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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

Comparison of numbers of predicted genes specifically expressed (A) or upregulated (B) during growth, starvation and conjugation.a, b: the search conditions were those listed in Table S5.
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pone-0004429-g005: Comparison of numbers of predicted genes specifically expressed (A) or upregulated (B) during growth, starvation and conjugation.a, b: the search conditions were those listed in Table S5.

Mentions: We used the search program to identify predicted genes that were specifically expressed (i.e., hybridization was detectable only) during growth, starvation or conjugation, or that were significantly up-regulated during these stages (see the search conditions in Table S5). In Figure 5, we have plotted the number of genes showing different levels of specific or up-regulated expression. The most striking feature of this analysis is the large number of genes whose expression is specific to, or highly induced (>5×) during conjugation and the remarkably high levels of expression of these induced/expressed genes. Thus, almost 500 genes are expressed at levels >5× corrected background during conjugation. That more genes are expressed during conjugation than during either growth or starvation (Figure 4) may not be so surprising if one considers an analogy to multicellular animals: ciliate conjugation encompasses meiosis, production of haploid pronuclei, pronuclear fusion and events with likely parallels to events occurring in early embryonic stages in animals (eg, histone transitions, chromatin remodeling, initiation of rRNA and mRNA transcription, cytoplasmic determination of germ-line and somatic nuclear lineages).


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)

Comparison of numbers of predicted genes specifically expressed (A) or upregulated (B) during growth, starvation and conjugation.a, b: the search conditions were those listed in Table S5.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0004429-g005: Comparison of numbers of predicted genes specifically expressed (A) or upregulated (B) during growth, starvation and conjugation.a, b: the search conditions were those listed in Table S5.
Mentions: We used the search program to identify predicted genes that were specifically expressed (i.e., hybridization was detectable only) during growth, starvation or conjugation, or that were significantly up-regulated during these stages (see the search conditions in Table S5). In Figure 5, we have plotted the number of genes showing different levels of specific or up-regulated expression. The most striking feature of this analysis is the large number of genes whose expression is specific to, or highly induced (>5×) during conjugation and the remarkably high levels of expression of these induced/expressed genes. Thus, almost 500 genes are expressed at levels >5× corrected background during conjugation. That more genes are expressed during conjugation than during either growth or starvation (Figure 4) may not be so surprising if one considers an analogy to multicellular animals: ciliate conjugation encompasses meiosis, production of haploid pronuclei, pronuclear fusion and events with likely parallels to events occurring in early embryonic stages in animals (eg, histone transitions, chromatin remodeling, initiation of rRNA and mRNA transcription, cytoplasmic determination of germ-line and somatic nuclear lineages).

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