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Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation.

Nugent RL, Johnsson A, Fleharty B, Gogol M, Xue-Franzén Y, Seidel C, Wright AP, Forsburg SL - BMC Genomics (2010)

Bottom Line: Comparison of phenotypes and expression profiles in single, double and triple mutants indicate that these HAT enzymes have overlapping functions.Consistent with this, overlapping specificity in histone H3 acetylation is observed.However, there is no evidence for overlap with another HAT enzyme, encoded by the essential mst1+ gene.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular and Computational Biology Section, University of Southern California, Los Angeles, California 90089-2910, USA.

ABSTRACT

Background: Histone acetyltransferase enzymes (HATs) are implicated in regulation of transcription. HATs from different families may overlap in target and substrate specificity.

Results: We isolated the elp3+ gene encoding the histone acetyltransferase subunit of the Elongator complex in fission yeast and characterized the phenotype of an Deltaelp3 mutant. We examined genetic interactions between Deltaelp3 and two other HAT mutants, Deltamst2 and Deltagcn5 and used whole genome microarray analysis to analyze their effects on gene expression.

Conclusions: Comparison of phenotypes and expression profiles in single, double and triple mutants indicate that these HAT enzymes have overlapping functions. Consistent with this, overlapping specificity in histone H3 acetylation is observed. However, there is no evidence for overlap with another HAT enzyme, encoded by the essential mst1+ gene.

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Related in: MedlinePlus

Validation of microarray results by qPCR. Genes that showed differential expression from microarray analysis were analyzed in different HAT mutants through qualitative PCR (qPCR). The log2 fold expression ratios from microarray and qPCR experiments for the mutants versus wild type were plotted. qPCR results are indicated by the blue bars, microarray by the purple bars. Strain list: Strain list: Δelp3 (FY 3851), Δgcn5 (FY2943), Δmst2 (FY1890), Δgcn5 Δelp3 (FY3847), Δgcn5 Δmst2(FY3361), Δmst2 Δelp3 (FY3850), Δgcn5 Δelp3 Δmst2 (3854).
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Figure 3: Validation of microarray results by qPCR. Genes that showed differential expression from microarray analysis were analyzed in different HAT mutants through qualitative PCR (qPCR). The log2 fold expression ratios from microarray and qPCR experiments for the mutants versus wild type were plotted. qPCR results are indicated by the blue bars, microarray by the purple bars. Strain list: Strain list: Δelp3 (FY 3851), Δgcn5 (FY2943), Δmst2 (FY1890), Δgcn5 Δelp3 (FY3847), Δgcn5 Δmst2(FY3361), Δmst2 Δelp3 (FY3850), Δgcn5 Δelp3 Δmst2 (3854).

Mentions: The few genes that were differentially expressed in Δelp3 and Δgcn5 showed significant over-representation in several functional ontology groups. In agreement with prior reports [27] we observed that Δgcn5 mutants de-repressed mating and meiosis genes. Specifically we found that gene ontology (GO) terms [34] related to mating and meiosis were found in the up-regulated genes, indicating that Gcn5 is required for repression of these genes. In Δelp3 mutants we found that genes significantly enriched in GO classes associated with trans-membrane transport were down-regulated and those associated with ion transport were up-regulated (Fig 2, Additional File 1). Interestingly, mei2, which has been shown to be repressed by Gcn5 [27] was down-regulated in Δelp3 (Fig. 3). This may indicate that Gcn5 and Elp3 target the same pathway but with opposite effects. The few genes that were differentially expressed in Δmst2 mutants provided no over-represented GO classes.


Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation.

Nugent RL, Johnsson A, Fleharty B, Gogol M, Xue-Franzén Y, Seidel C, Wright AP, Forsburg SL - BMC Genomics (2010)

Validation of microarray results by qPCR. Genes that showed differential expression from microarray analysis were analyzed in different HAT mutants through qualitative PCR (qPCR). The log2 fold expression ratios from microarray and qPCR experiments for the mutants versus wild type were plotted. qPCR results are indicated by the blue bars, microarray by the purple bars. Strain list: Strain list: Δelp3 (FY 3851), Δgcn5 (FY2943), Δmst2 (FY1890), Δgcn5 Δelp3 (FY3847), Δgcn5 Δmst2(FY3361), Δmst2 Δelp3 (FY3850), Δgcn5 Δelp3 Δmst2 (3854).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2823694&req=5

Figure 3: Validation of microarray results by qPCR. Genes that showed differential expression from microarray analysis were analyzed in different HAT mutants through qualitative PCR (qPCR). The log2 fold expression ratios from microarray and qPCR experiments for the mutants versus wild type were plotted. qPCR results are indicated by the blue bars, microarray by the purple bars. Strain list: Strain list: Δelp3 (FY 3851), Δgcn5 (FY2943), Δmst2 (FY1890), Δgcn5 Δelp3 (FY3847), Δgcn5 Δmst2(FY3361), Δmst2 Δelp3 (FY3850), Δgcn5 Δelp3 Δmst2 (3854).
Mentions: The few genes that were differentially expressed in Δelp3 and Δgcn5 showed significant over-representation in several functional ontology groups. In agreement with prior reports [27] we observed that Δgcn5 mutants de-repressed mating and meiosis genes. Specifically we found that gene ontology (GO) terms [34] related to mating and meiosis were found in the up-regulated genes, indicating that Gcn5 is required for repression of these genes. In Δelp3 mutants we found that genes significantly enriched in GO classes associated with trans-membrane transport were down-regulated and those associated with ion transport were up-regulated (Fig 2, Additional File 1). Interestingly, mei2, which has been shown to be repressed by Gcn5 [27] was down-regulated in Δelp3 (Fig. 3). This may indicate that Gcn5 and Elp3 target the same pathway but with opposite effects. The few genes that were differentially expressed in Δmst2 mutants provided no over-represented GO classes.

Bottom Line: Comparison of phenotypes and expression profiles in single, double and triple mutants indicate that these HAT enzymes have overlapping functions.Consistent with this, overlapping specificity in histone H3 acetylation is observed.However, there is no evidence for overlap with another HAT enzyme, encoded by the essential mst1+ gene.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular and Computational Biology Section, University of Southern California, Los Angeles, California 90089-2910, USA.

ABSTRACT

Background: Histone acetyltransferase enzymes (HATs) are implicated in regulation of transcription. HATs from different families may overlap in target and substrate specificity.

Results: We isolated the elp3+ gene encoding the histone acetyltransferase subunit of the Elongator complex in fission yeast and characterized the phenotype of an Deltaelp3 mutant. We examined genetic interactions between Deltaelp3 and two other HAT mutants, Deltamst2 and Deltagcn5 and used whole genome microarray analysis to analyze their effects on gene expression.

Conclusions: Comparison of phenotypes and expression profiles in single, double and triple mutants indicate that these HAT enzymes have overlapping functions. Consistent with this, overlapping specificity in histone H3 acetylation is observed. However, there is no evidence for overlap with another HAT enzyme, encoded by the essential mst1+ gene.

Show MeSH
Related in: MedlinePlus