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Splicing factor and exon profiling across human tissues.

de la Grange P, Gratadou L, Delord M, Dutertre M, Auboeuf D - Nucleic Acids Res. (2010)

Bottom Line: It has been shown that alternative splicing is especially prevalent in brain and testis when compared to other tissues.To test whether there is a specific propensity of these tissues to generate splicing variants, we used a single source of high-density microarray data to perform both splicing factor and exon expression profiling across 11 normal human tissues.In addition to providing a unique resource on expression profiling of alternative splicing variants and splicing factors across human tissues, this study demonstrates that the higher prevalence of alternative splicing in a subset of tissues originates from the larger number of genes, including splicing factors, being expressed than in other tissues.

View Article: PubMed Central - PubMed

Affiliation: GenoSplice technology, Centre Hayem, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010, Paris, France. didier.auboeuf@inserm.fr

ABSTRACT
It has been shown that alternative splicing is especially prevalent in brain and testis when compared to other tissues. To test whether there is a specific propensity of these tissues to generate splicing variants, we used a single source of high-density microarray data to perform both splicing factor and exon expression profiling across 11 normal human tissues. Paired comparisons between tissues and an original exon-based statistical group analysis demonstrated after extensive RT-PCR validation that the cerebellum, testis, and spleen had the largest proportion of differentially expressed alternative exons. Variations at the exon level correlated with a larger number of splicing factors being expressed at a high level in the cerebellum, testis and spleen than in other tissues. However, this splicing factor expression profile was similar to a more global gene expression pattern as a larger number of genes had a high expression level in the cerebellum, testis and spleen. In addition to providing a unique resource on expression profiling of alternative splicing variants and splicing factors across human tissues, this study demonstrates that the higher prevalence of alternative splicing in a subset of tissues originates from the larger number of genes, including splicing factors, being expressed than in other tissues.

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Identification of differentially expressed exons by paired comparisons. (A) Workflow. The exon and gene expression profiling across 11 normal tissues was performed using the same dataset from Affymetrix. Stringent criteria were used to select probes from genes expressed in at least two tissues in order to compare the exon content of well-expressed transcripts produced from annotated genes. Among 18 008 human genes annotated in FAST DB based on publicly available mRNA sequences, 13 843 genes were defined by >60% of high-quality probes. (B) Number of exons being differentially expressed when comparing two tissues as indicated. Fifty-five paired comparisons were performed by comparing each tissue to each other. Comparisons between two tissues were performed by considering only genes that were well expressed in both tissues. (C) Number of differentially expressed exons identified for each tissue. Each tissue contained a number of unique differentially expressed exons.
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Figure 1: Identification of differentially expressed exons by paired comparisons. (A) Workflow. The exon and gene expression profiling across 11 normal tissues was performed using the same dataset from Affymetrix. Stringent criteria were used to select probes from genes expressed in at least two tissues in order to compare the exon content of well-expressed transcripts produced from annotated genes. Among 18 008 human genes annotated in FAST DB based on publicly available mRNA sequences, 13 843 genes were defined by >60% of high-quality probes. (B) Number of exons being differentially expressed when comparing two tissues as indicated. Fifty-five paired comparisons were performed by comparing each tissue to each other. Comparisons between two tissues were performed by considering only genes that were well expressed in both tissues. (C) Number of differentially expressed exons identified for each tissue. Each tissue contained a number of unique differentially expressed exons.

Mentions: To identify differentially expressed exons across normal human tissues, we analyzed the publicly available dataset from Affymetrix (www.affymetrix.com) in which RNAs from 11 normal human tissues were hybridized on GeneChip® Human Exon 1.0 ST Arrays. Exon arrays contain multiple probes per exon, allowing to analyze gene expression at both transcript and exon levels (8). Using the EASANA® analysis system from GenoSplice technology (www.genosplice.com), 13 843 human genes were analyzed after the selection of ‘good-quality’ probes targeting well-annotated exons of genes with known mRNAs (Figure 1A). Fifty-five paired comparisons of the tissues with each others were performed in order to identify the largest number of differentially expressed exons across tissues. For each paired comparison of tissues, only genes significantly expressed in both tissues were considered for analysis at the exon level. A Student’s t-test was performed to test the difference between ‘splicing index values’ as previously reported (8). Differences between ‘splicing index values’ were considered statistically significant for fold-changes ≥1.5 and P-values ≤0.05.Figure 1.


