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Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain.

Sreenivasan R, Cai M, Bartfai R, Wang X, Christoffels A, Orban L - PLoS ONE (2008)

Bottom Line: We found that five members of the GTP-binding septin gene family, from which only one member (septin 4) has previously been implicated in reproduction in mice, were all strongly expressed in the gonads.Our microarray would be useful for studying gonad development, differentiation and function not only in zebrafish but also in related teleosts via cross-species hybridizations.Since several genes have been shown to play similar roles in gonadogenesis in zebrafish and other vertebrates, our array may even provide information on genetic disorders affecting gonadal phenotypes and fertility in mammals.

View Article: PubMed Central - PubMed

Affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.

ABSTRACT

Background: Our knowledge on zebrafish reproduction is very limited. We generated a gonad-derived cDNA microarray from zebrafish and used it to analyze large-scale gene expression profiles in adult gonads and other organs.

Methodology/principal findings: We have identified 116638 gonad-derived zebrafish expressed sequence tags (ESTs), 21% of which were isolated in our lab. Following in silico normalization, we constructed a gonad-derived microarray comprising 6370 unique, full-length cDNAs from differentiating and adult gonads. Labeled targets from adult gonad, brain, kidney and 'rest-of-body' from both sexes were hybridized onto the microarray. Our analyses revealed 1366, 881 and 656 differentially expressed transcripts (34.7% novel) that showed highest expression in ovary, testis and both gonads respectively. Hierarchical clustering showed correlation of the two gonadal transcriptomes and their similarities to those of the brains. In addition, we have identified 276 genes showing sexually dimorphic expression both between the brains and between the gonads. By in situ hybridization, we showed that the gonadal transcripts with the strongest array signal intensities were germline-expressed. We found that five members of the GTP-binding septin gene family, from which only one member (septin 4) has previously been implicated in reproduction in mice, were all strongly expressed in the gonads.

Conclusions/significance: We have generated a gonad-derived zebrafish cDNA microarray and demonstrated its usefulness in identifying genes with sexually dimorphic co-expression in both the gonads and the brains. We have also provided the first evidence of large-scale differential gene expression between female and male brains of a teleost. Our microarray would be useful for studying gonad development, differentiation and function not only in zebrafish but also in related teleosts via cross-species hybridizations. Since several genes have been shown to play similar roles in gonadogenesis in zebrafish and other vertebrates, our array may even provide information on genetic disorders affecting gonadal phenotypes and fertility in mammals.

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Related in: MedlinePlus

Hierarchical clustering of expression profiles for 6331 genes across eight different organs.Individual gene expression profiles are plotted horizontally against vertical columns of organ type. For each organ, profiles for the three biological replicates and each of their two technical replicates are displayed. Strongly expressed and weakly expressed genes with respect to the common reference are represented in red and green respectively. All organs showed a high level of correlation between biological and technical replicates. The gonads contained the highest number of strongly expressed transcripts. Many genes showed sexually dimorphic gene expression in the gonads and in other organs. Clustering showed correlation between expression profiles of different organs. Kidney targets clustered together with ‘rest-of-body’, while ovary and testis clustered with brain targets to form a distinct group. Refer to Fig. 2 for abbreviations.
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pone-0001791-g004: Hierarchical clustering of expression profiles for 6331 genes across eight different organs.Individual gene expression profiles are plotted horizontally against vertical columns of organ type. For each organ, profiles for the three biological replicates and each of their two technical replicates are displayed. Strongly expressed and weakly expressed genes with respect to the common reference are represented in red and green respectively. All organs showed a high level of correlation between biological and technical replicates. The gonads contained the highest number of strongly expressed transcripts. Many genes showed sexually dimorphic gene expression in the gonads and in other organs. Clustering showed correlation between expression profiles of different organs. Kidney targets clustered together with ‘rest-of-body’, while ovary and testis clustered with brain targets to form a distinct group. Refer to Fig. 2 for abbreviations.

Mentions: In order to compare transcriptional profiles across all eight organs, hierarchical clustering was performed with a similarity measure using Pearson correlation coefficient and a complete linkage algorithm on 6331 genes which had expression levels above those of negative controls. (All negative control probes, β-actin probes and probes corresponding to RNA spikes were eliminated from this analysis.) The resulting condition tree (Fig. 4) revealed similar expression levels between biological and technical replicates, highlighting the minimal inter- and intra-array hybridization variation. As expected from an array enriched in gonad-derived clones, the highest number of strongly-expressed transcripts was found in the ovary and testis. Although the organ pairs of the two sexes clustered together, distinct differences were observed for all four sample types tested, particularly between the ovary and testis. In addition, the gonad cluster grouped together with the brain cluster, indicating the similarity of the transcriptome among these organs (Fig. 4). The kidney and ‘rest of body’ profiles showed significantly different transcriptional profiles from those of the gonads and brains.


Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain.

