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Microarray analyses of gene expression during the Tetrahymena thermophila life cycle.

Miao W, Xiong J, Bowen J, Wang W, Liu Y, Braguinets O, Grigull J, Pearlman RE, Orias E, Gorovsky MA - PLoS ONE (2009)

Bottom Line: Strikingly, transcripts homologous to 1068 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation.Genes encoding proteins known to interact or to function in complexes show similar expression patterns, indicating that co-ordinate expression with putative genes of known function can identify genes with related functions.New candidate genes associated with the RNAi-like process of DNA elimination and with meiosis are identified and the late stages of conjugation are shown to be characterized by specific expression of an unexpectedly large and diverse number of genes not involved in nuclear functions.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Rochester, Rochester, New York, USA. miaowei530@yeah.net

ABSTRACT

Background: The model eukaryote, Tetrahymena thermophila, is the first ciliated protozoan whose genome has been sequenced, enabling genome-wide analysis of gene expression.

Methodology/principal findings: A genome-wide microarray platform containing the predicted coding sequences (putative genes) for T. thermophila is described, validated and used to study gene expression during the three major stages of the organism's life cycle: growth, starvation and conjugation.

Conclusions/significance: Of the approximately 27,000 predicted open reading frames, transcripts homologous to only approximately 5900 are not detectable in any of these life cycle stages, indicating that this single-celled organism does indeed contain a large number of functional genes. Transcripts from over 5000 predicted genes are expressed at levels >5x corrected background and 95 genes are expressed at >250x corrected background in all stages. Transcripts homologous to 91 predicted genes are specifically expressed and 155 more are highly up-regulated in growing cells, while 90 are specifically expressed and 616 are up-regulated during starvation. Strikingly, transcripts homologous to 1068 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation. The patterns of gene expression during conjugation correlate well with the developmental stages of meiosis, nuclear differentiation and DNA elimination. The relationship between gene expression and chromosome fragmentation is analyzed. Genes encoding proteins known to interact or to function in complexes show similar expression patterns, indicating that co-ordinate expression with putative genes of known function can identify genes with related functions. New candidate genes associated with the RNAi-like process of DNA elimination and with meiosis are identified and the late stages of conjugation are shown to be characterized by specific expression of an unexpectedly large and diverse number of genes not involved in nuclear functions.

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Heat map of 706 genes expressed during both starvation and conjugation but not during growth.Genes whose maximum expression levels during starvation and conjugation were >2× corrected background, and were less than 1× corrected background during growth, were included, Clustering type: Hierarchical, with Euclidean distance metric. Software, conditions and other symbols are as in Figure 6.
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pone-0004429-g008: Heat map of 706 genes expressed during both starvation and conjugation but not during growth.Genes whose maximum expression levels during starvation and conjugation were >2× corrected background, and were less than 1× corrected background during growth, were included, Clustering type: Hierarchical, with Euclidean distance metric. Software, conditions and other symbols are as in Figure 6.

Mentions: A second type of programmed genome rearrangement results in less precise elimination of a much greater percentage (∼15%) of the MIC genome, and is subject to epigenetic regulation. About 6,000 “internal eliminated sequences” (IESs) ranging from 0.5 to >20 kb in length, are removed, and the flanking macronucleus destined sequences (MDSs) are ligated. IES excision can occur reproducibly at a specific region or at a small number of alternative positions to remove most repetitive, non-genic sequences from the macronucleus. The discovery of an RNAi pathway involving 28 nt “scan RNAs” (scnRNAs) in genome rearrangement of Tetrahymena [21], [22] demonstrated that the mechanism by which IES-containing chromatin is targeted for elimination is strikingly similar to the mechanism by which centromeric heterochromatin is targeted for silencing in other organisms and provides a conserved mechanism by which ‘foreign’ genetic elements that invade eukaryotic genomes are identified for silencing or elimination[21]–[25]; see Figure 8 in [26] for the most recent description of this process.