Splicing factor and exon profiling across human tissues.

de la Grange P, Gratadou L, Delord M, Dutertre M, Auboeuf D - Nucleic Acids Res. (2010)

Identification of differentially expressed exons by paired comparisons. (A) Workflow. The exon and gene expression profiling across 11 normal tissues was performed using the same dataset from Affymetrix. Stringent criteria were used to select probes from genes expressed in at least two tissues in order to compare the exon content of well-expressed transcripts produced from annotated genes. Among 18 008 human genes annotated in FAST DB based on publicly available mRNA sequences, 13 843 genes were defined by >60% of high-quality probes. (B) Number of exons being differentially expressed when comparing two tissues as indicated. Fifty-five paired comparisons were performed by comparing each tissue to each other. Comparisons between two tissues were performed by considering only genes that were well expressed in both tissues. (C) Number of differentially expressed exons identified for each tissue. Each tissue contained a number of unique differentially expressed exons.
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Related In: Results  -  Collection

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Figure 1: Identification of differentially expressed exons by paired comparisons. (A) Workflow. The exon and gene expression profiling across 11 normal tissues was performed using the same dataset from Affymetrix. Stringent criteria were used to select probes from genes expressed in at least two tissues in order to compare the exon content of well-expressed transcripts produced from annotated genes. Among 18 008 human genes annotated in FAST DB based on publicly available mRNA sequences, 13 843 genes were defined by >60% of high-quality probes. (B) Number of exons being differentially expressed when comparing two tissues as indicated. Fifty-five paired comparisons were performed by comparing each tissue to each other. Comparisons between two tissues were performed by considering only genes that were well expressed in both tissues. (C) Number of differentially expressed exons identified for each tissue. Each tissue contained a number of unique differentially expressed exons.
Mentions: To identify differentially expressed exons across normal human tissues, we analyzed the publicly available dataset from Affymetrix (www.affymetrix.com) in which RNAs from 11 normal human tissues were hybridized on GeneChip® Human Exon 1.0 ST Arrays. Exon arrays contain multiple probes per exon, allowing to analyze gene expression at both transcript and exon levels (8). Using the EASANA® analysis system from GenoSplice technology (www.genosplice.com), 13 843 human genes were analyzed after the selection of ‘good-quality’ probes targeting well-annotated exons of genes with known mRNAs (Figure 1A). Fifty-five paired comparisons of the tissues with each others were performed in order to identify the largest number of differentially expressed exons across tissues. For each paired comparison of tissues, only genes significantly expressed in both tissues were considered for analysis at the exon level. A Student’s t-test was performed to test the difference between ‘splicing index values’ as previously reported (8). Differences between ‘splicing index values’ were considered statistically significant for fold-changes ≥1.5 and P-values ≤0.05.Figure 1.

Bottom Line: It has been shown that alternative splicing is especially prevalent in brain and testis when compared to other tissues.To test whether there is a specific propensity of these tissues to generate splicing variants, we used a single source of high-density microarray data to perform both splicing factor and exon expression profiling across 11 normal human tissues.In addition to providing a unique resource on expression profiling of alternative splicing variants and splicing factors across human tissues, this study demonstrates that the higher prevalence of alternative splicing in a subset of tissues originates from the larger number of genes, including splicing factors, being expressed than in other tissues.

View Article: PubMed Central - PubMed

Affiliation: GenoSplice technology, Centre Hayem, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010, Paris, France. didier.auboeuf@inserm.fr

ABSTRACT
It has been shown that alternative splicing is especially prevalent in brain and testis when compared to other tissues. To test whether there is a specific propensity of these tissues to generate splicing variants, we used a single source of high-density microarray data to perform both splicing factor and exon expression profiling across 11 normal human tissues. Paired comparisons between tissues and an original exon-based statistical group analysis demonstrated after extensive RT-PCR validation that the cerebellum, testis, and spleen had the largest proportion of differentially expressed alternative exons. Variations at the exon level correlated with a larger number of splicing factors being expressed at a high level in the cerebellum, testis and spleen than in other tissues. However, this splicing factor expression profile was similar to a more global gene expression pattern as a larger number of genes had a high expression level in the cerebellum, testis and spleen. In addition to providing a unique resource on expression profiling of alternative splicing variants and splicing factors across human tissues, this study demonstrates that the higher prevalence of alternative splicing in a subset of tissues originates from the larger number of genes, including splicing factors, being expressed than in other tissues.

Show MeSH
Related in: MedlinePlus