title: Emergence of differentially regulated pathways associated with the development of regional specificity in chicken skin.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan. d00b48009@ntu.edu.tw.|Genome and Systems Biology Degree Program, Academia Sinica, Taipei, Taiwan. d00b48009@ntu.edu.tw.
authors.forename: Kai-Wei
authors.initials: KW
authors.lastname: Chang
authors.affiliation: Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan. deschutes101@gmail.com.
authors.forename: Nancy A
authors.initials: NA
authors.lastname: Huang
authors.affiliation: Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan. ihliu@ntu.edu.tw.|Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan. ihliu@ntu.edu.tw.
authors.forename: I-Hsuan
authors.initials: IH
authors.lastname: Liu
authors.affiliation: Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan. weh15@ms26.hinet.net.
authors.forename: Yi-Hui
authors.initials: YH
authors.lastname: Wang
authors.affiliation: Department of Pathology, School of Medicine, University of Southern California, Los Angeles, CA, USA. Ping.Wu@med.usc.edu.
authors.forename: Ping
authors.initials: P
authors.lastname: Wu
authors.affiliation: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan. swallow77@msn.com.
authors.forename: Yen-Tzu
authors.initials: YT
authors.lastname: Tseng
authors.affiliation: Department of Pathology, School of Medicine, University of Southern California, Los Angeles, CA, USA. z10110045@email.ncku.edu.tw.|International Research Center for Wound Repair and Regeneration, National Cheng-Kung University, Tainan, Taiwan. z10110045@email.ncku.edu.tw.
authors.forename: Michael W
authors.initials: MW
authors.lastname: Hughes
authors.affiliation: Department of Pathology, School of Medicine, University of Southern California, Los Angeles, CA, USA. tjiang@usc.edu.
authors.forename: Ting Xin
authors.initials: TX
authors.lastname: Jiang
authors.affiliation: Institute of Biotechnology, National Taiwan University, Taipei, Taiwan. motion@ntu.edu.tw.|Agricultural Biotechnology Research Centre, Academia Sinica, Taipei, Taiwan. motion@ntu.edu.tw.|Center for Systems Biology, National Taiwan University, Taipei, Taiwan. motion@ntu.edu.tw.
authors.forename: Mong-Hsun
authors.initials: MH
authors.lastname: Tsai
authors.affiliation: Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, Taiwan. chienyuchen@ntu.edu.tw.|Center for Systems Biology, National Taiwan University, Taipei, Taiwan. chienyuchen@ntu.edu.tw.
authors.forename: Chien-Yu
authors.initials: CY
authors.lastname: Chen
authors.affiliation: Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan. yjoyang@ntu.edu.tw.|Center for Systems Biology, National Taiwan University, Taipei, Taiwan. yjoyang@ntu.edu.tw.
authors.forename: Yen-Jen
authors.initials: YJ
authors.lastname: Oyang
authors.affiliation: Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan. eclin01@ntu.edu.tw.
authors.forename: En-Chung
authors.initials: EC
authors.lastname: Lin
authors.affiliation: Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan. cmchuong@med.usc.edu.|Department of Pathology, School of Medicine, University of Southern California, Los Angeles, CA, USA. cmchuong@med.usc.edu.
authors.forename: Cheng-Ming
authors.initials: CM
authors.lastname: Chuong
authors.affiliation: Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan. shaupinglin@ntu.edu.tw.|Institute of Biotechnology, National Taiwan University, Taipei, Taiwan. shaupinglin@ntu.edu.tw.|Agricultural Biotechnology Research Centre, Academia Sinica, Taipei, Taiwan. shaupinglin@ntu.edu.tw.|Center for Systems Biology, National Taiwan University, Taipei, Taiwan. shaupinglin@ntu.edu.tw.
authors.forename: Shau-Ping
authors.initials: SP
authors.lastname: Lin
mesh_terms: D000818:Animals; D020746:Calcium Channels, L-Type / Q000235:genetics / Q000378:metabolism; D002454:Cell Differentiation / Q000235:genetics; D002642:Chick Embryo; D002645:Chickens / Q000235:genetics* / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D005241:Feathers / Q000378:metabolism; D016678:Genome; D006657:Histones / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D015398:Signal Transduction; D012867:Skin / Q000378:metabolism*; D016212:Transforming Growth Factor beta / Q000378:metabolism
chemical_list: D020746:Calcium Channels, L-Type; D002843:Chromatin; D006657:Histones; D016212:Transforming Growth Factor beta