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

Overview of attention for article published in BMC Genomics, January 2015
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Title
Emergence of differentially regulated pathways associated with the development of regional specificity in chicken skin
Published in
BMC Genomics, January 2015
DOI 10.1186/s12864-014-1202-9
Pubmed ID
Authors

Kai-Wei Chang, Nancy A Huang, I-Hsuan Liu, Yi-Hui Wang, Ping Wu, Yen-Tzu Tseng, Michael W Hughes, Ting Xin Jiang, Mong-Hsun Tsai, Chien-Yu Chen, Yen-Jen Oyang, En-Chung Lin, Cheng-Ming Chuong, Shau-Ping Lin

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.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 27 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Portugal 1 4%
Unknown 26 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 8 30%
Researcher 6 22%
Student > Master 3 11%
Student > Doctoral Student 3 11%
Professor 1 4%
Other 3 11%
Unknown 3 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 17 63%
Biochemistry, Genetics and Molecular Biology 4 15%
Computer Science 2 7%
Medicine and Dentistry 1 4%
Unknown 3 11%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 28 January 2015.
All research outputs
#3,322,126
of 4,684,537 outputs
Outputs from BMC Genomics
#3,445
of 4,358 outputs
Outputs of similar age
#111,744
of 161,102 outputs
Outputs of similar age from BMC Genomics
#225
of 269 outputs
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So far Altmetric has tracked 4,358 research outputs from this source. They receive a mean Attention Score of 3.8. This one is in the 10th percentile – i.e., 10% of its peers scored the same or lower than it.
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