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Global analysis of the small RNA transcriptome in different ploidies and genomic combinations of a vertebrate complex--the Squalius alburnoides.

Inácio A, Pinho J, Pereira PM, Comai L, Coelho MM - PLoS ONE (2012)

Bottom Line: Previously in this complex, it was showed that in response to the increase in genome dosage, triploids hybrids could regulate gene expression to a diploid state.However, an overall view indicates an up-regulation of several miRNAs in triploids and a global miRNA expression in triploids higher than the predicted from an additive model.Those results point to a participation of miRNAs in the cellular functional stability needed when the ploidy change.

View Article: PubMed Central - PubMed

Affiliation: Centro de Biologia Ambiental, Departamento de Biologia Animal da Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal. mainacio@fc.ul.pt

ABSTRACT
The Squalius alburnoides complex (Steindachner) is one of the most intricate hybrid polyploid systems known in vertebrates. In this complex, the constant switch of the genome composition in consecutive generations, very frequently involving a change on the ploidy level, promotes repetitive situations of potential genomic shock. Previously in this complex, it was showed that in response to the increase in genome dosage, triploids hybrids could regulate gene expression to a diploid state. In this work we compared the small RNA profiles in the different genomic compositions interacting in the complex in order to explore the miRNA involvement in gene expression regulation of triploids. Using high-throughput arrays and sequencing technologies we were able to verify that diploid and triploid hybrids shared most of their sequences and their miRNA expression profiles were high correlated. However, an overall view indicates an up-regulation of several miRNAs in triploids and a global miRNA expression in triploids higher than the predicted from an additive model. Those results point to a participation of miRNAs in the cellular functional stability needed when the ploidy change.

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Differences in global miRNA expression profile.Differences related to A) allopolyplodization and B) hybridization. C) Differential expression profile between the parental species. Logarithmized ratios of gene expression for each miRNA were plotted producing a characteristic crescent curve where positive values indicate miRNAs with a higher expression and negative values miRNAs with a lower expression. ♦ Represents the median and its position indicate if most of the values are positive or negative. The percentages of positive and negative values are indicated.
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pone-0041158-g006: Differences in global miRNA expression profile.Differences related to A) allopolyplodization and B) hybridization. C) Differential expression profile between the parental species. Logarithmized ratios of gene expression for each miRNA were plotted producing a characteristic crescent curve where positive values indicate miRNAs with a higher expression and negative values miRNAs with a lower expression. ♦ Represents the median and its position indicate if most of the values are positive or negative. The percentages of positive and negative values are indicated.

Mentions: Afterwards, we decided to analyze whether the global expression profile of miRNAs changes with ploidy increase in such a way that, by compensating the gene dosage, could enhance stability of the triploids. No major differences of miRNA expression levels were found in any of the possible comparisons, either in the microarrays or in the small RNAseq analysis. Indeed, the majority of fold changes were between 0.5 to 2 (Figure S1). Therefore, we focused on the moderate expression changes detected in the small RNAseq data, deciding that the lower sensitivity of microarrays and the decreased fidelity of Danio rerio miRNA chip could compromise accuracy. For the analysis, normalized counts of each miRNA in one library were divided by the corresponding expression value of the same miRNA in the other library; log ratios were plotted producing a characteristic crescent curve where positive values indicate miRNAs with a higher expression and negative values mRNAs with a lower expression (Figure 6). Results indicated that the increase in the ploidy level affected the miRNA transcriptome, since the analysis between diploids and triploid hybrids showed a significant difference in the number of up and down-expressed miRNAs (χ-test, p<0.001), with an higher amount of up-regulated miRNAs in triploids (72%) (Figure 6A). However, no conclusions about the absolute up-regulation in block of all miRNAs in PAAs can be made, since the same molar amount of small RNA library was used for sequencing. Nevertheless, small RNAseq reveals a change in the global profile of PAAs, with a higher percentage of miRNAs being up-regulated in comparison to any other diploid (Figure 6A). In support of this evidence, the majority of up-regulated miRNAs (93%) in PAA/PA were also up-regulated in at least one of the other comparisons (PAA/PP or PAA/AA) and 62% were up-regulated in all the three comparisons (Table S3). If we considered only the miRNAs that change their expression more than 1 fold, 21% are up-regulated in all the comparisons and correspond to 5 miRNAs: dre-mir-182, dre-mir-183, dre-mir-96, dre-mir-141 and dre-mir-192 (Table S3). No specific transcript or group of transcripts sharing the same gene ontology term was found to be targeted by all the 5 miRNAs (MicroCosm Targets Version 5 and [19]).


