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A gene expression atlas of the domestic pig.

Freeman TC, Ivens A, Baillie JK, Beraldi D, Barnett MW, Dorward D, Downing A, Fairbairn L, Kapetanovic R, Raza S, Tomoiu A, Alberio R, Wu C, Su AI, Summers KM, Tuggle CK, Archibald AL, Hume DA - BMC Biol. (2012)

Bottom Line: The analysis presented here provides a detailed functional clustering of the pig transcriptome where transcripts are grouped according to their expression pattern, so one can infer the function of an uncharacterized gene from the company it keeps and the locations in which it is expressed.In particular, we discuss the expression signatures associated with the gastrointestinal tract, an organ that was sampled at 15 sites along its length and whose biology in the pig is similar to human.As an important livestock animal with a physiology that is more similar than mouse to man, we provide a major new resource for understanding gene expression with respect to the known physiology of mammalian tissues and cells.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9PS, UK. tom.freeman@roslin.ed.ac.uk

ABSTRACT

Background: This work describes the first genome-wide analysis of the transcriptional landscape of the pig. A new porcine Affymetrix expression array was designed in order to provide comprehensive coverage of the known pig transcriptome. The new array was used to generate a genome-wide expression atlas of pig tissues derived from 62 tissue/cell types. These data were subjected to network correlation analysis and clustering.

Results: The analysis presented here provides a detailed functional clustering of the pig transcriptome where transcripts are grouped according to their expression pattern, so one can infer the function of an uncharacterized gene from the company it keeps and the locations in which it is expressed. We describe the overall transcriptional signatures present in the tissue atlas, where possible assigning those signatures to specific cell populations or pathways. In particular, we discuss the expression signatures associated with the gastrointestinal tract, an organ that was sampled at 15 sites along its length and whose biology in the pig is similar to human. We identify sets of genes that define specialized cellular compartments and region-specific digestive functions. Finally, we performed a network analysis of the transcription factors expressed in the gastrointestinal tract and demonstrate how they sub-divide into functional groups that may control cellular gastrointestinal development.

Conclusions: As an important livestock animal with a physiology that is more similar than mouse to man, we provide a major new resource for understanding gene expression with respect to the known physiology of mammalian tissues and cells. The data and analyses are available on the websites http://biogps.org and http://www.macrophages.com/pig-atlas.

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Diagram of pig GI tract and table of the cell populations/structures associatedwith specific regions. A. Schematic of the different regions of thepig GI tract with areas sampled for this study marked with a red dot. B.Table of the five main cell types and subdivisions thereof that make up the GItract and their expected presence in the samples analyzed here. GI,gastrointestinal.
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Figure 4: Diagram of pig GI tract and table of the cell populations/structures associatedwith specific regions. A. Schematic of the different regions of thepig GI tract with areas sampled for this study marked with a red dot. B.Table of the five main cell types and subdivisions thereof that make up the GItract and their expected presence in the samples analyzed here. GI,gastrointestinal.

Mentions: The pig's size and the feasibility of obtaining fresh tissues from healthy individualsoffer a unique opportunity to study the expression landscape of important organ systems.In common with humans, the pig is an omnivore and its gastrointestinal tract (GI) hasevolved to be able to masticate, digest and absorb a wide range of foodstuffs. In thisstudy, we collected samples along the entire length of the GI tract from the tongue tothe rectum, a total of 15 distinct regions (in duplicate), as shown in Figure 4a. The GI tract is lined with an epithelial layer whose cellularcomposition changes in line with the functional role of the GI compartment. The upper GItract is lined with a stratified squamous epithelium which transitions in the stomach toa columnar epithelium that runs through to the rectum. Even within the small intestine,enterocyte expression of solute transporters and digestive enzymes is tightly regulatedto reflect the changing nature of the luminal contents, as well as the migration ofcells up the crypt-villus axis [40]. Associated with the epithelium are various glandular cell types involvedwith enzyme secretion, lubrication, and endocrine control, and specialized structures,such as the pyloric and fundic glands of the stomach and sub-mucosal Brunner's glands ofthe duodenum. The lamina propria, which lies beneath the epithelium, is itself a complexmix of cells made up of endothelial, immune and connective tissues. The GI tract isalmost entirely surrounded by musculature (predominately smooth muscle) and regulated bythe enteric neural plexus. Therefore, the GI tract is composed of five major classes ofcell types: epithelia, glandular/endocrine epithelia, immune cells, neuronal cells andmesenchymal cells (muscle, connective tissue). The region-specific cellular compositionof the GI tract is summarized in Figure 4b.


A gene expression atlas of the domestic pig.

