1
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Chan YF, Lu CW, Kuo HC, Hung CM. A chromosome-level genome assembly of the Asian house martin implies potential genes associated with the feathered-foot trait. G3 (BETHESDA, MD.) 2024; 14:jkae077. [PMID: 38607414 PMCID: PMC11152083 DOI: 10.1093/g3journal/jkae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/04/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
The presence of feathers is a vital characteristic among birds, yet most modern birds had no feather on their feet. The discoveries of feathers on the hind limbs of basal birds and dinosaurs have sparked an interest in the evolutionary origin and genetic mechanism of feathered feet. However, the majority of studies investigating the genes associated with this trait focused on domestic populations. Understanding the genetic mechanism underpinned feathered-foot development in wild birds is still in its infancy. Here, we assembled a chromosome-level genome of the Asian house martin (Delichon dasypus) using the long-read High Fidelity sequencing approach to initiate the search for genes associated with its feathered feet. We employed the whole-genome alignment of D. dasypus with other swallow species to identify high-SNP regions and chromosomal inversions in the D. dasypus genome. After filtering out variations unrelated to D. dasypus evolution, we found six genes related to feather development near the high-SNP regions. We also detected three feather development genes in chromosomal inversions between the Asian house martin and the barn swallow genomes. We discussed their association with the wingless/integrated (WNT), bone morphogenetic protein, and fibroblast growth factor pathways and their potential roles in feathered-foot development. Future studies are encouraged to utilize the D. dasypus genome to explore the evolutionary process of the feathered-foot trait in avian species. This endeavor will shed light on the evolutionary path of feathers in birds.
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Affiliation(s)
- Yuan-Fu Chan
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Wei Lu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Hao-Chih Kuo
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
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2
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Chen CK, Chang YM, Jiang TX, Yue Z, Liu TY, Lu J, Yu Z, Lin JJ, Vu TD, Huang TY, Harn HIC, Ng CS, Wu P, Chuong CM, Li WH. Conserved regulatory switches for the transition from natal down to juvenile feather in birds. Nat Commun 2024; 15:4174. [PMID: 38755126 PMCID: PMC11099144 DOI: 10.1038/s41467-024-48303-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 04/24/2024] [Indexed: 05/18/2024] Open
Abstract
The transition from natal downs for heat conservation to juvenile feathers for simple flight is a remarkable environmental adaptation process in avian evolution. However, the underlying epigenetic mechanism for this primary feather transition is mostly unknown. Here we conducted time-ordered gene co-expression network construction, epigenetic analysis, and functional perturbations in developing feather follicles to elucidate four downy-juvenile feather transition events. We report that extracellular matrix reorganization leads to peripheral pulp formation, which mediates epithelial-mesenchymal interactions for branching morphogenesis. α-SMA (ACTA2) compartmentalizes dermal papilla stem cells for feather renewal cycling. LEF1 works as a key hub of Wnt signaling to build rachis and converts radial downy to bilateral symmetry. Novel usage of scale keratins strengthens feather sheath with SOX14 as the epigenetic regulator. We show that this primary feather transition is largely conserved in chicken (precocial) and zebra finch (altricial) and discuss the possibility that this evolutionary adaptation process started in feathered dinosaurs.
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Affiliation(s)
- Chih-Kuan Chen
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yao-Ming Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ting-Xin Jiang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - ZhiCao Yue
- Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen, Guangdong, China
- International Cancer Center, Shenzhen University Medical School, Shenzhen, Guangdong, China
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Shenzhen University Medical School, Shenzhen, Guangdong, China
| | - Tzu-Yu Liu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Jiayi Lu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zhou Yu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jinn-Jy Lin
- National Applied Research Laboratories, National Center for High-performance Computing, Hsinchu, Taiwan
| | - Trieu-Duc Vu
- Michigan Neuroscience Institute, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Tao-Yu Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hans I-Chen Harn
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chen Siang Ng
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
- Bioresource Conservation Research Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
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3
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Kiat Y, O’Connor JK. Functional constraints on the number and shape of flight feathers. Proc Natl Acad Sci U S A 2024; 121:e2306639121. [PMID: 38346196 PMCID: PMC10895369 DOI: 10.1073/pnas.2306639121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 12/30/2023] [Indexed: 02/15/2024] Open
Abstract
As a fundamental ecological aspect of most organisms, locomotor function significantly constrains morphology. At the same time, the evolution of novel locomotor abilities has produced dramatic morphological transformations, initiating some of the most significant diversifications in life history. Despite significant new fossil evidence, it remains unclear whether volant locomotion had a single or multiple origins in pennaraptoran dinosaurs and the volant abilities of individual taxa are controversial. The evolution of powered flight in modern birds involved exaptation of feathered surfaces extending off the limbs and tail yet most studies concerning flight potential in pennaraptorans do not account for the structure and morphology of the wing feathers themselves. Analysis of the number and shape of remex and rectrix feathers across a large dataset of extant birds indicates that the number of remiges and rectrices and the degree of primary vane asymmetry strongly correlate with locomotor ability revealing important functional constraints. Among these traits, phenotypic flexibility varies reflected by the different rates at which morphological changes evolve, such that some traits reflect the ancestral condition, whereas others reflect current locomotor function. While Mesozoic birds and Microraptor have remex morphologies consistent with extant volant birds, that of anchiornithines deviate significantly providing strong evidence this clade was not volant. The results of these analyses support a single origin of dinosaurian flight and indicate the early stages of feathered wing evolution are not sampled by the currently available fossil record.