Microarray analyses of gene expression during the Tetrahymena thermophila life cycle.

Miao W, Xiong J, Bowen J, Wang W, Liu Y, Braguinets O, Grigull J, Pearlman RE, Orias E, Gorovsky MA - PLoS ONE (2009)

Heat map of 706 genes expressed during both starvation and conjugation but not during growth.Genes whose maximum expression levels during starvation and conjugation were >2× corrected background, and were less than 1× corrected background during growth, were included, Clustering type: Hierarchical, with Euclidean distance metric. Software, conditions and other symbols are as in Figure 6.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2636879&req=5

pone-0004429-g008: Heat map of 706 genes expressed during both starvation and conjugation but not during growth.Genes whose maximum expression levels during starvation and conjugation were >2× corrected background, and were less than 1× corrected background during growth, were included, Clustering type: Hierarchical, with Euclidean distance metric. Software, conditions and other symbols are as in Figure 6.
Mentions: A second type of programmed genome rearrangement results in less precise elimination of a much greater percentage (∼15%) of the MIC genome, and is subject to epigenetic regulation. About 6,000 “internal eliminated sequences” (IESs) ranging from 0.5 to >20 kb in length, are removed, and the flanking macronucleus destined sequences (MDSs) are ligated. IES excision can occur reproducibly at a specific region or at a small number of alternative positions to remove most repetitive, non-genic sequences from the macronucleus. The discovery of an RNAi pathway involving 28 nt “scan RNAs” (scnRNAs) in genome rearrangement of Tetrahymena [21], [22] demonstrated that the mechanism by which IES-containing chromatin is targeted for elimination is strikingly similar to the mechanism by which centromeric heterochromatin is targeted for silencing in other organisms and provides a conserved mechanism by which ‘foreign’ genetic elements that invade eukaryotic genomes are identified for silencing or elimination[21]–[25]; see Figure 8 in [26] for the most recent description of this process.

Bottom Line: Strikingly, transcripts homologous to 1068 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation.Genes encoding proteins known to interact or to function in complexes show similar expression patterns, indicating that co-ordinate expression with putative genes of known function can identify genes with related functions.New candidate genes associated with the RNAi-like process of DNA elimination and with meiosis are identified and the late stages of conjugation are shown to be characterized by specific expression of an unexpectedly large and diverse number of genes not involved in nuclear functions.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Rochester, Rochester, New York, USA. miaowei530@yeah.net

ABSTRACT

Background: The model eukaryote, Tetrahymena thermophila, is the first ciliated protozoan whose genome has been sequenced, enabling genome-wide analysis of gene expression.

Methodology/principal findings: A genome-wide microarray platform containing the predicted coding sequences (putative genes) for T. thermophila is described, validated and used to study gene expression during the three major stages of the organism's life cycle: growth, starvation and conjugation.

Conclusions/significance: Of the approximately 27,000 predicted open reading frames, transcripts homologous to only approximately 5900 are not detectable in any of these life cycle stages, indicating that this single-celled organism does indeed contain a large number of functional genes. Transcripts from over 5000 predicted genes are expressed at levels >5x corrected background and 95 genes are expressed at >250x corrected background in all stages. Transcripts homologous to 91 predicted genes are specifically expressed and 155 more are highly up-regulated in growing cells, while 90 are specifically expressed and 616 are up-regulated during starvation. Strikingly, transcripts homologous to 1068 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation. The patterns of gene expression during conjugation correlate well with the developmental stages of meiosis, nuclear differentiation and DNA elimination. The relationship between gene expression and chromosome fragmentation is analyzed. Genes encoding proteins known to interact or to function in complexes show similar expression patterns, indicating that co-ordinate expression with putative genes of known function can identify genes with related functions. New candidate genes associated with the RNAi-like process of DNA elimination and with meiosis are identified and the late stages of conjugation are shown to be characterized by specific expression of an unexpectedly large and diverse number of genes not involved in nuclear functions.

Show MeSH
Related in: MedlinePlus