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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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Related in: MedlinePlus

Summary of the number of genes differentially expressed at two hour intervals during conjugation.Values above and below the “0 line” represent the number of up-regulated and down-regulated genes, respectively.
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pone-0004429-g014: Summary of the number of genes differentially expressed at two hour intervals during conjugation.Values above and below the “0 line” represent the number of up-regulated and down-regulated genes, respectively.

Mentions: One goal of our comprehensive microarray analyses of gene expression was to identify candidate genes involved in the striking developmental changes (cell pairing, meiosis, fertilization, RNAi-mediated scanning of MIC-specific sequences, chromosome fragmentation, telomere addition, rDNA amplification and the DNA splicing events of IES elimination) that occur during conjugation. As a first step toward this end, we divided the conjugation process into a series of 2 hr intervals and determined the number of genes showing significant changes in expression, either up or down from the beginning to the end of the time interval, ranging from 4 to 500 fold (Figure 14). Clearly, the first two hours of conjugation are marked by changes, both upward and downward in the expression of a large number (>3100) genes, with expression of >700 genes increasing >10× and expression of 17 genes increasing a remarkable >500× in only 2 hr. Subsequent intervals also show changes in large numbers of genes, although the numbers and extent of the changes diminish as conjugation proceeds.


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)

Summary of the number of genes differentially expressed at two hour intervals during conjugation.Values above and below the “0 line” represent the number of up-regulated and down-regulated genes, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0004429-g014: Summary of the number of genes differentially expressed at two hour intervals during conjugation.Values above and below the “0 line” represent the number of up-regulated and down-regulated genes, respectively.
Mentions: One goal of our comprehensive microarray analyses of gene expression was to identify candidate genes involved in the striking developmental changes (cell pairing, meiosis, fertilization, RNAi-mediated scanning of MIC-specific sequences, chromosome fragmentation, telomere addition, rDNA amplification and the DNA splicing events of IES elimination) that occur during conjugation. As a first step toward this end, we divided the conjugation process into a series of 2 hr intervals and determined the number of genes showing significant changes in expression, either up or down from the beginning to the end of the time interval, ranging from 4 to 500 fold (Figure 14). Clearly, the first two hours of conjugation are marked by changes, both upward and downward in the expression of a large number (>3100) genes, with expression of >700 genes increasing >10× and expression of 17 genes increasing a remarkable >500× in only 2 hr. Subsequent intervals also show changes in large numbers of genes, although the numbers and extent of the changes diminish as conjugation proceeds.

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