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Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.

Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG - PLoS Comput. Biol. (2009)

Bottom Line: These patterns of tissue-specific expression are more accurate than existing high-throughput experimental studies for nearly all tissues; they also complement existing experiments by addressing tissue-specific expression present at particular developmental stages and in small tissues.We used these predictions to address several experimentally challenging questions, including the identification of tissue-specific transcriptional motifs and the discovery of potential miRNA regulation specific to particular tissues.To our knowledge, this is the first study producing high-accuracy predictions of tissue-specific expression and interactions for a metazoan organism based on whole-animal data.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA.

ABSTRACT
Tissue-specific gene expression plays a fundamental role in metazoan biology and is an important aspect of many complex diseases. Nevertheless, an organism-wide map of tissue-specific expression remains elusive due to difficulty in obtaining these data experimentally. Here, we leveraged existing whole-animal Caenorhabditis elegans microarray data representing diverse conditions and developmental stages to generate accurate predictions of tissue-specific gene expression and experimentally validated these predictions. These patterns of tissue-specific expression are more accurate than existing high-throughput experimental studies for nearly all tissues; they also complement existing experiments by addressing tissue-specific expression present at particular developmental stages and in small tissues. We used these predictions to address several experimentally challenging questions, including the identification of tissue-specific transcriptional motifs and the discovery of potential miRNA regulation specific to particular tissues. We also investigate the role of tissue context in gene function through tissue-specific functional interaction networks. To our knowledge, this is the first study producing high-accuracy predictions of tissue-specific expression and interactions for a metazoan organism based on whole-animal data.

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Expression of GFP-reporter constructs.(A) K08B12.1 was predicted to express in hypodermis; the reporter construct expressed exclusively in hypodermis. Expression was variable, strongest in embryo-L1, though detectable in all stages. (B) F58H1.2 was predicted to express in hypodermis; the reporter construct expressed exclusively in hypodermis. Expression was variable, strongest in embryo-L1 and not detectable in adults. (C) F55H12.4 was predicted to express in the hypodermis. pF55H12.4::GFP expressed in hypodermis, vulva, anus, and to a lesser extent pharynx. Hypodermal expression was highly variable and was strongest in L4 and Adult stages. (D) C29F5.1 was predicted to express in muscle. The reporter construct was observed in body wall, vulval, and anal but not pharyngeal muscle in all stages. (E) F13D12.6 was predicted to express in the intestine and the reporter construct expressed exclusively in intestinal cells at all stages. (F) gnrr-1 was predicted to express in neurons. Strong expression of pgnrr-1::GFP was seen in various head neurons at all stages. Expression was also observed in the anterior pharynx and ventral nerve cord neurons. (A,B) Seam cell exclusion is observed in these lines, which is typical of hypodermally expressed genes; see Gilleard et al. [77] for examples of hypodermal expression.
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pcbi-1000417-g003: Expression of GFP-reporter constructs.(A) K08B12.1 was predicted to express in hypodermis; the reporter construct expressed exclusively in hypodermis. Expression was variable, strongest in embryo-L1, though detectable in all stages. (B) F58H1.2 was predicted to express in hypodermis; the reporter construct expressed exclusively in hypodermis. Expression was variable, strongest in embryo-L1 and not detectable in adults. (C) F55H12.4 was predicted to express in the hypodermis. pF55H12.4::GFP expressed in hypodermis, vulva, anus, and to a lesser extent pharynx. Hypodermal expression was highly variable and was strongest in L4 and Adult stages. (D) C29F5.1 was predicted to express in muscle. The reporter construct was observed in body wall, vulval, and anal but not pharyngeal muscle in all stages. (E) F13D12.6 was predicted to express in the intestine and the reporter construct expressed exclusively in intestinal cells at all stages. (F) gnrr-1 was predicted to express in neurons. Strong expression of pgnrr-1::GFP was seen in various head neurons at all stages. Expression was also observed in the anterior pharynx and ventral nerve cord neurons. (A,B) Seam cell exclusion is observed in these lines, which is typical of hypodermally expressed genes; see Gilleard et al. [77] for examples of hypodermal expression.

