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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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Relation between z-scores. Plot of z-scores of breeds and sexes (top), and between the breed z-scores and the standard deviation within probes of Probe × Tissue solutions (bottom).
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Figure 4: Relation between z-scores. Plot of z-scores of breeds and sexes (top), and between the breed z-scores and the standard deviation within probes of Probe × Tissue solutions (bottom).

Mentions: At a false discovery rate FDR < 0.05, we identified 19 and 33 genes differentially expressed between sexes and breeds, respectively. The complete lists together with tentative annotations [26] are in Tables 3 and 4. Two of the genes, orthologous to human genes in the HLA-A and HLA-B complex, were differentially expressed simultaneously between breeds and between sexes. However, there was no correlation overall between tissue, breed or sex effects. This was evident from the pattern in Figure 4, which displays the relation between zb and zs scores (top figure) and between zb scores and the standard deviation of the probe × tissue solutions (bottom figure). If there were a relation, we would see the dots around a diagonal rather than close to the axes. Thus, each of the factors studied here, sex and breed, influence the transcriptome through different genetic programmes.


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)

Relation between z-scores. Plot of z-scores of breeds and sexes (top), and between the breed z-scores and the standard deviation within probes of Probe × Tissue solutions (bottom).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Relation between z-scores. Plot of z-scores of breeds and sexes (top), and between the breed z-scores and the standard deviation within probes of Probe × Tissue solutions (bottom).
Mentions: At a false discovery rate FDR < 0.05, we identified 19 and 33 genes differentially expressed between sexes and breeds, respectively. The complete lists together with tentative annotations [26] are in Tables 3 and 4. Two of the genes, orthologous to human genes in the HLA-A and HLA-B complex, were differentially expressed simultaneously between breeds and between sexes. However, there was no correlation overall between tissue, breed or sex effects. This was evident from the pattern in Figure 4, which displays the relation between zb and zs scores (top figure) and between zb scores and the standard deviation of the probe × tissue solutions (bottom figure). If there were a relation, we would see the dots around a diagonal rather than close to the axes. Thus, each of the factors studied here, sex and breed, influence the transcriptome through different genetic programmes.

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