Emergence of differentially regulated pathways associated with the development of regional specificity in chicken skin

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.

The search for SNPs and genes associated with the feed conversion ratio using entropy analysis

“…CACNA2D1 is involved in the development of the skin epithelium in chicken embryos (Chang et al, 2015). GNAI1 is connected with many signalling pathways.…”

Genomic determinants of epidermal appendage patterning and structure in domestic birds

“…However, the molecular pathways that regulate epidermal appendage variation remain poorly understood. To identify regulatory pathways involved in the feather vs. scale fate decision, Chang et al (2015) compared transcriptome microarray datasets from feather-forming dorsal skin and scale-forming metatarsal skin harvested from chicken embryos at two developmental stages associated with the uncommitted or committed state. The authors used cosine similarity analysis to identify genes that are differentially expressed in feather vs. scale forming epidermis and mesenchyme (Chang et al, 2015).…”

“…To identify regulatory pathways involved in the feather vs. scale fate decision, Chang et al (2015) compared transcriptome microarray datasets from feather-forming dorsal skin and scale-forming metatarsal skin harvested from chicken embryos at two developmental stages associated with the uncommitted or committed state. The authors used cosine similarity analysis to identify genes that are differentially expressed in feather vs. scale forming epidermis and mesenchyme (Chang et al, 2015). In addition to the identification of genes with known roles in epidermal development, the authors discovered that genes involved in calcium signaling are significantly upregulated in developing scale-forming epithelium relative to feather-forming epithelium (Chang et al, 2015).…”

“…The authors used cosine similarity analysis to identify genes that are differentially expressed in feather vs. scale forming epidermis and mesenchyme (Chang et al, 2015). In addition to the identification of genes with known roles in epidermal development, the authors discovered that genes involved in calcium signaling are significantly upregulated in developing scale-forming epithelium relative to feather-forming epithelium (Chang et al, 2015). Although substantial functional experimentation is required to define the role of calcium signaling in the feather vs. scale fate decision, this research highlights the prospect of using genome-wide gene expression analyses to elucidate the molecular networks that regulate epidermal appendage fate.…”

“…Many excellent reviews summarize recent progress in this field, including a landmark volume edited by Chuong (1998). Other recent work and reviews tackle the molecular developmental basis of macropatterning of appendage distribution in different body regions (Chang et al, 2015; Lin et al, 2006), micropatterning determinants of epidermal placode spacing (Houghton et al, 2005; Hughes et al, 2011; Lin et al, 2009), and the evolution and development of structural variation among epidermal appendages within and among species (Chen et al, 2015; Dhouailly, 2009; Musser et al, 2015; Prin and Dhouailly, 2004; Prin et al, 2004; Sawyer et al, 2005). …”