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Ng CS, Chen CK, Fan WL, Wu P, Wu SM, Chen JJ, Lai YT, Mao CT, Lu MYJ, Chen DR, Lin ZS, Yang KJ, Sha YA, Tu TC, Chen CF, Chuong CM, Li WH. Transcriptomic analyses of regenerating adult feathers in chicken. BMC Genomics 2015; 16:756. [PMID: 26445093 PMCID: PMC4594745 DOI: 10.1186/s12864-015-1966-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 09/30/2015] [Indexed: 11/13/2022] Open
Abstract
Background Feathers have diverse forms with hierarchical branching patterns and are an excellent model for studying the development and evolution of morphological traits. The complex structure of feathers allows for various types of morphological changes to occur. The genetic basis of the structural differences between different parts of a feather and between different types of feather is a fundamental question in the study of feather diversity, yet there is only limited relevant information for gene expression during feather development. Results We conducted transcriptomic analysis of five zones of feather morphologies from two feather types at different times during their regeneration after plucking. The expression profiles of genes associated with the development of feather structure were examined. We compared the gene expression patterns in different types of feathers and different portions of a feather and identified morphotype-specific gene expression patterns. Many candidate genes were identified for growth control, morphogenesis, or the differentiation of specific structures of different feather types. Conclusion This study laid the ground work for studying the evolutionary origin and diversification of feathers as abundant data were produced for the study of feather morphogenesis. It significantly increased our understanding of the complex molecular and cellular events in feather development processes and provided a foundation for future studies on the development of other skin appendages. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1966-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chen Siang Ng
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Chih-Kuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617, Taiwan.
| | - Wen-Lang Fan
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. .,Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, 20401, Taiwan.
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
| | - Siao-Man Wu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Jiun-Jie Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Yu-Ting Lai
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Chi-Tang Mao
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Di-Rong Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Ze-Shiang Lin
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Kai-Jung Yang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Yuan-An Sha
- Department of Animal Science, National Chung Hsing University, Taichung, 40227, Taiwan.
| | - Tsung-Che Tu
- Department of Animal Science, National Chung Hsing University, Taichung, 40227, Taiwan.
| | - Chih-Feng Chen
- Department of Animal Science, National Chung Hsing University, Taichung, 40227, Taiwan. .,Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, 40227, Taiwan.
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA. .,Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, 40227, Taiwan. .,Integrative Stem Cell Center, China Medical University, Taichung, 40402, Taiwan.
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan. .,Center for the Integrative and Evolutionary Galliformes Genomics (iEGG Center), National Chung Hsing University, Taichung, 40227, Taiwan. .,Integrative Stem Cell Center, China Medical University, Taichung, 40402, Taiwan. .,Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA.
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Musser JM, Wagner GP, Prum RO. Nuclear β-catenin localization supports homology of feathers, avian scutate scales, and alligator scales in early development. Evol Dev 2015; 17:185-94. [PMID: 25963196 DOI: 10.1111/ede.12123] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Feathers are an evolutionary novelty found in all extant birds. Despite recent progress investigating feather development and a revolution in dinosaur paleontology, the relationship of feathers to other amniote skin appendages, particularly reptile scales, remains unclear. Disagreement arises primarily from the observation that feathers and avian scutate scales exhibit an anatomical placode-defined as an epidermal thickening-in early development, whereas alligator and other avian scales do not. To investigate the homology of feathers and archosaur scales we examined patterns of nuclear β-catenin localization during early development of feathers and different bird and alligator scales. In birds, nuclear β-catenin is first localized to the feather placode, and then exhibits a dynamic pattern of localization in both epidermis and dermis of the feather bud. We found that asymmetric avian scutate scales and alligator scales share similar patterns of nuclear β-catenin localization with feathers. This supports the hypothesis that feathers, scutate scales, and alligator scales are homologous during early developmental stages, and are derived from early developmental stages of an asymmetric scale present in the archosaur ancestor. Furthermore, given that the earliest stage of β-catenin localization in feathers and archosaur scales is also found in placodes of several mammalian skin appendages, including hair and mammary glands, we hypothesize that a common skin appendage placode originated in the common ancestor of all amniotes. We suggest a skin placode should not be defined by anatomical features, but as a local, organized molecular signaling center from which an epidermal appendage develops.