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Affiliation(s)
- Yosef Kiat
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL60605
| | - Jingmai K. O’Connor
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL60605
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4
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Chuang T, Cheng JW, Chuong CM, Juan WT. Autofluorescence microscopy as a non-invasive probe to characterize the complex mechanical properties of keratin-based integumentary organs: A feather paradigm. CHINESE JOURNAL OF PHYSICS 2023; 86:561-571. [PMID: 38370512 PMCID: PMC10868595 DOI: 10.1016/j.cjph.2023.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Integumentary organs exhibit diverse morphologies and functions. The complex mechanical property of the architecture is mainly contributed by the ingenious multiscale assembly of keratins. A cross-scale characterization on keratin integration in an integument system will help us understand the principles on how keratin-based bio-architecture are built and function in nature. In this study, we used feather as a model integument organ. We develop autofluorescence (AF) microscopy to study the characteristics of its keratin assemblies over a wide range of length scales. The AF intensity of each feather component, following the hierarchy from the rachis to barb to barbule, decreased with the physical dimension. By combining the analysis of AF signal and tensile testing, we can probe regional material density and the associated mechanical strength in a composite feather. We further demonstrated that the AF micro-images could resolve subtle variations in the defective keratin assembly in feathers from frizzled chicken variants with a mutation in α-keratin 75. The distinction between AF patterns and the morphological features of feather components across different length scales indicated a synergetic interplay between material integration and complex morphogenesis during feather development. The work shows AF microscopy can serve as an easy and non-invasive approach to study multiscale keratin organizations and the associated bio-mechanical properties in diverse integumentary organs. This approach will facilitate our learning of many bio-inspired designs in diverse animal integumentary organs/appendages.
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Affiliation(s)
- T.C. Chuang
- Integrative Stem Cell Center, China Medical University Hospital, Taichung 40447, Taiwan
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung 40402, Taiwan
| | - Jiun-Wei Cheng
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung 40402, Taiwan
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA
| | - Wen-Tau Juan
- Integrative Stem Cell Center, China Medical University Hospital, Taichung 40447, Taiwan
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung 40402, Taiwan
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5
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Li WH, Chuong CM, Chen CK, Wu P, Jiang TX, Harn HIC, Liu TY, Yu Z, Lu J, Chang YM, Yue Z, Lin J, Vu TD, Huang TY, Ng CS. Transition from natal downs to juvenile feathers: conserved regulatory switches in Neoaves. RESEARCH SQUARE 2023:rs.3.rs-3382427. [PMID: 37886492 PMCID: PMC10602114 DOI: 10.21203/rs.3.rs-3382427/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The transition from natal downs for heat conservation to juvenile feathers for simple flight is a remarkable environmental adaptation process in avian evolution. However, the underlying epigenetic mechanism for this primary feather transition is mostly unknown. Here we conducted time-ordered gene co-expression network construction, epigenetic analysis, and functional perturbations in developing feather follicles to elucidate four downy-juvenile feather transition events. We discovered that LEF1 works as a key hub of Wnt signaling to build rachis and converts radial downy to bilateral symmetry. Extracellular matrix reorganization leads to peripheral pulp formation, which mediates epithelial -mesenchymal interactions for branching morphogenesis. ACTA2 compartments dermal papilla stem cells for feather cycling. Novel usage of scale keratins strengthens feather sheath with SOX14 as the epigenetic regulator. We found this primary feather transition largely conserved in chicken (precocious) and zebra finch (altricial) and discussed the possibility that this evolutionary adaptation process started in feathered dinosaurs.
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Affiliation(s)
| | | | | | - Ping Wu
- University of Southern California
| | | | - Hans I-Chen Harn
- Department of Pathology, Keck School of Medicine, University of Southern California
| | - Tzu-Yu Liu
- Department of Pathology, Keck School of Medicine, University of Southern California
| | - Zhou Yu
- Department of Pathology, Keck School of Medicine, University of Southern California
| | - Jiayi Lu
- Department of Pathology, Keck School of Medicine, University of Southern California
| | | | | | | | - Trieu-Duc Vu
- Foundation for Advancement of International Science
| | - Tao-Yu Huang
- Biodiversity Research Center, Academia Sinica, Taipei
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6
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Zheng X, Zhang Y, Zhang Y, Chen J, Nie R, Li J, Zhang H, Wu C. HOXB8 overexpression induces morphological changes in chicken mandibular skin: an RNA-seq analysis. Poult Sci 2023; 102:102971. [PMID: 37562126 PMCID: PMC10432836 DOI: 10.1016/j.psj.2023.102971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 07/19/2023] [Accepted: 07/23/2023] [Indexed: 08/12/2023] Open
Abstract
The Huiyang beard chicken is a well-known Chinese local breed known for its elongated feathers gathered from both sides of the face (muffs) and below the beak (beard), as well as short wattles (SW). The muff and beard (Mb) mutation is caused by ectopic upregulation of the homeobox B8 (HOXB8) gene in the mandibular skin; and the chi-square test showed a significant correlation between SW and Mb genotypes. However, the underlying molecular mechanisms that regulate Mb and SW variations remain unclear. In this study, we investigated the transcriptomes of the mandibular skin and wattles of chickens with and without the Mb genotype to elucidate the molecular basis of these traits. Our results show that HOXB8 is expressed at significantly higher levels in both the mandibular skin and wattles of Mb chickens than in those of wild-type chickens, indicating that HOXB8 regulates both the Mb and SW phenotypes. Key genes for keratin synthesis were highly expressed in the mandibular skin of Mb chickens, suggesting that HOXB8 may play a role in feather development. In wattles, changes in the expression of extracellular matrix synthesis genes may contribute to SW traits. DNA-binding motif analyses revealed that differentially expressed genes were likely to be directly regulated by HOXB8 binding, indicating that HOXB8 may directly or indirectly regulate feather follicle development and wattle growth. Our study identified both known and novel targets, including several genes not previously implicated in feather development and mesenchymal formation. These findings provide insights into the molecular mechanisms of skin appendage variation in birds and offer potential applications in breeding poultry breeds with unique phenotypes.
