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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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Differential GO categories across embryo layers. Percentage of the most frequent GO categories within extreme genes for each embryonic layer (A, ectoderm; B, mesoderm; C, endoderm; D, all genes in A, B and C). 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 3: Differential GO categories across embryo layers. Percentage of the most frequent GO categories within extreme genes for each embryonic layer (A, ectoderm; B, mesoderm; C, endoderm; D, all genes in A, B and C). 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 sought to investigate more in detail the genetic basis of the tissue arrangement by embryonic layers, and to pick up genes that can be differentially expressed in concerted action within each embryonic layer. To that end, we obtained the extreme gene probes differentiating the ectoderm tissues (olfactory bulb, hypothalamus, pineal gland, adenohypophysis and neurohypophysis), mesoderm (muscle and fat), and endoderm (liver, stomach and ileum). An extreme probe for each embryo layer was defined as for individual tissues, i.e., a probe whose all expression levels for that group of tissues were either smaller or larger than the levels for the rest of tissues (Material and Methods). We excluded thyroid and adrenal glands for being mixed tissues and blood, for outlier. The complete list in additional file 1. A pie-plot with differential gene ontology (GO) frequencies obtained with onto-express [25] is in Figure 3. A wide variety of GO were over represented in each layer; this fact, together with a large percentage of unknown or unannotated genes makes it somewhat difficult to interpret the results in detail.


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)

Differential GO categories across embryo layers. Percentage of the most frequent GO categories within extreme genes for each embryonic layer (A, ectoderm; B, mesoderm; C, endoderm; D, all genes in A, B and C). 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 3: Differential GO categories across embryo layers. Percentage of the most frequent GO categories within extreme genes for each embryonic layer (A, ectoderm; B, mesoderm; C, endoderm; D, all genes in A, B and C). 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 sought to investigate more in detail the genetic basis of the tissue arrangement by embryonic layers, and to pick up genes that can be differentially expressed in concerted action within each embryonic layer. To that end, we obtained the extreme gene probes differentiating the ectoderm tissues (olfactory bulb, hypothalamus, pineal gland, adenohypophysis and neurohypophysis), mesoderm (muscle and fat), and endoderm (liver, stomach and ileum). An extreme probe for each embryo layer was defined as for individual tissues, i.e., a probe whose all expression levels for that group of tissues were either smaller or larger than the levels for the rest of tissues (Material and Methods). We excluded thyroid and adrenal glands for being mixed tissues and blood, for outlier. The complete list in additional file 1. A pie-plot with differential gene ontology (GO) frequencies obtained with onto-express [25] is in Figure 3. A wide variety of GO were over represented in each layer; this fact, together with a large percentage of unknown or unannotated genes makes it somewhat difficult to interpret the results in detail.

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