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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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NJ tree of tissues using the 1- Distance. The four groups in Table 1 are indicated by symbols: brain (open squares), endocrine (grey squares), structural (grey triangles) and metabolic (black circles).
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Figure 2: NJ tree of tissues using the 1- Distance. The four groups in Table 1 are indicated by symbols: brain (open squares), endocrine (grey squares), structural (grey triangles) and metabolic (black circles).

Mentions: The trees depicted in Figure 1 were obtained with the original data (after RMA transformation). A better alternative to study relationships between tissues is to consider the Probe × Tissue solutions obtained from model (2), as these solutions are corrected for 'noisy' factors such as sex, breed and global tissue effects. Thus we constructed a NJ-tree of tissue transcriptomes using the 1- distance (see methods). This tree is shown in Figure 2. Although the pattern was similar to the NJ-tree in Figure 1, this tree provided a clearer picture of relationships between tissues. For instance, it emphasized that blood is the most distant tissue, corroborated also by the fact that blood harbored the largest number of extreme probes (Table 1). We defined a tissue's extreme probe as a probe for which all four mRNA levels of the tissue were either smaller or larger than the remaining mRNA levels (Material and Methods). In contrast, the two adrenal tissues and both fats were the closest pair of tissues. The brain is not a uniform organ, and this well known fact [21-23] was corroborated by a relevant variability within the different brain tissues sampled. Olfactory bulb was neighbor to hypothalamus. The two pituitaries, adenohypohysis and neurohypohysis, exhibited neighbor but distinct transcriptomes. This result agrees with the fact that both organs carry out very different physiological functions and have separate embryonic origins from the ectoderm layer (from an ectodermal outpocketing of the stomodeum and neural ectoderm, respectively). In fact, it was more interesting to note that neurohypophysis and hypothalamus were relatively distant. A close relationship might have been expected because neurohypophysis consists primarily of axonic projections of the hypothalamus. The pineal gland exhibited an intermediate transcriptome between hypophyses and hypothalamus – olfactory bulb.


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)

NJ tree of tissues using the 1- Distance. The four groups in Table 1 are indicated by symbols: brain (open squares), endocrine (grey squares), structural (grey triangles) and metabolic (black circles).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: NJ tree of tissues using the 1- Distance. The four groups in Table 1 are indicated by symbols: brain (open squares), endocrine (grey squares), structural (grey triangles) and metabolic (black circles).
Mentions: The trees depicted in Figure 1 were obtained with the original data (after RMA transformation). A better alternative to study relationships between tissues is to consider the Probe × Tissue solutions obtained from model (2), as these solutions are corrected for 'noisy' factors such as sex, breed and global tissue effects. Thus we constructed a NJ-tree of tissue transcriptomes using the 1- distance (see methods). This tree is shown in Figure 2. Although the pattern was similar to the NJ-tree in Figure 1, this tree provided a clearer picture of relationships between tissues. For instance, it emphasized that blood is the most distant tissue, corroborated also by the fact that blood harbored the largest number of extreme probes (Table 1). We defined a tissue's extreme probe as a probe for which all four mRNA levels of the tissue were either smaller or larger than the remaining mRNA levels (Material and Methods). In contrast, the two adrenal tissues and both fats were the closest pair of tissues. The brain is not a uniform organ, and this well known fact [21-23] was corroborated by a relevant variability within the different brain tissues sampled. Olfactory bulb was neighbor to hypothalamus. The two pituitaries, adenohypohysis and neurohypohysis, exhibited neighbor but distinct transcriptomes. This result agrees with the fact that both organs carry out very different physiological functions and have separate embryonic origins from the ectoderm layer (from an ectodermal outpocketing of the stomodeum and neural ectoderm, respectively). In fact, it was more interesting to note that neurohypophysis and hypothalamus were relatively distant. A close relationship might have been expected because neurohypophysis consists primarily of axonic projections of the hypothalamus. The pineal gland exhibited an intermediate transcriptome between hypophyses and hypothalamus – olfactory bulb.

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