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Affiliation(s)
- Xiaotong Zheng
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, Jiangsu Province, China
| | - Ying Zhang
- China Agricultural Museum, Beijing 100026, China
| | - Yawen Zhang
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jianfei Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, Jiangsu Province, China
| | - Ruixue Nie
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Junying Li
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hao Zhang
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Changxin Wu
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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7
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Alonso-Alvarez C, Andrade P, Cantarero A, Morales J, Carneiro M. Relocation to avoid costs: A hypothesis on red carotenoid-based signals based on recent CYP2J19 gene expression data. Bioessays 2022; 44:e2200037. [PMID: 36209392 DOI: 10.1002/bies.202200037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/25/2022] [Accepted: 09/22/2022] [Indexed: 11/11/2022]
Abstract
In many vertebrates, the enzymatic oxidation of dietary yellow carotenoids generates red keto-carotenoids giving color to ornaments. The oxidase CYP2J19 is here a key effector. Its purported intracellular location suggests a shared biochemical pathway between trait expression and cell functioning. This might guarantee the reliability of red colorations as individual quality signals independent of production costs. We hypothesize that the ornament type (feathers vs. bare parts) and production costs (probably CYP2J19 activity compromising vital functions) could have promoted tissue-specific gene relocation. We review current avian tissue-specific CYP2J19 expression data. Among the ten red-billed species showing CYP2J19 bill expression, only one showed strong hepatic expression. Moreover, a phylogenetically-controlled analysis of 25 red-colored species shows that those producing red bare parts are less likely to have strong hepatic CYP2J19 expression than species with only red plumages. Thus, both production costs and shared pathways might have contributed to the evolution of red signals.
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Affiliation(s)
- Carlos Alonso-Alvarez
- Department of Evolutionary Ecology, National Museum of Natural Sciences - CSIC. C/ José Gutiérrez Abascal 2, Madrid, Spain
| | - Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Alejandro Cantarero
- Department of Evolutionary Ecology, National Museum of Natural Sciences - CSIC. C/ José Gutiérrez Abascal 2, Madrid, Spain.,Department of Physiology, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - Judith Morales
- Department of Evolutionary Ecology, National Museum of Natural Sciences - CSIC. C/ José Gutiérrez Abascal 2, Madrid, Spain
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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8
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Lin GW, Liang YC, Wu P, Chen CK, Lai YC, Jiang TX, Haung YH, Chuong CM. Regional specific differentiation of integumentary organs: SATB2 is involved in α- and β-keratin gene cluster switching in the chicken. Dev Dyn 2022; 251:1490-1508. [PMID: 34240503 PMCID: PMC8742846 DOI: 10.1002/dvdy.396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Animals develop skin regional specificities to best adapt to their environments. Birds are excellent models in which to study the epigenetic mechanisms that facilitate these adaptions. Patients suffering from SATB2 mutations exhibit multiple defects including ectodermal dysplasia-like changes. The preferential expression of SATB2, a chromatin regulator, in feather-forming compared to scale-forming regions, suggests it functions in regional specification of chicken skin appendages by acting on either differentiation or morphogenesis. RESULTS Retrovirus mediated SATB2 misexpression in developing feathers, beaks, and claws causes epidermal differentiation abnormalities (e.g. knobs, plaques) with few organ morphology alterations. Chicken β-keratins are encoded in 5 sub-clusters (Claw, Feather, Feather-like, Scale, and Keratinocyte) on Chromosome 25 and a large Feather keratin cluster on Chromosome 27. Type I and II α-keratin clusters are located on Chromosomes 27 and 33, respectively. Transcriptome analyses showed these keratins (1) are often tuned up or down collectively as a sub-cluster, and (2) these changes occur in a temporo-spatial specific manner. CONCLUSIONS These results suggest an organizing role of SATB2 in cluster-level gene co-regulation during skin regional specification.