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Affiliation(s)
- Jacob M Musser
- Department of Ecology and Evolutionary Biology, and Peabody Museum of Natural History, Yale University, 21 Sachem St, New Haven, CT 06511, USA.,Systems Biology Institute, Yale University, 840 West Campus Drive, West Haven, CT 06516, USA
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, and Peabody Museum of Natural History, Yale University, 21 Sachem St, New Haven, CT 06511, USA.,Systems Biology Institute, Yale University, 840 West Campus Drive, West Haven, CT 06516, USA
| | - Richard O Prum
- Department of Ecology and Evolutionary Biology, and Peabody Museum of Natural History, Yale University, 21 Sachem St, New Haven, CT 06511, USA
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Musser JM, Wagner GP. Character trees from transcriptome data: Origin and individuation of morphological characters and the so-called "species signal". JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:588-604. [PMID: 26175303 DOI: 10.1002/jez.b.22636] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 05/29/2015] [Indexed: 01/01/2023]
Abstract
We elaborate a framework for investigating the evolutionary history of morphological characters. We argue that morphological character trees generated by phylogenetic analysis of transcriptomes provide a useful tool for identifying causal gene expression differences underlying the development and evolution of morphological characters. They also enable rigorous testing of different models of morphological character evolution and origination, including the hypothesis that characters originate via divergence of repeated ancestral characters. Finally, morphological character trees provide evidence that character transcriptomes undergo concerted evolution. We argue that concerted evolution of transcriptomes can explain the so-called "species signal" found in several recent comparative transcriptome studies. The species signal is the phenomenon that transcriptomes cluster by species rather than character type, even though the characters are older than the respective species. We suggest the species signal is a natural consequence of concerted gene expression evolution resulting from mutations that alter gene regulatory network interactions shared by the characters under comparison. Thus, character trees generated from transcriptomes allow us to investigate the variational independence, or individuation, of morphological characters at the level of genetic programs.
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Affiliation(s)
- Jacob M Musser
- Yale Systems Biology Institute, West Haven, Connecticut.,Yale Peabody Museum of Natural History, New Haven, Connecticut.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Günter P Wagner
- Yale Systems Biology Institute, West Haven, Connecticut.,Yale Peabody Museum of Natural History, New Haven, Connecticut.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut.,Department of Obstetrics Gynecology and Reproductive Sciences, Yale Medical School, New Haven, Connecticut.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan
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AP2γ regulates neural and epidermal development downstream of the BMP pathway at early stages of ectodermal patterning. Cell Res 2012; 22:1546-61. [PMID: 22945355 DOI: 10.1038/cr.2012.122] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bone morphogenetic protein (BMP) inhibits neural specification and induces epidermal differentiation during ectodermal patterning. However, the mechanism of this process is not well understood. Here we show that AP2γ, a transcription factor activator protein (AP)-2 family member, is upregulated by BMP4 during neural differentiation of pluripotent stem cells. Knockdown of AP2γ facilitates mouse embryonic stem cell (ESC) neural fate determination and impairs epidermal differentiation, whereas AP2γ overexpression inhibits neural conversion and promotes epidermal commitment. In the early chick embryo, AP2γ is expressed in the entire epiblast before HH stage 3 and gradually shifts to the putative epidermal ectoderm during HH stage 4. In the future neural plate AP2γ inhibits excessive neural expansion and it also promotes epidermal development in the surface ectoderm. Moreover, AP2γ knockdown in ESCs and chick embryos partially rescued the neural inhibition and epidermal induction effects of BMP4. Mechanistic studies showed that BMP4 directly regulates AP2γ expression through Smad1 binding to the AP2γ promoter. Taken together, we propose that during the early stages of ectodermal patterning in the chick embryo, AP2γ acts downstream of the BMP pathway to restrict precocious neural expansion in the prospective neural plate and initiates epidermal differentiation in the future epidermal ectoderm.
