Figure 1.
Geographic locations of sampled Amazighs groups in Morocco.
A total of 52 peripheral blood samples were collected: 20 urban samples from the town of Anza (Latitude: 29.367°, Longitude: −9.633°), 15 rural samples from the rural village of Sebt-Nabor (Latitude: 31.450°, Longitude: −9.650°), and 17 nomadic samples from the Sahara desert in eastern Morocco (Latitude: 31.809°, Longitude −4.603°). Subsets of these were used in the gene expression profiling, genotyping and methylation profiling as described in Table S5.
Table 1.
Number of differentially expressed genes.
Figure 2.
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.
Figure 3.
Sex and location effects on methylation patterns.
Two-way clustering of differentially methylated CpG sites at P<0.05 (ANOVA) for the sex effect (A) and for the location effect (B). Sample labels indicate their sex and location (M: male, F: female, E: nomad, SN: rural, and A: urban). There is clear separation of the sexes in (A), and a suggestion of a signature of urban living for a dozen or so genes in (B) highlighted as the Anza-enriched cluster.
Figure 4.
Functional analysis of differentially expressed genes.
(A) Differential expression of the FOS and MYC networks and enriched disease classes. The Ingenuity Pathways Knowledge Base (IPKB) was used to generate networks of interacting genes that are overrepresented in the set of transcripts differentially expressed (based on a 1% FDR cutoff) between the urban and rural samples. The top two networks are focused on the FOS and MYC transcription factors, and every one of the genes that the IPKB indicate as interacting either genetically or biochemically are differentially expressed in this comparison. Network connectivity is indicated as solid edges for direct interactions, and dashed edges for indirect interactions. Transcripts are displayed in green for down-regulated and red for up-regulated, while cellular compartments in which the gene products are localized are also indicated. Gold edges highlight shared interactions. The list of genes, their fold change and P values are listed in Table S3. (B) Overrepresentation of disease classes affected by differentially expressed genes. Some of the Ingenuity Knowledge Database disease bio-function categories enriched (P<0.05) in differentially expressed transcripts (1% FDR) in the three lifestyle pairwise comparisons (grey, urban vs. rural; blue, nomadic vs. urban; green, nomadic vs. rural). Fisher's exact test was used to calculate the P value associated with the probability that the number of genes in each biological function and/or disease assigned to that data set is greater or less than expected by chance given the numbers of genes expressed in leukocytes.