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Affiliation(s)
- Gee-Way Lin
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
| | - Ya-Chen Liang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Integrative Stem Cell Center, China Medical University and Hospital, China Medical University, Taichung 40447, Taiwan
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Chih-Kuan Chen
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- The IEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402204, Taiwan
| | - Yung-Chih Lai
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Integrative Stem Cell Center, China Medical University and Hospital, China Medical University, Taichung 40447, Taiwan
- Institute of New Drug Development, China Medical University, Taichung 40402, Taiwan
| | - Ting-Xin Jiang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yen-Hua Haung
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan
- TMU Research Center of Cell Therapy and Regeneration Medicine, Taipei Medical University, Taipei, 11031, Taiwan
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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9
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Niiyama S, Ishimatsu-Tsuji Y, Kishimoto J. Niche formed by bone morphogenetic protein antagonists gremlin 1 and gremlin 2 in human hair follicles. Health Sci Rep 2022; 5:e486. [PMID: 35036581 PMCID: PMC8753488 DOI: 10.1002/hsr2.486] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/18/2021] [Accepted: 10/07/2021] [Indexed: 01/01/2023] Open
Affiliation(s)
- Shiro Niiyama
- Department of Dermatology Toho University Ohashi Medical Center Tokyo Japan
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10
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Wu P, Jiang TX, Lei M, Chen CK, Hsieh Li SM, Widelitz RB, Chuong CM. Cyclic growth of dermal papilla and regeneration of follicular mesenchymal components during feather cycling. Development 2021; 148:dev198671. [PMID: 34344024 PMCID: PMC10656464 DOI: 10.1242/dev.198671] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 07/08/2021] [Indexed: 01/23/2023]
Abstract
How dermis maintains tissue homeostasis in cyclic growth and wounding is a fundamental unsolved question. Here, we study how dermal components of feather follicles undergo physiological (molting) and plucking injury-induced regeneration in chickens. Proliferation analyses reveal quiescent, transient-amplifying (TA) and long-term label-retaining dermal cell (LRDC) states. During the growth phase, LRDCs are activated to make new dermal components with distinct cellular flows. Dermal TA cells, enriched in the proximal follicle, generate both peripheral pulp, which extends distally to expand the epithelial-mesenchymal interactive interface for barb patterning, and central pulp, which provides nutrition. Entering the resting phase, LRDCs, accompanying collar bulge epidermal label-retaining cells, descend to the apical dermal papilla. In the next cycle, these apical dermal papilla LRDCs are re-activated to become new pulp progenitor TA cells. In the growth phase, lower dermal sheath can generate dermal papilla and pulp. Transcriptome analyses identify marker genes and highlight molecular signaling associated with dermal specification. We compare the cyclic topological changes with those of the hair follicle, a convergently evolved follicle configuration. This work presents a model for analyzing homeostasis and tissue remodeling of mesenchymal progenitors.
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Affiliation(s)
- Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ting-Xin Jiang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Mingxing Lei
- 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
- Integrative Stem Cell Center, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
| | - Chih-Kuan Chen
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- The IEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
| | - Shu-Man Hsieh Li
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
- Department of Biochemistry, National Defense Medical Center, Taipei 114, Taiwan
| | - Randall B. Widelitz
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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11
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Chen CK, Juan WT, Liang YC, Wu P, Chuong CM. Making region-specific integumentary organs in birds: evolution and modifications. Curr Opin Genet Dev 2021; 69:103-111. [PMID: 33780743 DOI: 10.1016/j.gde.2021.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/20/2021] [Accepted: 02/24/2021] [Indexed: 11/16/2022]
Abstract
Birds are the most diversified terrestrial vertebrates due to highly diverse integumentary organs that enable robust adaptability to various eco-spaces. Here we show that this complexity is built upon multi-level regional specifications. Across-the-body (macro-) specification includes the evolution of beaks and feathers as new integumentary organs that are formed with regional specificity. Within-an-organ (micro-) specification involves further modifications of organ shapes. We review recent progress in elucidating the molecular mechanisms underlying feather diversification as an example. (1) β-Keratin gene clusters are regulated by typical enhancers or high order chromatin looping to achieve macro- and micro-level regional specification, respectively. (2) Multi-level symmetry-breaking of feather branches confers new functional forms. (3) Complex color patterns are produced by combinations of macro-patterning and micro-patterning processes. The integration of these findings provides new insights toward the principle of making a robustly adaptive bio-interface.
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Affiliation(s)
- Chih-Kuan Chen
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; The IEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
| | - Wen-Tau Juan
- Integrative Stem Cell Center, China Medical University Hospital, Taichung 40447, Taiwan
| | - Ya-Chen Liang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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12
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Kim D, Garza LA. Hypothesis: Wound-induced TLR3 activation stimulates endogenous retinoic acid synthesis and signalling during regeneration. Exp Dermatol 2020; 28:450-452. [PMID: 30927295 DOI: 10.1111/exd.13931] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 03/13/2019] [Indexed: 12/20/2022]
Abstract
Although the mechanism is unclear, it has been shown that genetically normal adult mice with a large wound form de novo morphogenesis of hair follicles in wound-induced hair neogenesis (WIHN)(1). We focused on how tissues recognize damage signals and identified that double-stranded RNA (dsRNA)-mediated toll-like receptor 3 (TLR3) activation stimulates WIHN. Here, we propose a hypothesis that TLR3 stimulates retinoic acid synthesis and signalling to allow for regeneration, suggesting that common clinical methods of facial rejuvenation in human subjects through damage (such as lasers or dermabrasion), and the use of topical retinoids reflect the same biologic pathway.