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Tríbulo C, Guadalupe Barrionuevo M, Agüero TH, Sánchez SS, Calcaterra NB, Aybar MJ. ΔNp63is regulated by BMP4 signaling and is required for early epidermal development inXenopus. Dev Dyn 2011; 241:257-69. [DOI: 10.1002/dvdy.23706] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2011] [Indexed: 11/09/2022] Open
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Ugur SA, Tolun A. Homozygous WNT10b mutation and complex inheritance in Split-Hand/Foot Malformation. Hum Mol Genet 2008; 17:2644-53. [PMID: 18515319 DOI: 10.1093/hmg/ddn164] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Split-Hand/Foot Malformation (SHFM) is a complex limb malformation affecting the central rays of the autopod. We studied a large consanguineous kindred afflicted with autosomal recessive SHFM. Twelve affected members had central feet reductions with or without hand involvement while the remaining one had the mildest phenotype and atypical SHFM. We identified by homozygosity mapping a novel SHFM locus at 12q13.11-q13 with a maximum multipoint lod score of 5.47 and by subsequent candidate gene approach a homozygous missense WNT10b mutation (p.R332W) in all affected individuals but the atypical case plus in an asymptomatic female. We propose that either a second locus contributes to the manifestation of SHFM phenotype or a suppressor locus prevented trait manifestation in the non-penetrant female. We also investigated linkage to the five known SHFM loci. Four of the loci were excluded, while in TP63 [tumor protein p63 (SHFM4)], the only known gene responsible for SHFM, we detected in most affected subjects a rare insertion variant (rs34201045) at the alternate promoter used for transcription of the N-terminal-truncated p63 isotype. This is the first reported WNT10b mutation on the pathogenesis of limb development and recessive mutation in SHFM.
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Affiliation(s)
- Sibel Aylin Ugur
- Department of Molecular Biology and Genetics, Boaziçi University, Istanbul 34342, Turkey.
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Mercader N. Early steps of paired fin development in zebrafish compared with tetrapod limb development. Dev Growth Differ 2007; 49:421-37. [PMID: 17587327 DOI: 10.1111/j.1440-169x.2007.00942.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The development of zebrafish paired fins and tetrapod forelimbs and hindlimbs show striking similarities at the molecular level. In recent years, the zebrafish, Danio rerio has become a valuable model for the study of the development of vertebrate paired appendages and several large-scale mutagenesis screens have identified novel fin mutants. This review summarizes recent advances in research into zebrafish paired fin development and highlights features that are shared with and distinct from limb development in other main animal models.
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Affiliation(s)
- Nadia Mercader
- European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany.
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Abstract
The epidermis is a stratified epithelium that functions as a barrier protecting the organism from dehydration, mechanical trauma, and microbial insults. This barrier function is established during embryogenesis through a complex and tightly controlled stratification program. Whereas the morphological changes that occur during epidermal development have been extensively studied, the molecular mechanisms that govern this process remain poorly understood. In this review we summarize the current advances that have been made in understanding the molecular mechanisms that regulate epidermal morphogenesis.
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Affiliation(s)
- Maranke I Koster
- Department of Dermatology and Charles C. Gates Program in Regenerative Medicine and Stem Cell Biology, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80010, USA.
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Liu G, Moro A, Zhang JJR, Cheng W, Qiu W, Kim PCW. The role of Shh transcription activator Gli2 in chick cloacal development. Dev Biol 2006; 303:448-60. [PMID: 17239843 DOI: 10.1016/j.ydbio.2006.10.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 09/19/2006] [Accepted: 10/27/2006] [Indexed: 12/25/2022]
Abstract
Patterning and differentiation along the dorsal-ventral (D-V) axis lead to cloacal partitioning into ventral urinary and dorsal alimentary tracts in most mammals, but not birds and fish. We previously reported that the major activator of Sonic hedgehog (Shh) signaling transcription factor Gli2 plays an essential role in cloacal partitioning along the D-V axis in a mouse model. Here, we report that chick cloacal patterning and differentiation is along the anterior-posterior axis. During chick cloacal formation, Shh is expressed strongly in hindgut endoderm; Gli2 is very weakly detected in the surrounding hindgut mesoderm. In the mesoderm of the cloacal region, the over-expression of the constitutively active form of mouse Gli2 has been shown to: not induce cloacal partitioning along the D-V axis; induce expression of Ptch1, Gli2, bmp4, wnt5a, and hoxd-13, which have been previously shown to play a role in hindgut patterning; increase cell proliferation; and reduce apoptosis. Interestingly, p63 expression in the cloacal endoderm is also up-regulated, suggesting an interaction between the Shh and p63 pathways. In conclusion, Gli2 alone is insufficient to induce partitioning along the D-V axis in the chick embryo. However, Gli2 regulates both epithelial and mesenchymal cell proliferation and apoptosis during cloacal development.