Mentions: We experimentally verified tissue-specific expression of six top genes with previously unreported tissue-specific predictions by creating transgenic lines carrying promoter-GFP constructs (Figure 3). Three of these genes were predicted to express in hypodermis. We chose to focus on hypodermis since, to our knowledge, no large-scale study investigating hypodermal expression has been reported. Promoter-GFP constructs of two of the predicted hypodermal genes, K08B12.1 and F58H1.2, were most prominently expressed in the hypodermis at earlier stages (Figure 3A and 3B and Figure S4). The third gene, F55H12.4, showed strongest hypodermal expression during L4 and adult stages (Figure 3C). We also verified the expression of genes that we predicted to be expressed in muscle (C29F5.1, Figure 3D), intestine (F13D12.6, Figure 3E), and neurons (gnrr-1, Figure 3F). The tissue specific expression of gnrr-1, a homolog of the human gonadotropin releasing receptor, was previously studied using antibody staining [36]. While our algorithm predicted with high confidence that gnrr-1 expresses in neurons, neuronal expression was not reported in that study, and the gene was not included in the Von Stetina et al. list of neuronally-enriched genes [22]. Nevertheless, our promoter-GFP (Pgnnr-1::gfp) construct expressed primarily in head neurons and ventral cord neurons (Figure 3D), validating our prediction. It is likely that the protein product of gnrr-1 is heavily post-translationally modified, as species of multiple molecular weights are observed [36]. Thus, it is possible that differences in such modification explain the discrepancy between our gene expression results and the previous antibody staining experiment, due to epitope differences. Furthermore, gnrr-1 is strongly over-expressed in L1 and L2 larval stages in multiple developmental microarray time courses, which is the pattern observed for many neuronal genes


Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.

Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG - PLoS Comput. Biol. (2009)

Expression of GFP-reporter constructs.(A) K08B12.1 was predicted to express in hypodermis; the reporter construct expressed exclusively in hypodermis. Expression was variable, strongest in embryo-L1, though detectable in all stages. (B) F58H1.2 was predicted to express in hypodermis; the reporter construct expressed exclusively in hypodermis. Expression was variable, strongest in embryo-L1 and not detectable in adults. (C) F55H12.4 was predicted to express in the hypodermis. pF55H12.4::GFP expressed in hypodermis, vulva, anus, and to a lesser extent pharynx. Hypodermal expression was highly variable and was strongest in L4 and Adult stages. (D) C29F5.1 was predicted to express in muscle. The reporter construct was observed in body wall, vulval, and anal but not pharyngeal muscle in all stages. (E) F13D12.6 was predicted to express in the intestine and the reporter construct expressed exclusively in intestinal cells at all stages. (F) gnrr-1 was predicted to express in neurons. Strong expression of pgnrr-1::GFP was seen in various head neurons at all stages. Expression was also observed in the anterior pharynx and ventral nerve cord neurons. (A,B) Seam cell exclusion is observed in these lines, which is typical of hypodermally expressed genes; see Gilleard et al. [77] for examples of hypodermal expression.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2692103&req=5