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Affiliation(s)
- Dongwon Kim
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Luis A Garza
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland
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13
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Zheng X, Zhang B, Zhang Y, Zhong H, Nie R, Li J, Zhang H, Wu C. Transcriptome analysis of feather follicles reveals candidate genes and pathways associated with pheomelanin pigmentation in chickens. Sci Rep 2020; 10:12088. [PMID: 32694523 PMCID: PMC7374586 DOI: 10.1038/s41598-020-68931-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 07/03/2020] [Indexed: 11/20/2022] Open
Abstract
Yellow plumage is common in chickens, especially in breeds such as the Huiyang Bearded chicken, which is indigenous to China. We evaluated plumage colour distribution in F1, F2, and F3 populations of an Huiyang Bearded chicken × White Leghorn chicken cross, the heredity of the yellow plumage trait was distinguished from that of the gold plumage and other known plumage colours. Microscopic analysis of the feather follicles indicated that pheomelanin particles were formed in yellow but not in white feathers. To screen genes related to formation of the pheomelanin particles, we generated transcriptome data from yellow and white feather follicles from 7- and 11-week-old F3 chickens using RNA-seq. We identified 27 differentially expressed genes (DEGs) when comparing the yellow and white feather follicles. These DEGs were enriched in the Gene Ontology classes ‘melanosome’ and ‘melanosome organization’ related to the pigmentation process. Down-regulation of TYRP1, DCT, PMEL, MLANA, and HPGDS, verified using quantitative reverse transcription PCR, may lead to reduced eumelanin and increased pheomelanin synthesis in yellow plumage. Owing to the presence of the Dominant white locus, both white and yellow plumage lack eumelanin, and white feathers showed no pigments. Our results provide an understanding of yellow plumage formation in chickens.
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Affiliation(s)
- Xiaotong Zheng
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yawen Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Haian Zhong
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ruixue Nie
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Changxin Wu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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14
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Sun L, Zhou T, Wan QH, Fang SG. Transcriptome Comparison Reveals Key Components of Nuptial Plumage Coloration in Crested Ibis. Biomolecules 2020; 10:E905. [PMID: 32549189 PMCID: PMC7356354 DOI: 10.3390/biom10060905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/02/2020] [Accepted: 06/13/2020] [Indexed: 11/16/2022] Open
Abstract
Nuptial plumage coloration is critical in the mating choice of the crested ibis. This species has a characteristic nuptial plumage that develops from the application of a black sticky substance, secreted by a patch of skin in the throat and neck region. We aimed to identify the genes regulating its coloring, by comparing skin transcriptomes between ibises during the breeding and nonbreeding seasons. In breeding season skins, key eumelanin synthesis genes, TYR, DCT, and TYRP1 were upregulated. Tyrosine metabolism, which is closely related to melanin synthesis, was also upregulated, as were transporter proteins belonging to multiple SLC families, which might act during melanosome transportation to keratinocytes. These results indicate that eumelanin is likely an important component of the black substance. In addition, we observed upregulation in lipid metabolism in breeding season skins. We suggest that the lipids contribute to an oil base, which imbues the black substance with water insolubility and enhances its adhesion to feather surfaces. In nonbreeding season skins, we observed upregulation in cell adhesion molecules, which play critical roles in cell interactions. A number of molecules involved in innervation and angiogenesis were upregulated, indicating an ongoing expansion of nerves and blood vessels in sampled skins. Feather β keratin, a basic component of avian feather filament, was also upregulated. These results are consistent with feather regeneration in the black skin of nonbreeding season ibises. Our results provide the first molecular evidence indicating that eumelanin is the key component of ibis coloration.
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Affiliation(s)
| | | | | | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (L.S.); (T.Z.); (Q.-H.W.)
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15
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The Making of a Flight Feather: Bio-architectural Principles and Adaptation. Cell 2020; 179:1409-1423.e17. [PMID: 31778655 DOI: 10.1016/j.cell.2019.11.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 08/09/2019] [Accepted: 11/01/2019] [Indexed: 01/14/2023]
Abstract
The evolution of flight in feathered dinosaurs and early birds over millions of years required flight feathers whose architecture features hierarchical branches. While barb-based feather forms were investigated, feather shafts and vanes are understudied. Here, we take a multi-disciplinary approach to study their molecular control and bio-architectural organizations. In rachidial ridges, epidermal progenitors generate cortex and medullary keratinocytes, guided by Bmp and transforming growth factor β (TGF-β) signaling that convert rachides into adaptable bilayer composite beams. In barb ridges, epidermal progenitors generate cylindrical, plate-, or hooklet-shaped barbule cells that form fluffy branches or pennaceous vanes, mediated by asymmetric cell junction and keratin expression. Transcriptome analyses and functional studies show anterior-posterior Wnt2b signaling within the dermal papilla controls barbule cell fates with spatiotemporal collinearity. Quantitative bio-physical analyses of feathers from birds with different flight characteristics and feathers in Burmese amber reveal how multi-dimensional functionality can be achieved and may inspire future composite material designs. VIDEO ABSTRACT.
