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A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs.

Idaghdour Y, Storey JD, Jadallah SJ, Gibson G - PLoS Genet. (2008)

Bottom Line: Genome-wide polymorphism analysis indicates that genetic differentiation in the total sample is limited and is unlikely to explain the expression divergence.Methylation profiling of 1,505 CpG sites suggests limited contribution of methylation to the observed differences in gene expression.Our results show a strong genome-wide gene expression signature of regional population differences that presumably include lifestyle, geography, and biotic factors, implying that these can play at least as great a role as genetic divergence in modulating gene expression variation in humans.

View Article: PubMed Central - PubMed

Affiliation: North Carolina State University, Raleigh, North Carolina, United States of America.

ABSTRACT
The different environments that humans experience are likely to impact physiology and disease susceptibility. In order to estimate the magnitude of the impact of environment on transcript abundance, we examined gene expression in peripheral blood leukocyte samples from 46 desert nomadic, mountain agrarian and coastal urban Moroccan Amazigh individuals. Despite great expression heterogeneity in humans, as much as one third of the leukocyte transcriptome was found to be associated with differences among regions. Genome-wide polymorphism analysis indicates that genetic differentiation in the total sample is limited and is unlikely to explain the expression divergence. Methylation profiling of 1,505 CpG sites suggests limited contribution of methylation to the observed differences in gene expression. Genetic network analysis further implies that specific aspects of immune function are strongly affected by regional factors and may influence susceptibility to respiratory and inflammatory disease. Our results show a strong genome-wide gene expression signature of regional population differences that presumably include lifestyle, geography, and biotic factors, implying that these can play at least as great a role as genetic divergence in modulating gene expression variation in humans.

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Related in: MedlinePlus

Volcano plots of statistical significance versus magnitude of differential expression between locations.(A) For each transcript, significance is shown as the negative logarithm of the P value on the y-axis, and the log base 2 of magnitude of mean expression difference is on the x-axis. Dashed lines indicate the threshold for significance (green: P<0.05, blue: 1% FDR, and red: Bonferroni adjusted P<0.05). The Venn diagram (B) shows the numbers of differentially expressed genes at 1% FDR for each comparison and the overlaps between them.
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pgen-1000052-g002: Volcano plots of statistical significance versus magnitude of differential expression between locations.(A) For each transcript, significance is shown as the negative logarithm of the P value on the y-axis, and the log base 2 of magnitude of mean expression difference is on the x-axis. Dashed lines indicate the threshold for significance (green: P<0.05, blue: 1% FDR, and red: Bonferroni adjusted P<0.05). The Venn diagram (B) shows the numbers of differentially expressed genes at 1% FDR for each comparison and the overlaps between them.

Mentions: Given the geographical distance between the sampled localities (urban to rural: 150 km; urban to nomadic: 560 km; rural to nomadic: 650 km), and the scope of the differences in lifestyle, we expected the nomadic sample to be the most differentiated. However, volcano plots of significance against the magnitude of gene expression divergence for each pairwise comparison of regions (Figure 2A) imply that the nomads diverge less from both the rural and urban individuals, than the urban diverge from rural individuals. We also examined the differentiation of all three regions (Figure 2B), which shows that the majority of the differences between nomadic and rural individuals are also observed in contrasts of these two localities with the urban sample.


A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs.

Idaghdour Y, Storey JD, Jadallah SJ, Gibson G - PLoS Genet. (2008)

Volcano plots of statistical significance versus magnitude of differential expression between locations.(A) For each transcript, significance is shown as the negative logarithm of the P value on the y-axis, and the log base 2 of magnitude of mean expression difference is on the x-axis. Dashed lines indicate the threshold for significance (green: P<0.05, blue: 1% FDR, and red: Bonferroni adjusted P<0.05). The Venn diagram (B) shows the numbers of differentially expressed genes at 1% FDR for each comparison and the overlaps between them.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2290968&req=5

pgen-1000052-g002: Volcano plots of statistical significance versus magnitude of differential expression between locations.(A) For each transcript, significance is shown as the negative logarithm of the P value on the y-axis, and the log base 2 of magnitude of mean expression difference is on the x-axis. Dashed lines indicate the threshold for significance (green: P<0.05, blue: 1% FDR, and red: Bonferroni adjusted P<0.05). The Venn diagram (B) shows the numbers of differentially expressed genes at 1% FDR for each comparison and the overlaps between them.
Mentions: Given the geographical distance between the sampled localities (urban to rural: 150 km; urban to nomadic: 560 km; rural to nomadic: 650 km), and the scope of the differences in lifestyle, we expected the nomadic sample to be the most differentiated. However, volcano plots of significance against the magnitude of gene expression divergence for each pairwise comparison of regions (Figure 2A) imply that the nomads diverge less from both the rural and urban individuals, than the urban diverge from rural individuals. We also examined the differentiation of all three regions (Figure 2B), which shows that the majority of the differences between nomadic and rural individuals are also observed in contrasts of these two localities with the urban sample.

Bottom Line: Genome-wide polymorphism analysis indicates that genetic differentiation in the total sample is limited and is unlikely to explain the expression divergence.Methylation profiling of 1,505 CpG sites suggests limited contribution of methylation to the observed differences in gene expression.Our results show a strong genome-wide gene expression signature of regional population differences that presumably include lifestyle, geography, and biotic factors, implying that these can play at least as great a role as genetic divergence in modulating gene expression variation in humans.

View Article: PubMed Central - PubMed

Affiliation: North Carolina State University, Raleigh, North Carolina, United States of America.

ABSTRACT
The different environments that humans experience are likely to impact physiology and disease susceptibility. In order to estimate the magnitude of the impact of environment on transcript abundance, we examined gene expression in peripheral blood leukocyte samples from 46 desert nomadic, mountain agrarian and coastal urban Moroccan Amazigh individuals. Despite great expression heterogeneity in humans, as much as one third of the leukocyte transcriptome was found to be associated with differences among regions. Genome-wide polymorphism analysis indicates that genetic differentiation in the total sample is limited and is unlikely to explain the expression divergence. Methylation profiling of 1,505 CpG sites suggests limited contribution of methylation to the observed differences in gene expression. Genetic network analysis further implies that specific aspects of immune function are strongly affected by regional factors and may influence susceptibility to respiratory and inflammatory disease. Our results show a strong genome-wide gene expression signature of regional population differences that presumably include lifestyle, geography, and biotic factors, implying that these can play at least as great a role as genetic divergence in modulating gene expression variation in humans.

Show MeSH
Related in: MedlinePlus