Limits...
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.

Show MeSH
Sample clustering using differentially expressed genes. Genes differentially expressed between sexes (top) and breeds (bottom).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2335121&req=5

Figure 5: Sample clustering using differentially expressed genes. Genes differentially expressed between sexes (top) and breeds (bottom).

Mentions: We performed a clustering of probes and samples using only the differentially expressed genes from Tables 3 and 4. Results were drawn in Figure 5, where the discrimination between sexes (top) and breeds (bottom) is neat and clearly visible. This clustering contrasts with that in Figure 1 where all probes were employed. The discrepancy occurs because the expression pattern of most genes is primarily affected by the tissue and not so much by sex or breed, as discussed. However, as Figure 5 clearly shows, this does not mean that a careful selection of probes does not allow us to discriminate samples between according to sex or breed.


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)

Sample clustering using differentially expressed genes. Genes differentially expressed between sexes (top) and breeds (bottom).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Sample clustering using differentially expressed genes. Genes differentially expressed between sexes (top) and breeds (bottom).
Mentions: We performed a clustering of probes and samples using only the differentially expressed genes from Tables 3 and 4. Results were drawn in Figure 5, where the discrimination between sexes (top) and breeds (bottom) is neat and clearly visible. This clustering contrasts with that in Figure 1 where all probes were employed. The discrepancy occurs because the expression pattern of most genes is primarily affected by the tissue and not so much by sex or breed, as discussed. However, as Figure 5 clearly shows, this does not mean that a careful selection of probes does not allow us to discriminate samples between according to sex or breed.

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