pcbi-1000417-g003: Expression of GFP-reporter constructs.(A) K08B12.1 was predicted to express in hypodermis; the reporter construct expressed exclusively in hypodermis. Expression was variable, strongest in embryo-L1, though detectable in all stages. (B) F58H1.2 was predicted to express in hypodermis; the reporter construct expressed exclusively in hypodermis. Expression was variable, strongest in embryo-L1 and not detectable in adults. (C) F55H12.4 was predicted to express in the hypodermis. pF55H12.4::GFP expressed in hypodermis, vulva, anus, and to a lesser extent pharynx. Hypodermal expression was highly variable and was strongest in L4 and Adult stages. (D) C29F5.1 was predicted to express in muscle. The reporter construct was observed in body wall, vulval, and anal but not pharyngeal muscle in all stages. (E) F13D12.6 was predicted to express in the intestine and the reporter construct expressed exclusively in intestinal cells at all stages. (F) gnrr-1 was predicted to express in neurons. Strong expression of pgnrr-1::GFP was seen in various head neurons at all stages. Expression was also observed in the anterior pharynx and ventral nerve cord neurons. (A,B) Seam cell exclusion is observed in these lines, which is typical of hypodermally expressed genes; see Gilleard et al. [77] for examples of hypodermal expression.
Mentions: We experimentally verified tissue-specific expression of six top genes with previously unreported tissue-specific predictions by creating transgenic lines carrying promoter-GFP constructs (Figure 3). Three of these genes were predicted to express in hypodermis. We chose to focus on hypodermis since, to our knowledge, no large-scale study investigating hypodermal expression has been reported. Promoter-GFP constructs of two of the predicted hypodermal genes, K08B12.1 and F58H1.2, were most prominently expressed in the hypodermis at earlier stages (Figure 3A and 3B and Figure S4). The third gene, F55H12.4, showed strongest hypodermal expression during L4 and adult stages (Figure 3C). We also verified the expression of genes that we predicted to be expressed in muscle (C29F5.1, Figure 3D), intestine (F13D12.6, Figure 3E), and neurons (gnrr-1, Figure 3F). The tissue specific expression of gnrr-1, a homolog of the human gonadotropin releasing receptor, was previously studied using antibody staining [36]. While our algorithm predicted with high confidence that gnrr-1 expresses in neurons, neuronal expression was not reported in that study, and the gene was not included in the Von Stetina et al. list of neuronally-enriched genes [22]. Nevertheless, our promoter-GFP (Pgnnr-1::gfp) construct expressed primarily in head neurons and ventral cord neurons (Figure 3D), validating our prediction. It is likely that the protein product of gnrr-1 is heavily post-translationally modified, as species of multiple molecular weights are observed [36]. Thus, it is possible that differences in such modification explain the discrepancy between our gene expression results and the previous antibody staining experiment, due to epitope differences. Furthermore, gnrr-1 is strongly over-expressed in L1 and L2 larval stages in multiple developmental microarray time courses, which is the pattern observed for many neuronal genes

Bottom Line: These patterns of tissue-specific expression are more accurate than existing high-throughput experimental studies for nearly all tissues; they also complement existing experiments by addressing tissue-specific expression present at particular developmental stages and in small tissues.We used these predictions to address several experimentally challenging questions, including the identification of tissue-specific transcriptional motifs and the discovery of potential miRNA regulation specific to particular tissues.To our knowledge, this is the first study producing high-accuracy predictions of tissue-specific expression and interactions for a metazoan organism based on whole-animal data.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA.

ABSTRACT
Tissue-specific gene expression plays a fundamental role in metazoan biology and is an important aspect of many complex diseases. Nevertheless, an organism-wide map of tissue-specific expression remains elusive due to difficulty in obtaining these data experimentally. Here, we leveraged existing whole-animal Caenorhabditis elegans microarray data representing diverse conditions and developmental stages to generate accurate predictions of tissue-specific gene expression and experimentally validated these predictions. These patterns of tissue-specific expression are more accurate than existing high-throughput experimental studies for nearly all tissues; they also complement existing experiments by addressing tissue-specific expression present at particular developmental stages and in small tissues. We used these predictions to address several experimentally challenging questions, including the identification of tissue-specific transcriptional motifs and the discovery of potential miRNA regulation specific to particular tissues. We also investigate the role of tissue context in gene function through tissue-specific functional interaction networks. To our knowledge, this is the first study producing high-accuracy predictions of tissue-specific expression and interactions for a metazoan organism based on whole-animal data.

Show MeSH
Related in: MedlinePlus