Abstract
BackgroundRegional specificity allows different skin regions to exhibit different characteristics, enabling complementary functions to make effective use of the integumentary surface. Chickens exhibit a high degree of regional specificity in the skin and can serve as a good model for when and how these regional differences begin to emerge.ResultsWe used developing feather and scale regions in embryonic chickens as a model to gauge the differences in their molecular pathways. We employed cosine similarity analysis to identify the differentially regulated and co-regulated genes. We applied low cell techniques for expression validation and chromatin immunoprecipitation (ChIP)-based enhancer identification to overcome limited cell availabilities from embryonic chicken skin.We identified a specific set of genes demonstrating a high correlation as being differentially expressed during feather and scale development and maturation. Some members of the WNT, TGF-beta/BMP, and Notch family known to be involved in feathering skin differentiation were found to be differentially regulated. Interestingly, we also found genes along calcium channel pathways that are differentially regulated. From the analysis of differentially regulated pathways, we used calcium signaling pathways as an example for further verification. Some voltage-gated calcium channel subunits, particularly CACNA1D, are expressed spatio-temporally in the skin epithelium. These calcium signaling pathway members may be involved in developmental decisions, morphogenesis, or epithelial maturation. We further characterized enhancers associated with histone modifications, including H3K4me1, H3K27ac, and H3K27me3, near calcium channel-related genes and identified signature intensive hotspots that may be correlated with certain voltage-gated calcium channel genes.ConclusionWe demonstrated the applicability of cosine similarity analysis for identifying novel regulatory pathways that are differentially regulated during development. Our study concerning the effects of signaling pathways and histone signatures on enhancers suggests that voltage-gated calcium signaling may be involved in early skin development. This work lays the foundation for studying the roles of these gene pathways and their genomic regulation during the establishment of skin regional specificity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-014-1202-9) contains supplementary material, which is available to authorized users.
Highlights
Regional specificity allows different skin regions to exhibit different characteristics, enabling complementary functions to make effective use of the integumentary surface
We found that most of the developmentally associated genes identified from Gene Set Enrichment Analysis (GSEA) were involved in regulatory networks, such as Bone morphogenetic protein (BMP)-Sonic hedgehog (SHH), Wingless-type MMTV integration site family (WNT), Delta-Notch, and retinoic acid pathways, which have been well described in regional skin development [12,14,15,16,17,35,36] (Additional file 1: Figure S1)
We measured the expression correlations between genes that were differentially expressed in feathers and scales (E7fe vs. Embryonic day 9 feather-growing skin epithelium (E9fe), Embryonic day 7 feather-growing skin mesenchyme (E7fm) vs. Embryonic day 9 feather-growing skin mesenchyme (E9fm), E9 metatarsal skin epithelial (E9se) vs. E11 metatarsal skin epithelial (E11se), and E9 metatarsal skin mesenchymal (E9sm) vs. E11 metatarsal skin mesenchymal (E11sm)) [21]
Summary
Regional specificity allows different skin regions to exhibit different characteristics, enabling complementary functions to make effective use of the integumentary surface. The integument system (skin) is essential for an individual to interact with the environment and plays a role in functions such as protection, sensation, thermoregulation, camouflage, and mating. These functions are achieved through evolutionally specialized skin and its appendages located in a regional-specific manner. In humans, these regions include the scalp, face, eyebrow, and sweat glands for communication and metabolic homeostasis. Feathers provide thermal insulation, protection, communication, and the ability to fly To form these specialized skin ectodermal organs during development, the ectoderm gradually becomes diversified through interactions with the dermis [1].
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