Expression Changes of Structural Protein Genes May Be Related to Adaptive Skin Characteristics Specific to Humans

Abstract

Human skin is morphologically and physiologically different from the skin of other primates. However, the genetic causes underlying human-specific skin characteristics remain unclear. Here, we quantitatively demonstrate that the epidermis and dermis of human skin are significantly thicker than those of three Old World monkey species. In addition, we indicate that the topography of the epidermal basement membrane zone shows a rete ridge in humans but is flat in the Old World monkey species examined. Subsequently, we comprehensively compared gene expression levels between human and nonhuman great ape skin using next-generation cDNA sequencing (RNA-Seq). We identified four structural protein genes associated with the epidermal basement membrane zone or elastic fibers in the dermis (COL18A1, LAMB2, CD151, and BGN) that were expressed significantly greater in humans than in nonhuman great apes, suggesting that these differences may be related to the rete ridge and rich elastic fibers present in human skin. The rete ridge may enhance the strength of adhesion between the epidermis and dermis in skin. This ridge, along with a thick epidermis and rich elastic fibers might contribute to the physical strength of human skin with a low amount of hair. To estimate transcriptional regulatory regions for COL18A1, LAMB2, CD151, and BGN, we examined conserved noncoding regions with histone modifications that can activate transcription in skin cells. Human-specific substitutions in these regions, especially those located in binding sites of transcription factors which function in skin, may alter the gene expression patterns and give rise to the human-specific adaptive skin characteristics.

Keywords: elastic fibers; epidermal basement membrane zone; primates; rete ridge; transcriptional regulatory region.

Fig. 1.

—Phylogenetic relationships between human, nonhuman great apes, and rhesus macaque. A phylogenetic tree was constructed using the Neighbor-Joining method and the pair-wise nucleotide divergence of whole genome sequences (Scally et al. 2012). The scale bar represents 0.005 substitutions per site. The distance on each branch was calculated by the Fitch–Margoliash algorithm (Fitch and Margoliash 1967) using the pair-wise nucleotide divergence.

Fig. 2.

—The thickness and epidermal BM zone topography of skin in humans and three Old World monkey species. The comparison of thickness of the epidermis (a) and dermis (b). Pa, Ca, Cp, and Hs indicate Papio anubis, Cercopithecus albogularis, Chlorocebus pygerythrus, and Homo sapiens, respectively. The numbers of individuals used for measurements are shown under each species name abbreviation. Photographs of hematoxylin–eosin stained histologic skin sections are from H. sapiens (c), P. anubis (d), C. albogularis (e), and Ch. pygerythrus (f). Scale bars are shown in each panel. ep. and d. indicate the epidermis and dermis, respectively. *P < 0.05, **P < 0.01, and ***P < 0.001, t-test with Bonferroni correction.

Fig. 3.

—Volcano plots for the gene expression differences between humans and nonhuman great apes. Each blue dot represents the gene expressed in the skin. The normalized RPKM values are based on the mapping to the reference genome of (a) human, (b) chimpanzee, (c) gorilla, and (d) orangutan. The log 2-fold changes of average normalized RPKM values of nonhuman great apes compared with those of humans and the −log 10 P values resulting from Baggerley’s test comparing average normalized RPKM values between humans and nonhuman great apes for each gene are plotted on the x and y axis, respectively. Differentially expressed genes between humans and nonhuman great apes selected in this study are shown by black and red dots. The gene names colored in red indicate structural protein genes.

Fig. 4.

—The positions of the putative transcriptional regulatory regions with the candidate substitutions. The exons of (a) COL18A1, (b) LAMB2, (c) CD151, and (d) BGN genes are shown in orange in each panel. The symbols “<” and “>” indicate the direction of the genes. All genes (except genes of interest) are shown by gray arrows. White arrowheads at the end of horizontal lines indicate that the genes are continuous beyond the schematic representation. Orange vertical lines indicate the position of the putative transcriptional regulatory regions numbered by Roman numerals. The zoomed-in view around these regions are shown in the rectangles of each panel. H3K4m1, H3K4m2, H3K4m3, H3K9ac, and H3K27ac indicate monomethylation of histone H3 lysine 4, dimethylation of histone H3 lysine 4, trimethylation of histone H3 lysine 4, acetylation of histone H3 lysine 9, and acetylation of histone H3 lysine 27, respectively. The positions and density of the gray scale bars indicate the positions and intensity of histone modifications shown at the side of the bars, respectively. The skin cell strains referred for the histone modifications were as below: a: NHEK, b: NHDF-Ad, c: NHEK, and d: NHDF-Ad. For LAMB2 and BGN, we also referred to the NHEK strain, in which the genes are also expressed (supplementary fig. S4b and d, Supplementary Material online). The red arrowheads indicate the numbers of the candidate substitutions located in each putative transcriptional regulatory region. A substitution in COL18A1 region I was later removed from the candidate substitutions because of the high ancestral allele frequency in the locus.