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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

The expression profiles of TWI1 (TTHERM_01161040) co-expressed genes.Stages are as described in Materials and Methods.
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pone-0004429-g015: The expression profiles of TWI1 (TTHERM_01161040) co-expressed genes.Stages are as described in Materials and Methods.

Mentions: The first gene we examined was TWI1, which encodes an essential argonaute family protein that is associated with the small RNAs (scnRNAs) required for targeting the IES sequences for elimination [7], [21]. This gene has the added advantage that four proteins (CnjBp, Wag1p, Ema1p and Giw1p) have been shown to be physically associated with Twi1p by co-immunoprecipitation and TAP-tagging ([26], J. Bednenko, K. Mochizuki and M. Gorovsky, unpublished observations), allowing a test of whether co-expression can identify genes that encode proteins that likely have shared functions. Figure 15 illustrates the expression pattern during growth, starvation and conjugation of TWI1 and of 18 other proteins whose expression patterns correlate highly (R>0.9) with TWI1 (Table 5). Both CnjB and WAG1 are found among these 18 genes, and expression of a third gene, EMA1, that encodes a protein known to be physically associated with Twi1p is also highly correlated (R = 0.85 ), but GIW1 was not found (R<0.8). Of the eighteen TWI1 co-expressed genes (R>0.9), 6 had no known homologs, while the other 12 were all homologous to proteins associated with DNA-related properties. These results indicate that co-expression analysis is able to identify genes that have shared functions, arguing that the other 16 genes listed in Table 5 are candidates for further investigation into the process of IES elimination.


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)

The expression profiles of TWI1 (TTHERM_01161040) co-expressed genes.Stages are as described in Materials and Methods.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0004429-g015: The expression profiles of TWI1 (TTHERM_01161040) co-expressed genes.Stages are as described in Materials and Methods.
Mentions: The first gene we examined was TWI1, which encodes an essential argonaute family protein that is associated with the small RNAs (scnRNAs) required for targeting the IES sequences for elimination [7], [21]. This gene has the added advantage that four proteins (CnjBp, Wag1p, Ema1p and Giw1p) have been shown to be physically associated with Twi1p by co-immunoprecipitation and TAP-tagging ([26], J. Bednenko, K. Mochizuki and M. Gorovsky, unpublished observations), allowing a test of whether co-expression can identify genes that encode proteins that likely have shared functions. Figure 15 illustrates the expression pattern during growth, starvation and conjugation of TWI1 and of 18 other proteins whose expression patterns correlate highly (R>0.9) with TWI1 (Table 5). Both CnjB and WAG1 are found among these 18 genes, and expression of a third gene, EMA1, that encodes a protein known to be physically associated with Twi1p is also highly correlated (R = 0.85 ), but GIW1 was not found (R<0.8). Of the eighteen TWI1 co-expressed genes (R>0.9), 6 had no known homologs, while the other 12 were all homologous to proteins associated with DNA-related properties. These results indicate that co-expression analysis is able to identify genes that have shared functions, arguing that the other 16 genes listed in Table 5 are candidates for further investigation into the process of IES elimination.

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