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Using regulatory and epistatic networks to extend the findings of a genome scan: identifying the gene drivers of pigmentation in merino sheep.

García-Gámez E, Reverter A, Whan V, McWilliam SM, Arranz JJ, International Sheep Genomics ConsortiumKijas J - PLoS ONE (2011)

Bottom Line: We combined these results with gene expression data from five tissue types analysed with a skin-specific microarray.Likewise, by testing two-loci models derived from all pair-wise comparisons across piebald-associated SNP, we generated an epistatic network.Further, we report a number of differentially expressed genes in regions containing highly associated SNP including ATRN, DOCK7, FGFR1OP, GLI3, SILV and TBX15.

View Article: PubMed Central - PubMed

Affiliation: Livestock Industries, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, Queensland, Australia.

ABSTRACT
Extending genome wide association analysis by the inclusion of gene expression data may assist in the dissection of complex traits. We examined piebald, a pigmentation phenotype in both human and Merino sheep, by analysing multiple data types using a systems approach. First, a case control analysis of 49,034 ovine SNP was performed which confirmed a multigenic basis for the condition. We combined these results with gene expression data from five tissue types analysed with a skin-specific microarray. Promoter sequence analysis of differentially expressed genes allowed us to reverse-engineer a regulatory network. Likewise, by testing two-loci models derived from all pair-wise comparisons across piebald-associated SNP, we generated an epistatic network. At the intersection of both networks, we identified thirteen genes with insulin-like growth factor binding protein 7 (IGFBP7), platelet-derived growth factor alpha (PDGFRA) and the tetraspanin platelet activator CD9 at the kernel of the intersection. Further, we report a number of differentially expressed genes in regions containing highly associated SNP including ATRN, DOCK7, FGFR1OP, GLI3, SILV and TBX15. The application of network theory facilitated co-analysis of genetic variation with gene expression, recapitulated aspects of the known molecular biology of skin pigmentation and provided insights into the transcription regulation and epistatic interactions involved in piebald Merino sheep.

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Gene expression relating to pigmentation.(A) Design of the microarray experiment, showing hybridizations (arrows) between five tissue types. Samples were labelled with either red (arrow head) or green dye (arrow tail) and the experiment was repeated in a dye swap using samples from independent biological replicates. A total of 20 hybridizations were performed to compare the following tissue types: white skin tissue from 4 pooled non-pigmented animals (NOR); black skin tissue from a piebald animal (PBB); white skin tissue from a piebald animal (PBW); black skin tissue from a recessive black animal (RSB) and white skin tissue sampled from the inguinal, non-pigmented area from a recessive black animal (RSW). Each sample intervened in four hybridizations (two labelled red and two labelled green). (B) Plot of SNP allele frequency difference between piebald and normal animals (Y-axis) and differential gene expression in contrast 3 (NOR versus PBW) (X-axis) for a set of 1,935 genes. Red symbols represent genes which were both differentially expressed (piebald versus normal) and have a SNP within 2.5 Kb. Black symbols represent genes which either displayed differential expression (P<0.01) or are located within 1 Mb of an associated SNP. The remaining green symbols represent genes which were neither differentially expressed nor located near associated SNP.
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pone-0021158-g002: Gene expression relating to pigmentation.(A) Design of the microarray experiment, showing hybridizations (arrows) between five tissue types. Samples were labelled with either red (arrow head) or green dye (arrow tail) and the experiment was repeated in a dye swap using samples from independent biological replicates. A total of 20 hybridizations were performed to compare the following tissue types: white skin tissue from 4 pooled non-pigmented animals (NOR); black skin tissue from a piebald animal (PBB); white skin tissue from a piebald animal (PBW); black skin tissue from a recessive black animal (RSB) and white skin tissue sampled from the inguinal, non-pigmented area from a recessive black animal (RSW). Each sample intervened in four hybridizations (two labelled red and two labelled green). (B) Plot of SNP allele frequency difference between piebald and normal animals (Y-axis) and differential gene expression in contrast 3 (NOR versus PBW) (X-axis) for a set of 1,935 genes. Red symbols represent genes which were both differentially expressed (piebald versus normal) and have a SNP within 2.5 Kb. Black symbols represent genes which either displayed differential expression (P<0.01) or are located within 1 Mb of an associated SNP. The remaining green symbols represent genes which were neither differentially expressed nor located near associated SNP.

Mentions: We sought to interpret these genetic associations using gene expression obtained from five skin tissue types isolated from non-pigmented, piebald and also recessive black individuals known to be under the control of Agouti (Figure 1A, 2A). The five tissue types were white skin tissue from non-pigmented sheep (NOR); black skin tissue from a piebald animal (PBB); white skin tissue from a piebald animal (PBW); black skin tissue from a recessive black animal (RSB) and white skin tissue from the non-pigmented region of a recessive black animal (RSW). Seven contrasts between tissue types (named DE1–DE7, see Methods section) were examined using a microarray containing 3,685 unique skin-specific genes. Of these, 54 genes displayed differential expression (DE) in ≥4 contrasts and hierarchical cluster analysis revealed coexpression across tissue types (Figure S2). A set of 19 genes, including 11 keratin family members displayed coordinated down regulation in piebald tissue, again indicating no single gene alone appeared responsible for the trait.


