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

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• 作者：Kai-Wei Chang (1) (2)
  Nancy A Huang (3)
  I-Hsuan Liu (4) (5)
  Yi-Hui Wang (4)
  Ping Wu (6)
  Yen-Tzu Tseng (7)
  Michael W Hughes (6) (8)
  Ting Xin Jiang (6)
  Mong-Hsun Tsai (10) (11) (7)
  Chien-Yu Chen (11) (9)
  Yen-Jen Oyang (11) (3)
  En-Chung Lin (4)
  Cheng-Ming Chuong (5) (6)
  Shau-Ping Lin (10) (11) (5) (7)
  
  1. Genome and Systems Biology Degree Program ; National Taiwan University ; Taipei ; Taiwan
  2. Genome and Systems Biology Degree Program ; Academia Sinica ; Taipei ; Taiwan
  3. Department of Computer Science and Information Engineering ; National Taiwan University ; Taipei ; Taiwan
  4. Department of Animal Science and Technology ; National Taiwan University ; Taipei ; Taiwan
  5. Research Center for Developmental Biology and Regenerative Medicine ; National Taiwan University ; Taipei ; Taiwan
  6. Department of Pathology ; School of Medicine ; University of Southern California ; Los Angeles ; CA ; USA
  7. Institute of Biotechnology ; National Taiwan University ; Taipei ; Taiwan
  8. International Research Center for Wound Repair and Regeneration ; National Cheng-Kung University ; Tainan ; Taiwan
  10. Agricultural Biotechnology Research Centre ; Academia Sinica ; Taipei ; Taiwan
  11. Center for Systems Biology ; National Taiwan University ; Taipei ; Taiwan
  9. Department of Bio-Industrial Mechatronics Engineering ; National Taiwan University ; Taipei ; Taiwan
  
• 关键词：Development ; Chicken ; Skin ; Cosine similarity ; Calcium ; Histone modifications
• 刊名：BMC Genomics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：16
• 期：1
• 全文大小：1,873 KB
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• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background Regional 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. Results We 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. Conclusion We 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.