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16
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The Wnt/β-catenin signaling pathway is involved in regulating feather growth of embryonic chicks. Poult Sci 2020; 99:2315-2323. [PMID: 32359566 PMCID: PMC7597444 DOI: 10.1016/j.psj.2020.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/06/2019] [Accepted: 01/20/2020] [Indexed: 02/07/2023] Open
Abstract
Avian feathers have robust growth and regeneration capability and serve as a useful model for decoding hair morphogenesis and other developmental studies. However, the molecular signaling involved in regulating the development of feather follicles is unclear. The purpose of this study was to investigate the role of the Wnt/β-catenin pathway in regulating feather morphogenesis in embryonic chicks through in ovo injection of different doses of Dickkopf-1 (DKK1, a specific inhibitor of the target of the Wnt/β-catenin pathway). A total of 120 fertilized embryo eggs were randomly divided into 4 treatments, including a noninjection group (control group) and groups injected with 100 μL of phosphate-buffered saline (PBS)/egg (PBS control group), 100 μL of PBS/egg containing 600-ng DKK1/egg (600-ng DKK1 group), and 100-μL PBS/egg containing 1,200-ng DKK1/egg (1,200-ng DKK1 group). Feathers and skin tissues were sampled on embryonic (E) day 15 and the day of hatching to examine the feather mass, diameter and density of feather follicles, and the protein expression of the Wnt/β-catenin pathway. The results showed that, compared with CON and PBS treatment, the injection of DKK1 into the yolk sac of chick embryos had no significant effect on the hatching rate and embryo weight (P > 0.05), while it significantly decreased the relative mass of feathers in the whole body (P < 0.05). The high dose of DKK1 (1,200-ng DKK1/egg) decreased the relative mass of feathers on the back, chest, belly, neck, wings, head, and legs, which was more obvious than that in the 600-ng DKK1 group, which presented a dose-dependent effect. In addition, DKK1 injection significantly downregulated the protein expression levels of β-catenin, transcription factor 4, Cyclin D1, and c-Myc (P < 0.05). The immunofluorescence result of β-catenin was consistent with the Western blotting assay results. Altogether, these observations suggested that the Wnt/β-catenin signaling pathway is involved in regulating feather follicle development and feather growth during the embryonic development of chicks.
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17
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Eliason CM, Clarke JA. Cassowary gloss and a novel form of structural color in birds. SCIENCE ADVANCES 2020; 6:eaba0187. [PMID: 32426504 PMCID: PMC7220335 DOI: 10.1126/sciadv.aba0187] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/13/2020] [Indexed: 06/11/2023]
Abstract
One of the two lineages of extant birds resulting from its deepest split, Palaeognathae, has been reported not to exhibit structural coloration in feathers, affecting inferences of ancestral coloration mechanisms in extant birds. Structural coloration in facial skin and eggshells has been shown in this lineage, but has not been reported in feathers. We present the first evidence for two distinct mechanisms of structural color in palaeognath feathers. One extinct volant clade, Lithornithidae, shows evidence of elongate melanin-containing organelles uniquely associated with glossy/iridescent color, a structural color mechanism found in fossil outgroups and neognath birds. We also demonstrate a structural basis for the exceptional gloss in extant cassowary feathers. We propose gloss as an intermediate phenotype between matte and iridescent plumage, conferred by a thick and smooth feather rachis. Rachis-based structural color has not been previously investigated. The new data illuminate the relationships between avian melanin-based coloration and feather structure.
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Affiliation(s)
- Chad M. Eliason
- Grainger Bioinformatics Center, Field Museum of Natural History, Chicago, IL, USA
- Jackson School of Geosciences and Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Julia A. Clarke
- Jackson School of Geosciences and Integrative Biology, University of Texas at Austin, Austin, TX, USA
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18
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Chen MJ, Xie WY, Jiang SG, Wang XQ, Yan HC, Gao CQ. Molecular Signaling and Nutritional Regulation in the Context of Poultry Feather Growth and Regeneration. Front Physiol 2020; 10:1609. [PMID: 32038289 PMCID: PMC6985464 DOI: 10.3389/fphys.2019.01609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 12/23/2019] [Indexed: 12/03/2022] Open
Abstract
The normal growth and regeneration of feathers is important for improving the welfare and economic value of poultry. Feather follicle stem cells are the basis for driving feather development and are regulated by various molecular signaling pathways in the feather follicle microenvironment. To date, the roles of the Wnt, Bone Morphogenetic Protein (BMP), Notch, and Sonic Hedgehog (SHH) signaling pathways in the regulation of feather growth and regeneration are among the best understood. While these pathways regulate feather morphogenesis in different stages, their dysregulation results in a low feather growth rate, poor quality of plumage, and depilation. Additionally, exogenous nutrient intervention can affect the feather follicle cycle, promote the formation of the feather shaft and feather branches, preventing plumage abnormalities. This review focuses on our understanding of the signaling pathways involved in the transcriptional control of feather morphogenesis and explores the impact of nutritional factors on feather growth and regeneration in poultry. This work may help to develop novel mechanisms by which follicle stem cells can be manipulated to produce superior plumage that enhances poultry carcass quality.