Global analysis of the small RNA transcriptome in different ploidies and genomic combinations of a vertebrate complex--the Squalius alburnoides.

Inácio A, Pinho J, Pereira PM, Comai L, Coelho MM - PLoS ONE (2012)

Differences in global miRNA expression profile.Differences related to A) allopolyplodization and B) hybridization. C) Differential expression profile between the parental species. Logarithmized ratios of gene expression for each miRNA were plotted producing a characteristic crescent curve where positive values indicate miRNAs with a higher expression and negative values miRNAs with a lower expression. ♦ Represents the median and its position indicate if most of the values are positive or negative. The percentages of positive and negative values are indicated.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3399795&req=5

pone-0041158-g006: Differences in global miRNA expression profile.Differences related to A) allopolyplodization and B) hybridization. C) Differential expression profile between the parental species. Logarithmized ratios of gene expression for each miRNA were plotted producing a characteristic crescent curve where positive values indicate miRNAs with a higher expression and negative values miRNAs with a lower expression. ♦ Represents the median and its position indicate if most of the values are positive or negative. The percentages of positive and negative values are indicated.
Mentions: Afterwards, we decided to analyze whether the global expression profile of miRNAs changes with ploidy increase in such a way that, by compensating the gene dosage, could enhance stability of the triploids. No major differences of miRNA expression levels were found in any of the possible comparisons, either in the microarrays or in the small RNAseq analysis. Indeed, the majority of fold changes were between 0.5 to 2 (Figure S1). Therefore, we focused on the moderate expression changes detected in the small RNAseq data, deciding that the lower sensitivity of microarrays and the decreased fidelity of Danio rerio miRNA chip could compromise accuracy. For the analysis, normalized counts of each miRNA in one library were divided by the corresponding expression value of the same miRNA in the other library; log ratios were plotted producing a characteristic crescent curve where positive values indicate miRNAs with a higher expression and negative values mRNAs with a lower expression (Figure 6). Results indicated that the increase in the ploidy level affected the miRNA transcriptome, since the analysis between diploids and triploid hybrids showed a significant difference in the number of up and down-expressed miRNAs (χ-test, p<0.001), with an higher amount of up-regulated miRNAs in triploids (72%) (Figure 6A). However, no conclusions about the absolute up-regulation in block of all miRNAs in PAAs can be made, since the same molar amount of small RNA library was used for sequencing. Nevertheless, small RNAseq reveals a change in the global profile of PAAs, with a higher percentage of miRNAs being up-regulated in comparison to any other diploid (Figure 6A). In support of this evidence, the majority of up-regulated miRNAs (93%) in PAA/PA were also up-regulated in at least one of the other comparisons (PAA/PP or PAA/AA) and 62% were up-regulated in all the three comparisons (Table S3). If we considered only the miRNAs that change their expression more than 1 fold, 21% are up-regulated in all the comparisons and correspond to 5 miRNAs: dre-mir-182, dre-mir-183, dre-mir-96, dre-mir-141 and dre-mir-192 (Table S3). No specific transcript or group of transcripts sharing the same gene ontology term was found to be targeted by all the 5 miRNAs (MicroCosm Targets Version 5 and [19]).

Bottom Line: Previously in this complex, it was showed that in response to the increase in genome dosage, triploids hybrids could regulate gene expression to a diploid state.However, an overall view indicates an up-regulation of several miRNAs in triploids and a global miRNA expression in triploids higher than the predicted from an additive model.Those results point to a participation of miRNAs in the cellular functional stability needed when the ploidy change.

View Article: PubMed Central - PubMed

Affiliation: Centro de Biologia Ambiental, Departamento de Biologia Animal da Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal. mainacio@fc.ul.pt

ABSTRACT
The Squalius alburnoides complex (Steindachner) is one of the most intricate hybrid polyploid systems known in vertebrates. In this complex, the constant switch of the genome composition in consecutive generations, very frequently involving a change on the ploidy level, promotes repetitive situations of potential genomic shock. Previously in this complex, it was showed that in response to the increase in genome dosage, triploids hybrids could regulate gene expression to a diploid state. In this work we compared the small RNA profiles in the different genomic compositions interacting in the complex in order to explore the miRNA involvement in gene expression regulation of triploids. Using high-throughput arrays and sequencing technologies we were able to verify that diploid and triploid hybrids shared most of their sequences and their miRNA expression profiles were high correlated. However, an overall view indicates an up-regulation of several miRNAs in triploids and a global miRNA expression in triploids higher than the predicted from an additive model. Those results point to a participation of miRNAs in the cellular functional stability needed when the ploidy change.

Show MeSH
Related in: MedlinePlus