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Transcriptome architecture across tissues in the pig.

Ferraz AL, Ojeda A, López-Béjar M, Fernandes LT, Castelló A, Folch JM, Pérez-Enciso M - BMC Genomics (2008)

Bottom Line: Artificial selection has resulted in animal breeds with extreme phenotypes.For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively.The interaction in gene x tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain. splinter_zoo2@yahoo.com.br

ABSTRACT

Background: Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues?

Results: In order to gain insight on these issues, we conducted microarray expression profiling of 16 different tissues from four animals of two extreme pig breeds, Large White and Iberian, two males and two females. Mixed model analysis and neighbor - joining trees showed that tissues with similar developmental origin clustered closer than those with different embryonic origins. Often a sound biological interpretation was possible for overrepresented gene ontology categories within differentially expressed genes between groups of tissues. For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively. Tissue accounted for ~11 times more variability than sex or breed. Nevertheless, we were able to confidently identify genes with differential expression across tissues between breeds (33 genes) and between sexes (19 genes). The genes primarily affected by sex were overall different than those affected by breed or tissue. Interaction with tissue can be important for differentially expressed genes between breeds but not so much for genes whose expression differ between sexes.

Conclusion: Embryonic development leaves an enduring footprint on the transcriptome. The interaction in gene x tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome.

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Proportion of functional annotation categories. Percentage of the most frequent GO categories within the most significant differentially expressed genes between sexes (Table 3) and between breeds (Table 4). The number in each category is the false discovery rate (FDR) that the category is over represented with respect to the GO frequency across all genes in the microarray. The FDR is shown only if < 0.20.
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Figure 6: Proportion of functional annotation categories. Percentage of the most frequent GO categories within the most significant differentially expressed genes between sexes (Table 3) and between breeds (Table 4). The number in each category is the false discovery rate (FDR) that the category is over represented with respect to the GO frequency across all genes in the microarray. The FDR is shown only if < 0.20.

Mentions: We carried a GO automatic annotation [25] with the 19 most differentially expressed genes between sexes and 33 between breeds. The corresponding plots are in Figure 6. In neither case, sex or breed, was a given biological process GO clearly over represented (except the class of unknown/others which pools unknown and minoritary GO classes). As a result, the discussion should be considered as tentative or provisional. Nevertheless, we found defense genes to be over represented for both sex and breed specific genes. For sex, there was a significant excess of transcription and translation related genes. Some of these genes are sex linked (EIF1AY, UTX, ZFX), as mentioned above, so an over representation of this ontology is not unexpected. The GO biological processes were more scattered for breed than for sex (Figure 6B vs. 6A). Interestingly, there were more genes involved in nervous system development and cell differentiation than expected among breed specific genes. This might provide some clues as to what are the primary changes exerted by selection and breeding in the organism' transcriptome but further work is needed to get a definitive answer.


Transcriptome architecture across tissues in the pig.

Ferraz AL, Ojeda A, López-Béjar M, Fernandes LT, Castelló A, Folch JM, Pérez-Enciso M - BMC Genomics (2008)

Proportion of functional annotation categories. Percentage of the most frequent GO categories within the most significant differentially expressed genes between sexes (Table 3) and between breeds (Table 4). The number in each category is the false discovery rate (FDR) that the category is over represented with respect to the GO frequency across all genes in the microarray. The FDR is shown only if < 0.20.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2335121&req=5

Figure 6: Proportion of functional annotation categories. Percentage of the most frequent GO categories within the most significant differentially expressed genes between sexes (Table 3) and between breeds (Table 4). The number in each category is the false discovery rate (FDR) that the category is over represented with respect to the GO frequency across all genes in the microarray. The FDR is shown only if < 0.20.
Mentions: We carried a GO automatic annotation [25] with the 19 most differentially expressed genes between sexes and 33 between breeds. The corresponding plots are in Figure 6. In neither case, sex or breed, was a given biological process GO clearly over represented (except the class of unknown/others which pools unknown and minoritary GO classes). As a result, the discussion should be considered as tentative or provisional. Nevertheless, we found defense genes to be over represented for both sex and breed specific genes. For sex, there was a significant excess of transcription and translation related genes. Some of these genes are sex linked (EIF1AY, UTX, ZFX), as mentioned above, so an over representation of this ontology is not unexpected. The GO biological processes were more scattered for breed than for sex (Figure 6B vs. 6A). Interestingly, there were more genes involved in nervous system development and cell differentiation than expected among breed specific genes. This might provide some clues as to what are the primary changes exerted by selection and breeding in the organism' transcriptome but further work is needed to get a definitive answer.

Bottom Line: Artificial selection has resulted in animal breeds with extreme phenotypes.For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively.The interaction in gene x tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain. splinter_zoo2@yahoo.com.br

ABSTRACT

Background: Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues?

Results: In order to gain insight on these issues, we conducted microarray expression profiling of 16 different tissues from four animals of two extreme pig breeds, Large White and Iberian, two males and two females. Mixed model analysis and neighbor - joining trees showed that tissues with similar developmental origin clustered closer than those with different embryonic origins. Often a sound biological interpretation was possible for overrepresented gene ontology categories within differentially expressed genes between groups of tissues. For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively. Tissue accounted for ~11 times more variability than sex or breed. Nevertheless, we were able to confidently identify genes with differential expression across tissues between breeds (33 genes) and between sexes (19 genes). The genes primarily affected by sex were overall different than those affected by breed or tissue. Interaction with tissue can be important for differentially expressed genes between breeds but not so much for genes whose expression differ between sexes.

Conclusion: Embryonic development leaves an enduring footprint on the transcriptome. The interaction in gene x tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome.

Show MeSH