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Affiliation(s)
- Meng-Jie Chen
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Wen-Yan Xie
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Shi-Guang Jiang
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiu-Qi Wang
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Hui-Chao Yan
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Chun-Qi Gao
- College of Animal Science, South China Agricultural University/Guangdong Provincial Key Laboratory of Animal Nutrition Control/Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
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19
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Wang X, Li D, Song S, Zhang Y, Li Y, Wang X, Liu D, Zhang C, Cao Y, Fu Y, Han R, Li W, Liu X, Sun G, Li G, Tian Y, Li Z, Kang X. Combined transcriptomics and proteomics forecast analysis for potential genes regulating the Columbian plumage color in chickens. PLoS One 2019; 14:e0210850. [PMID: 31693656 PMCID: PMC6834273 DOI: 10.1371/journal.pone.0210850] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 10/18/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Coloration is one of the most recognizable characteristics in chickens, and clarifying the coloration mechanisms will help us understand feather color formation. "Yufen I" is a commercial egg-laying chicken breed in China that was developed by a three-line cross using lines H, N and D. Columbian plumage is a typical feather character of the "Yufen I" H line. To elucidate the molecular mechanism underlying the pigmentation of Columbian plumage, this study utilizes high-throughput sequencing technology to compare the transcriptome and proteome differences in the follicular tissue of different feathers, including the dorsal neck with black and white striped feather follicles (Group A) and the ventral neck with white feather follicles (Group B) in the "Yufen I" H line. RESULTS In this study, we identified a total of 21,306 genes and 5,203 proteins in chicken feather follicles. Among these, 209 genes and 382 proteins were differentially expressed in two locations, Group A and Group B, respectively. A total of 8 differentially expressed genes (DEGs) and 9 differentially expressed proteins (DEPs) were found to be involved in the melanogenesis pathway. Additionally, a specifically expressed MED23 gene and a differentially expressed GNAQ protein were involved in melanin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis mapped 190 DEGs and 322 DEPs to 175 and 242 pathways, respectively, and there were 166 pathways correlated with both DEGs and DEPs. 49 DEPs/DEGs overlapped and were enriched for 12 pathways. Transcriptomic and proteomic analyses revealed that the following pathways were activated: melanogenesis, cardiomyocyte adrenergic, calcium and cGMP-PKG. The expression of DEGs was validated by real-time quantitative polymerase chain reaction (qRT-PCR) that produced results similar to those from RNA-seq. In addition, we found that the expression of the MED23, FZD10, WNT7B and WNT11 genes peaked at approximately 8 weeks in the "Yufen I" H line, which is consistent with the molting cycle. As both groups showed significant differences in terms of the expression of the studied genes, this work opens up avenues for research in the future to assess their exact function in determining plumage color. CONCLUSION Common DEGs and DEPs were enriched in the melanogenesis pathway. MED23 and GNAQ were also reported to play a crucial role in melanin synthesis. In addition, this study is the first to reveal gene and protein variations in in the "Yufen I" H line during Columbian feather color development and to discover principal genes and proteins that will aid in functional genomics studies in the future. The results of the present study provide a significant conceptual basis for the future breeding schemes with the "Yufen I" H line and provide a basis for research on the mechanisms of feather pigmentation.
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Affiliation(s)
- Xinlei Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
| | - Donghua Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Sufang Song
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
| | - Yanhua Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yuanfang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiangnan Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Danli Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Chenxi Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yanfang Cao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yawei Fu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Wenting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiaojun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
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20
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Feather Evolution from Precocial to Altricial Birds. Zool Stud 2019; 58:e24. [PMID: 31966325 DOI: 10.6620/zs.2019.58-24] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/16/2019] [Indexed: 12/28/2022]
Abstract
Birds are the most abundant terrestrial vertebrates and their diversity is greatly shaped by the feathers. How avian evolution is linked to feather evolution has long been a fascinating question. Numerous excellent studies have shed light on this complex relationship by investigating feather diversity and its underlying molecular mechanisms. However, most have focused on adult domestic birds, and the contribution of feather diversity to environmental adaptation has not been well-studied. In this review, we described bird diversity using the traditional concept of the altricial-precocial spectrum in bird hatchlings. We combined the spectrum with a recently published avian phylogeny to profile the spectrum evolution. We then focused on the discrete diagnostic character of the spectrum, the natal down, and propose a hypothesis for the precocial-to-altricial evolution. For the underlying molecular mechanisms in feather diversity and bird evolution, we reviewed the literature and constructed the known mechanisms for feather tract definition and natal down development. Finally, we suggested some future directions for research on altricial-precocial divergence, which may expand our understanding of the relationship between natal down diversity and bird evolution.
