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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 the expression of 91 growth-specific genes.Genes expressed at levels >2× corrected background (see Figure 5A) are included. Clustering done using ArrayStar 2 (Clustering type: K-mean, Distance metric: standard Pearson). The heat map uses colors to display the relative values of all tiles within a given experimental condition wih blue indicating low expression, yellow indicating intermediate expression and red indicating high expression. The numerical values give the actual values on a log 2 scale that are associated with each color. Stages are as described in Materials and Methods. The color scale is shown by the bar at the top right corner of the figure.
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pone-0004429-g006: Heat map of the expression of 91 growth-specific genes.Genes expressed at levels >2× corrected background (see Figure 5A) are included. Clustering done using ArrayStar 2 (Clustering type: K-mean, Distance metric: standard Pearson). The heat map uses colors to display the relative values of all tiles within a given experimental condition wih blue indicating low expression, yellow indicating intermediate expression and red indicating high expression. The numerical values give the actual values on a log 2 scale that are associated with each color. Stages are as described in Materials and Methods. The color scale is shown by the bar at the top right corner of the figure.

Mentions: Heat maps and cluster analyses indicate that groups of genes in growing, starved and conjugating cells have distinct patterns of expression (Figures 6, 7, 8, 9). In growing cells (Figure 6), analyses of 91 growth-specific genes indicate that there are eight distinct clusters. Genes in cluster a are expressed relatively uniformly in L-l, L-m and L-h stages of growth (see Materials and Methods for a characterization of these stages). Genes in clusters c, d, e, f, g, and h are expressed in L-l stage growing cultures but the expression of these genes declines as growth proceeds. The disappearance of transcripts in L-h cells of clusters d and e is particularly striking, suggesting these genes are not expressed in stationary phase cells. Genes in cluster b show increased expression as the culture grows. The specific genes associated with each of these clusters are listed in Table S6; their continued investigation should provide insights into the specific changes that accompany altered growth states in Tetrahymena.


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 the expression of 91 growth-specific genes.Genes expressed at levels >2× corrected background (see Figure 5A) are included. Clustering done using ArrayStar 2 (Clustering type: K-mean, Distance metric: standard Pearson). The heat map uses colors to display the relative values of all tiles within a given experimental condition wih blue indicating low expression, yellow indicating intermediate expression and red indicating high expression. The numerical values give the actual values on a log 2 scale that are associated with each color. Stages are as described in Materials and Methods. The color scale is shown by the bar at the top right corner of the figure.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0004429-g006: Heat map of the expression of 91 growth-specific genes.Genes expressed at levels >2× corrected background (see Figure 5A) are included. Clustering done using ArrayStar 2 (Clustering type: K-mean, Distance metric: standard Pearson). The heat map uses colors to display the relative values of all tiles within a given experimental condition wih blue indicating low expression, yellow indicating intermediate expression and red indicating high expression. The numerical values give the actual values on a log 2 scale that are associated with each color. Stages are as described in Materials and Methods. The color scale is shown by the bar at the top right corner of the figure.
Mentions: Heat maps and cluster analyses indicate that groups of genes in growing, starved and conjugating cells have distinct patterns of expression (Figures 6, 7, 8, 9). In growing cells (Figure 6), analyses of 91 growth-specific genes indicate that there are eight distinct clusters. Genes in cluster a are expressed relatively uniformly in L-l, L-m and L-h stages of growth (see Materials and Methods for a characterization of these stages). Genes in clusters c, d, e, f, g, and h are expressed in L-l stage growing cultures but the expression of these genes declines as growth proceeds. The disappearance of transcripts in L-h cells of clusters d and e is particularly striking, suggesting these genes are not expressed in stationary phase cells. Genes in cluster b show increased expression as the culture grows. The specific genes associated with each of these clusters are listed in Table S6; their continued investigation should provide insights into the specific changes that accompany altered growth states in Tetrahymena.

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