Freeman TC, Ivens A, Baillie JK, Beraldi D, Barnett MW, Dorward D, Downing A, Fairbairn L, Kapetanovic R, Raza S, Tomoiu A, Alberio R, Wu C, Su AI, Summers KM, Tuggle CK, Archibald AL, Hume DA - BMC Biol. (2012)

Diagram of pig GI tract and table of the cell populations/structures associatedwith specific regions. A. Schematic of the different regions of thepig GI tract with areas sampled for this study marked with a red dot. B.Table of the five main cell types and subdivisions thereof that make up the GItract and their expected presence in the samples analyzed here. GI,gastrointestinal.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814290&req=5

Figure 4: Diagram of pig GI tract and table of the cell populations/structures associatedwith specific regions. A. Schematic of the different regions of thepig GI tract with areas sampled for this study marked with a red dot. B.Table of the five main cell types and subdivisions thereof that make up the GItract and their expected presence in the samples analyzed here. GI,gastrointestinal.
Mentions: The pig's size and the feasibility of obtaining fresh tissues from healthy individualsoffer a unique opportunity to study the expression landscape of important organ systems.In common with humans, the pig is an omnivore and its gastrointestinal tract (GI) hasevolved to be able to masticate, digest and absorb a wide range of foodstuffs. In thisstudy, we collected samples along the entire length of the GI tract from the tongue tothe rectum, a total of 15 distinct regions (in duplicate), as shown in Figure 4a. The GI tract is lined with an epithelial layer whose cellularcomposition changes in line with the functional role of the GI compartment. The upper GItract is lined with a stratified squamous epithelium which transitions in the stomach toa columnar epithelium that runs through to the rectum. Even within the small intestine,enterocyte expression of solute transporters and digestive enzymes is tightly regulatedto reflect the changing nature of the luminal contents, as well as the migration ofcells up the crypt-villus axis [40]. Associated with the epithelium are various glandular cell types involvedwith enzyme secretion, lubrication, and endocrine control, and specialized structures,such as the pyloric and fundic glands of the stomach and sub-mucosal Brunner's glands ofthe duodenum. The lamina propria, which lies beneath the epithelium, is itself a complexmix of cells made up of endothelial, immune and connective tissues. The GI tract isalmost entirely surrounded by musculature (predominately smooth muscle) and regulated bythe enteric neural plexus. Therefore, the GI tract is composed of five major classes ofcell types: epithelia, glandular/endocrine epithelia, immune cells, neuronal cells andmesenchymal cells (muscle, connective tissue). The region-specific cellular compositionof the GI tract is summarized in Figure 4b.

Bottom Line: The analysis presented here provides a detailed functional clustering of the pig transcriptome where transcripts are grouped according to their expression pattern, so one can infer the function of an uncharacterized gene from the company it keeps and the locations in which it is expressed.In particular, we discuss the expression signatures associated with the gastrointestinal tract, an organ that was sampled at 15 sites along its length and whose biology in the pig is similar to human.As an important livestock animal with a physiology that is more similar than mouse to man, we provide a major new resource for understanding gene expression with respect to the known physiology of mammalian tissues and cells.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9PS, UK. tom.freeman@roslin.ed.ac.uk

ABSTRACT

Background: This work describes the first genome-wide analysis of the transcriptional landscape of the pig. A new porcine Affymetrix expression array was designed in order to provide comprehensive coverage of the known pig transcriptome. The new array was used to generate a genome-wide expression atlas of pig tissues derived from 62 tissue/cell types. These data were subjected to network correlation analysis and clustering.

Results: The analysis presented here provides a detailed functional clustering of the pig transcriptome where transcripts are grouped according to their expression pattern, so one can infer the function of an uncharacterized gene from the company it keeps and the locations in which it is expressed. We describe the overall transcriptional signatures present in the tissue atlas, where possible assigning those signatures to specific cell populations or pathways. In particular, we discuss the expression signatures associated with the gastrointestinal tract, an organ that was sampled at 15 sites along its length and whose biology in the pig is similar to human. We identify sets of genes that define specialized cellular compartments and region-specific digestive functions. Finally, we performed a network analysis of the transcription factors expressed in the gastrointestinal tract and demonstrate how they sub-divide into functional groups that may control cellular gastrointestinal development.

Conclusions: As an important livestock animal with a physiology that is more similar than mouse to man, we provide a major new resource for understanding gene expression with respect to the known physiology of mammalian tissues and cells. The data and analyses are available on the websites http://biogps.org and http://www.macrophages.com/pig-atlas.

Show MeSH
Related in: MedlinePlus