Using regulatory and epistatic networks to extend the findings of a genome scan: identifying the gene drivers of pigmentation in merino sheep.

García-Gámez E, Reverter A, Whan V, McWilliam SM, Arranz JJ, International Sheep Genomics ConsortiumKijas J - PLoS ONE (2011)

Gene expression relating to pigmentation.(A) Design of the microarray experiment, showing hybridizations (arrows) between five tissue types. Samples were labelled with either red (arrow head) or green dye (arrow tail) and the experiment was repeated in a dye swap using samples from independent biological replicates. A total of 20 hybridizations were performed to compare the following tissue types: white skin tissue from 4 pooled non-pigmented animals (NOR); black skin tissue from a piebald animal (PBB); white skin tissue from a piebald animal (PBW); black skin tissue from a recessive black animal (RSB) and white skin tissue sampled from the inguinal, non-pigmented area from a recessive black animal (RSW). Each sample intervened in four hybridizations (two labelled red and two labelled green). (B) Plot of SNP allele frequency difference between piebald and normal animals (Y-axis) and differential gene expression in contrast 3 (NOR versus PBW) (X-axis) for a set of 1,935 genes. Red symbols represent genes which were both differentially expressed (piebald versus normal) and have a SNP within 2.5 Kb. Black symbols represent genes which either displayed differential expression (P<0.01) or are located within 1 Mb of an associated SNP. The remaining green symbols represent genes which were neither differentially expressed nor located near associated SNP.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3119053&req=5

pone-0021158-g002: Gene expression relating to pigmentation.(A) Design of the microarray experiment, showing hybridizations (arrows) between five tissue types. Samples were labelled with either red (arrow head) or green dye (arrow tail) and the experiment was repeated in a dye swap using samples from independent biological replicates. A total of 20 hybridizations were performed to compare the following tissue types: white skin tissue from 4 pooled non-pigmented animals (NOR); black skin tissue from a piebald animal (PBB); white skin tissue from a piebald animal (PBW); black skin tissue from a recessive black animal (RSB) and white skin tissue sampled from the inguinal, non-pigmented area from a recessive black animal (RSW). Each sample intervened in four hybridizations (two labelled red and two labelled green). (B) Plot of SNP allele frequency difference between piebald and normal animals (Y-axis) and differential gene expression in contrast 3 (NOR versus PBW) (X-axis) for a set of 1,935 genes. Red symbols represent genes which were both differentially expressed (piebald versus normal) and have a SNP within 2.5 Kb. Black symbols represent genes which either displayed differential expression (P<0.01) or are located within 1 Mb of an associated SNP. The remaining green symbols represent genes which were neither differentially expressed nor located near associated SNP.
Mentions: We sought to interpret these genetic associations using gene expression obtained from five skin tissue types isolated from non-pigmented, piebald and also recessive black individuals known to be under the control of Agouti (Figure 1A, 2A). The five tissue types were white skin tissue from non-pigmented sheep (NOR); black skin tissue from a piebald animal (PBB); white skin tissue from a piebald animal (PBW); black skin tissue from a recessive black animal (RSB) and white skin tissue from the non-pigmented region of a recessive black animal (RSW). Seven contrasts between tissue types (named DE1–DE7, see Methods section) were examined using a microarray containing 3,685 unique skin-specific genes. Of these, 54 genes displayed differential expression (DE) in ≥4 contrasts and hierarchical cluster analysis revealed coexpression across tissue types (Figure S2). A set of 19 genes, including 11 keratin family members displayed coordinated down regulation in piebald tissue, again indicating no single gene alone appeared responsible for the trait.

Bottom Line: We combined these results with gene expression data from five tissue types analysed with a skin-specific microarray.Likewise, by testing two-loci models derived from all pair-wise comparisons across piebald-associated SNP, we generated an epistatic network.Further, we report a number of differentially expressed genes in regions containing highly associated SNP including ATRN, DOCK7, FGFR1OP, GLI3, SILV and TBX15.

View Article: PubMed Central - PubMed

Affiliation: Livestock Industries, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, Queensland, Australia.

ABSTRACT
Extending genome wide association analysis by the inclusion of gene expression data may assist in the dissection of complex traits. We examined piebald, a pigmentation phenotype in both human and Merino sheep, by analysing multiple data types using a systems approach. First, a case control analysis of 49,034 ovine SNP was performed which confirmed a multigenic basis for the condition. We combined these results with gene expression data from five tissue types analysed with a skin-specific microarray. Promoter sequence analysis of differentially expressed genes allowed us to reverse-engineer a regulatory network. Likewise, by testing two-loci models derived from all pair-wise comparisons across piebald-associated SNP, we generated an epistatic network. At the intersection of both networks, we identified thirteen genes with insulin-like growth factor binding protein 7 (IGFBP7), platelet-derived growth factor alpha (PDGFRA) and the tetraspanin platelet activator CD9 at the kernel of the intersection. Further, we report a number of differentially expressed genes in regions containing highly associated SNP including ATRN, DOCK7, FGFR1OP, GLI3, SILV and TBX15. The application of network theory facilitated co-analysis of genetic variation with gene expression, recapitulated aspects of the known molecular biology of skin pigmentation and provided insights into the transcription regulation and epistatic interactions involved in piebald Merino sheep.

Show MeSH