Sreenivasan R, Cai M, Bartfai R, Wang X, Christoffels A, Orban L - PLoS ONE (2008)

Hierarchical clustering of expression profiles for 6331 genes across eight different organs.Individual gene expression profiles are plotted horizontally against vertical columns of organ type. For each organ, profiles for the three biological replicates and each of their two technical replicates are displayed. Strongly expressed and weakly expressed genes with respect to the common reference are represented in red and green respectively. All organs showed a high level of correlation between biological and technical replicates. The gonads contained the highest number of strongly expressed transcripts. Many genes showed sexually dimorphic gene expression in the gonads and in other organs. Clustering showed correlation between expression profiles of different organs. Kidney targets clustered together with ‘rest-of-body’, while ovary and testis clustered with brain targets to form a distinct group. Refer to Fig. 2 for abbreviations.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2262149&req=5

pone-0001791-g004: Hierarchical clustering of expression profiles for 6331 genes across eight different organs.Individual gene expression profiles are plotted horizontally against vertical columns of organ type. For each organ, profiles for the three biological replicates and each of their two technical replicates are displayed. Strongly expressed and weakly expressed genes with respect to the common reference are represented in red and green respectively. All organs showed a high level of correlation between biological and technical replicates. The gonads contained the highest number of strongly expressed transcripts. Many genes showed sexually dimorphic gene expression in the gonads and in other organs. Clustering showed correlation between expression profiles of different organs. Kidney targets clustered together with ‘rest-of-body’, while ovary and testis clustered with brain targets to form a distinct group. Refer to Fig. 2 for abbreviations.
Mentions: In order to compare transcriptional profiles across all eight organs, hierarchical clustering was performed with a similarity measure using Pearson correlation coefficient and a complete linkage algorithm on 6331 genes which had expression levels above those of negative controls. (All negative control probes, β-actin probes and probes corresponding to RNA spikes were eliminated from this analysis.) The resulting condition tree (Fig. 4) revealed similar expression levels between biological and technical replicates, highlighting the minimal inter- and intra-array hybridization variation. As expected from an array enriched in gonad-derived clones, the highest number of strongly-expressed transcripts was found in the ovary and testis. Although the organ pairs of the two sexes clustered together, distinct differences were observed for all four sample types tested, particularly between the ovary and testis. In addition, the gonad cluster grouped together with the brain cluster, indicating the similarity of the transcriptome among these organs (Fig. 4). The kidney and ‘rest of body’ profiles showed significantly different transcriptional profiles from those of the gonads and brains.

Bottom Line: We found that five members of the GTP-binding septin gene family, from which only one member (septin 4) has previously been implicated in reproduction in mice, were all strongly expressed in the gonads.Our microarray would be useful for studying gonad development, differentiation and function not only in zebrafish but also in related teleosts via cross-species hybridizations.Since several genes have been shown to play similar roles in gonadogenesis in zebrafish and other vertebrates, our array may even provide information on genetic disorders affecting gonadal phenotypes and fertility in mammals.

View Article: PubMed Central - PubMed

Affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.

ABSTRACT

Background: Our knowledge on zebrafish reproduction is very limited. We generated a gonad-derived cDNA microarray from zebrafish and used it to analyze large-scale gene expression profiles in adult gonads and other organs.

Methodology/principal findings: We have identified 116638 gonad-derived zebrafish expressed sequence tags (ESTs), 21% of which were isolated in our lab. Following in silico normalization, we constructed a gonad-derived microarray comprising 6370 unique, full-length cDNAs from differentiating and adult gonads. Labeled targets from adult gonad, brain, kidney and 'rest-of-body' from both sexes were hybridized onto the microarray. Our analyses revealed 1366, 881 and 656 differentially expressed transcripts (34.7% novel) that showed highest expression in ovary, testis and both gonads respectively. Hierarchical clustering showed correlation of the two gonadal transcriptomes and their similarities to those of the brains. In addition, we have identified 276 genes showing sexually dimorphic expression both between the brains and between the gonads. By in situ hybridization, we showed that the gonadal transcripts with the strongest array signal intensities were germline-expressed. We found that five members of the GTP-binding septin gene family, from which only one member (septin 4) has previously been implicated in reproduction in mice, were all strongly expressed in the gonads.

Conclusions/significance: We have generated a gonad-derived zebrafish cDNA microarray and demonstrated its usefulness in identifying genes with sexually dimorphic co-expression in both the gonads and the brains. We have also provided the first evidence of large-scale differential gene expression between female and male brains of a teleost. Our microarray would be useful for studying gonad development, differentiation and function not only in zebrafish but also in related teleosts via cross-species hybridizations. Since several genes have been shown to play similar roles in gonadogenesis in zebrafish and other vertebrates, our array may even provide information on genetic disorders affecting gonadal phenotypes and fertility in mammals.

Show MeSH
Related in: MedlinePlus