip are shown in red and other genes are shown in grey. The position of the meu5 transcript is indicated with an arrow. (B) Overlap between Meu5p-associated transcripts and middle genes. (C) Overlap between Meu5p-associated transcripts and genes downregulated in meu5Δ cells (in pat1-synchronized meiosis). Labelling of the Venn diagrams is as in Figure 1C.
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f2: Meu5p associates with transcripts encoded by middle genes and regulates their expression. (A) Meu5p targets are expressed at low levels in meu5Δ cells. Comparison of expression levels between wild-type and meu5Δ pat1-synchronized meiotic cells (data as in Figure 1B). Meu5p-associated transcripts identified by RIp-chip are shown in red and other genes are shown in grey. The position of the meu5 transcript is indicated with an arrow. (B) Overlap between Meu5p-associated transcripts and middle genes. (C) Overlap between Meu5p-associated transcripts and genes downregulated in meu5Δ cells (in pat1-synchronized meiosis). Labelling of the Venn diagrams is as in Figure 1C.

Mentions: To discover direct targets of Meu5p, we purified TAP-tagged Meu5p and used DNA microarrays to identify the transcripts present in the immunoprecipitate. We carried out the experiment in synchronized pat1 diploids (at the same time point used for expression analysis) as well as in unsynchronized h90 haploid cells undergoing meiosis. Meu5p-TAP co-purified with 82 transcripts (Figure 2A; Supplementary Figure S2 and Table S2), which were not present in control immunoprecipitates (Amorim and Mata, 2009; data not shown). These mRNAs were strongly enriched in middle genes (Figure 2B; P-value 3 × 10−58) and in genes whose expression was reduced in meu5Δ meiotic cells (Figure 2C; P-value 10−112). Indeed, 87% of the Meu5p-bound transcripts were middle genes.


Global coordination of transcriptional control and mRNA decay during cellular differentiation.

Amorim MJ, Cotobal C, Duncan C, Mata J - Mol. Syst. Biol. (2010)

Meu5p associates with transcripts encoded by middle genes and regulates their expression. (A) Meu5p targets are expressed at low levels in meu5Δ cells. Comparison of expression levels between wild-type and meu5Δ pat1-synchronized meiotic cells (data as in Figure 1B). Meu5p-associated transcripts identified by RIp-chip are shown in red and other genes are shown in grey. The position of the meu5 transcript is indicated with an arrow. (B) Overlap between Meu5p-associated transcripts and middle genes. (C) Overlap between Meu5p-associated transcripts and genes downregulated in meu5Δ cells (in pat1-synchronized meiosis). Labelling of the Venn diagrams is as in Figure 1C.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2913401&req=5

f2: Meu5p associates with transcripts encoded by middle genes and regulates their expression. (A) Meu5p targets are expressed at low levels in meu5Δ cells. Comparison of expression levels between wild-type and meu5Δ pat1-synchronized meiotic cells (data as in Figure 1B). Meu5p-associated transcripts identified by RIp-chip are shown in red and other genes are shown in grey. The position of the meu5 transcript is indicated with an arrow. (B) Overlap between Meu5p-associated transcripts and middle genes. (C) Overlap between Meu5p-associated transcripts and genes downregulated in meu5Δ cells (in pat1-synchronized meiosis). Labelling of the Venn diagrams is as in Figure 1C.
Mentions: To discover direct targets of Meu5p, we purified TAP-tagged Meu5p and used DNA microarrays to identify the transcripts present in the immunoprecipitate. We carried out the experiment in synchronized pat1 diploids (at the same time point used for expression analysis) as well as in unsynchronized h90 haploid cells undergoing meiosis. Meu5p-TAP co-purified with 82 transcripts (Figure 2A; Supplementary Figure S2 and Table S2), which were not present in control immunoprecipitates (Amorim and Mata, 2009; data not shown). These mRNAs were strongly enriched in middle genes (Figure 2B; P-value 3 × 10−58) and in genes whose expression was reduced in meu5Δ meiotic cells (Figure 2C; P-value 10−112). Indeed, 87% of the Meu5p-bound transcripts were middle genes.

Bottom Line: Their levels and half-lives were reduced in meu5 mutants, demonstrating that Meu5p stabilizes its targets.In the absence of meu5, all Mei4p targets were expressed with similar kinetics, indicating that Meu5p alters the global features of the gene expression program.Our data provide insight into the topology of regulatory networks integrating transcriptional and posttranscriptional controls.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.

ABSTRACT
The function of transcription in dynamic gene expression programs has been extensively studied, but little is known about how it is integrated with RNA turnover at the genome-wide level. We investigated these questions using the meiotic gene expression program of Schizosaccharomyces pombe. We identified over 80 transcripts that co-purify with the meiotic-specific Meu5p RNA-binding protein. Their levels and half-lives were reduced in meu5 mutants, demonstrating that Meu5p stabilizes its targets. Most Meu5p-bound RNAs were also targets of the Mei4p transcription factor, which induces the transient expression of approximately 500 meiotic genes. Although many Mei4p targets showed sharp expression peaks, Meu5p targets had broad expression profiles. In the absence of meu5, all Mei4p targets were expressed with similar kinetics, indicating that Meu5p alters the global features of the gene expression program. As Mei4p activates meu5 transcription, Mei4p, Meu5p and their common targets form a feed-forward loop, a motif common in transcriptional networks but not studied in the context of mRNA decay. Our data provide insight into the topology of regulatory networks integrating transcriptional and posttranscriptional controls.

Show MeSH
Related in: MedlinePlus