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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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Stages of conjugation in Tetrahymena.
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pone-0004429-g010: Stages of conjugation in Tetrahymena.

Mentions: Figure 9 illustrates the heat map and cluster analysis of 503 conjugation-specific genes. A number of distinct patterns of expression can be observed. Eight genes (indicated by the red arrow) are expressed almost exclusively at C-0, suggesting that they respond rapidly and transiently to the mixing of cells of different mating types. Genes in cluster a show high levels of conjugation-specific expression and, once expression is initiated, are expressed for long periods. Included in this cluster are previously characterized, conjugation-specific genes, including DCL1 [52], [53], TWI1 [7], PDD2 [54], [55], PDD3 [56], GIW1 (K. Mochizuki, personal communication), LIA1, LIA3 and LIA5 [51]. Three other published conjugation genes, PDD1 [57], ASI1 [58] and ASI2 [59] were found in the conjugation-induced genes (data not shown). Thus, all of the published and known conjugation genes were found in either the conjugation-specific or conjugation-inducible genes. Cluster a can be further divided into 2 sub-clusters. Most genes in cluster a2 initiate expression between 0 and 2 hours after cells are mixed, when the early steps in RNAi mediated IES elimination [7], [52], [53] and in meiosis are initiated (Figure 10). Most genes in cluster a1 initiate expression between 4 and 6 hours, during later stages of meiosis, pronuclear formation, nuclear exchange and fertilization (Figure 10), and when the scanning events of IES elimination are occurring [21]. Most genes in the b cluster are expressed at lower levels than those in the a cluster and are expressed more transiently. Most genes in cluster b3 initiate expression between 0 and 2 hr and transcripts from these genes have largely disappeared by 8 hr. RNAs from most genes in cluster b2 begin accumulating between 4 and 6 hr after cells are mixed and disappear between 10 and 12 hr. Genes in cluster b1 begin being expressed shortly after those in cluster b2 (between 6 and 8 hr). RNAs from some of the genes in this cluster become undetectable by 14–16 hr while others are detectable up to 18 hr, when our analysis was terminated.


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)

Stages of conjugation in Tetrahymena.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0004429-g010: Stages of conjugation in Tetrahymena.
Mentions: Figure 9 illustrates the heat map and cluster analysis of 503 conjugation-specific genes. A number of distinct patterns of expression can be observed. Eight genes (indicated by the red arrow) are expressed almost exclusively at C-0, suggesting that they respond rapidly and transiently to the mixing of cells of different mating types. Genes in cluster a show high levels of conjugation-specific expression and, once expression is initiated, are expressed for long periods. Included in this cluster are previously characterized, conjugation-specific genes, including DCL1 [52], [53], TWI1 [7], PDD2 [54], [55], PDD3 [56], GIW1 (K. Mochizuki, personal communication), LIA1, LIA3 and LIA5 [51]. Three other published conjugation genes, PDD1 [57], ASI1 [58] and ASI2 [59] were found in the conjugation-induced genes (data not shown). Thus, all of the published and known conjugation genes were found in either the conjugation-specific or conjugation-inducible genes. Cluster a can be further divided into 2 sub-clusters. Most genes in cluster a2 initiate expression between 0 and 2 hours after cells are mixed, when the early steps in RNAi mediated IES elimination [7], [52], [53] and in meiosis are initiated (Figure 10). Most genes in cluster a1 initiate expression between 4 and 6 hours, during later stages of meiosis, pronuclear formation, nuclear exchange and fertilization (Figure 10), and when the scanning events of IES elimination are occurring [21]. Most genes in the b cluster are expressed at lower levels than those in the a cluster and are expressed more transiently. Most genes in cluster b3 initiate expression between 0 and 2 hr and transcripts from these genes have largely disappeared by 8 hr. RNAs from most genes in cluster b2 begin accumulating between 4 and 6 hr after cells are mixed and disappear between 10 and 12 hr. Genes in cluster b1 begin being expressed shortly after those in cluster b2 (between 6 and 8 hr). RNAs from some of the genes in this cluster become undetectable by 14–16 hr while others are detectable up to 18 hr, when our analysis was terminated.

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