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Affiliation(s)
- Guodong Liu
- Department of Surgery, Programs of Infection, Immunity, Injury and Repair, The Hospital for Sick Children, 555 University Ave, Suite 1526, Toronto, Ontario, Canada M5G 1X8
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Vanhoutteghem A, Djian P. Basonuclin 2: an extremely conserved homolog of the zinc finger protein basonuclin. Proc Natl Acad Sci U S A 2004; 101:3468-73. [PMID: 14988505 PMCID: PMC373485 DOI: 10.1073/pnas.0400268101] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2003] [Indexed: 11/18/2022] Open
Abstract
Basonuclin is a zinc finger protein specific to basal keratinocytes and germ cells. In keratinocytes, basonuclin behaves as a stem cell marker and is thought to be a transcription factor that maintains proliferative capacity and prevents terminal differentiation. The human gene is located on chromosome 15. We have discovered in the chicken the existence of basonuclin 2, a basonuclin homolog. We also report the entire sequence of mouse and human basonuclin 2; the corresponding genes are located on mouse chromosome 4 and human chromosome 9. Although the amino acid sequence of basonuclin 2 differs extensively from that of basonuclin 1, the two proteins share essential features. Both contain three paired zinc fingers, a nuclear localization signal, and a serine stripe. The basonuclin 2 mRNA has a wider tissue distribution than the basonuclin 1 mRNA: it is particularly abundant in testis, kidney, uterus, and intestine. The extreme conservation of the basonuclin 2 amino acid sequence across vertebrates suggests that basonuclin 2 serves an important function, presumably as a regulatory protein of DNA transcription.
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Affiliation(s)
- Amandine Vanhoutteghem
- Unité Propre de Recherche 2228 du Centre National de la Recherche Scientifique, Institut Interdisciplinaire des Sciences du Vivant des Saints-Pères, Université René Descartes, 75006 Paris, France
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Tao H, Yoshimoto Y, Yoshioka H, Nohno T, Noji S, Ohuchi H. FGF10 is a mesenchymally derived stimulator for epidermal development in the chick embryonic skin. Mech Dev 2002; 116:39-49. [PMID: 12128204 DOI: 10.1016/s0925-4773(02)00131-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of avian cutaneous appendages, feathers and scales, is known to arise from the epithelial-mesenchymal interaction. Here we show that FGF10 is associated with this developmental process as an early signal from mesenchymal cells underlying nascent cutaneous placodes. Expression of Fgf10 was detected in the mesenchymal cells underneath the developing placodes. Forced expression of Fgf10 in the femoral skin suppressed expression of Shh and a zinc finger gene snail-related (cSnR), while induced expression of Bmp2 in the interbud region, resulting in thickening of the epidermal layer. Furthermore, forced expression of Fgf10 in the foot skin caused marked ingrowings of the epidermis. The cells in the epidermal ingrowings expressed beta-catenin, proliferating cell nuclear antigen, and an epidermal stem cell marker p63. These results support the idea that FGF10 is a mesenchymally derived stimulator of epidermal development through crosstalk with bone morphogenetic protein (BMP), beta-catenin, and other signaling pathways.
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Affiliation(s)
- Hirotaka Tao
- Department of Biological Science and Technology, Faculty of Engineering, The University of Tokushima, 2-1 Minami-Jyosanjima-cho, Japan
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