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21
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Qiu Y, Chen W, Nie Q. STOCHASTIC DYNAMICS OF CELL LINEAGE IN TISSUE HOMEOSTASIS. DISCRETE AND CONTINUOUS DYNAMICAL SYSTEMS-SERIES B 2019; 24:3971-3994. [PMID: 32269502 PMCID: PMC7141575 DOI: 10.3934/dcdsb.2018339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
During epithelium tissue maintenance, lineages of cells differentiate and proliferate in a coordinated way to provide the desirable size and spatial organization of different types of cells. While mathematical models through deterministic description have been used to dissect role of feedback regulations on tissue layer size and stratification, how the stochastic effects influence tissue maintenance remains largely unknown. Here we present a stochastic continuum model for cell lineages to investigate how both layer thickness and layer stratification are affected by noise. We find that the cell-intrinsic noise often causes reduction and oscillation of layer size whereas the cell-extrinsic noise increases the thickness, and sometimes, leads to uncontrollable growth of the tissue layer. The layer stratification usually deteriorates as the noise level increases in the cell lineage systems. Interestingly, the morphogen noise, which mixes both cell-intrinsic noise and cell-extrinsic noise, can lead to larger size of layer with little impact on the layer stratification. By investigating different combinations of the three types of noise, we find the layer thickness variability is reduced when cell-extrinsic noise level is high or morphogen noise level is low. Interestingly, there exists a tradeoff between low thickness variability and strong layer stratification due to competition among the three types of noise, suggesting robust layer homeostasis requires balanced levels of different types of noise in the cell lineage systems.
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Affiliation(s)
- Yuchi Qiu
- Department of Mathematics, University of California, Irvine Irvine, CA 92697, USA
| | - Weitao Chen
- Department of Mathematics, University of California, Riverside Riverside, CA 92507, USA
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22
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Wu P, Yan J, Lai YC, Ng CS, Li A, Jiang X, Elsey RM, Widelitz R, Bajpai R, Li WH, Chuong CM. Multiple Regulatory Modules Are Required for Scale-to-Feather Conversion. Mol Biol Evol 2019; 35:417-430. [PMID: 29177513 DOI: 10.1093/molbev/msx295] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The origin of feathers is an important question in Evo-Devo studies, with the eventual evolution of vaned feathers which are aerodynamic, allowing feathered dinosaurs and early birds to fly and venture into new ecological niches. Studying how feathers and scales are developmentally specified provides insight into how a new organ may evolve. We identified feather-associated genes using genomic analyses. The candidate genes were tested by expressing them in chicken and alligator scale forming regions. Ectopic expression of these genes induced intermediate morphotypes between scales and feathers which revealed several major morphogenetic events along this path: Localized growth zone formation, follicle invagination, epithelial branching, feather keratin differentiation, and dermal papilla formation. In addition to molecules known to induce feathers on scales (retinoic acid, β-catenin), we identified novel scale-feather converters (Sox2, Zic1, Grem1, Spry2, Sox18) which induce one or more regulatory modules guiding these morphogenetic events. Some morphotypes resemble filamentous appendages found in feathered dinosaur fossils, whereas others exhibit characteristics of modern avian feathers. We propose these morpho-regulatory modules were used to diversify archosaur scales and to initiate feather evolution. The regulatory combination and hierarchical integration may have led to the formation of extant feather forms. Our study highlights the importance of integrating discoveries between developmental biology and paleontology.
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Affiliation(s)
- Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jie Yan
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yung-Chih Lai
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA.,Integrative Stem Cell Center, China Medical University Hospital, China Medical University, Taichung, Taiwan.,Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Chen Siang Ng
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Ang Li
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Xueyuan Jiang
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Ruth M Elsey
- Louisiana Department of Wildlife and Fisheries, Rockefeller Wildlife Refuge, Grand Chenier, LA
| | - Randall Widelitz
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Ruchi Bajpai
- Center for Craniofacial Molecular Biology and Department of Biochemistry, University of Southern California, Los Angeles, CA
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA.,Integrative Stem Cell Center, China Medical University Hospital, China Medical University, Taichung, Taiwan.,Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan.,International Laboratory for Wound Repair and Regenerative Research, Graduated Institute of Clinical Medicine, National Cheng Kung University, Tainan, Taiwan.,Integrative and Evolutionary Galliformes Genomics Research Center (iEGG), National Chung-Hsing University, Taichung, Taiwan
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23
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Widelitz RB, Lin GW, Lai YC, Mayer JA, Tang PC, Cheng HC, Jiang TX, Chen CF, Chuong CM. Morpho-regulation in diverse chicken feather formation: Integrating branching modules and sex hormone-dependent morpho-regulatory modules. Dev Growth Differ 2018; 61:124-138. [PMID: 30569461 DOI: 10.1111/dgd.12584] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022]
Abstract
Many animals can change the size, shape, texture and color of their regenerated coats in response to different ages, sexes, or seasonal environmental changes. Here, we propose that the feather core branching morphogenesis module can be regulated by sex hormones or other environmental factors to change feather forms, textures or colors, thus generating a large spectrum of complexity for adaptation. We use sexual dimorphisms of the chicken to explore the role of hormones. A long-standing question is whether the sex-dependent feather morphologies are autonomously controlled by the male or female cell types, or extrinsically controlled and reversible. We have recently identified core feather branching molecular modules which control the anterior-posterior (bone morphogenetic orotein [BMP], Wnt gradient), medio-lateral (Retinoic signaling, Gremlin), and proximo-distal (Sprouty, BMP) patterning of feathers. We hypothesize that morpho-regulation, through quantitative modulation of existing parameters, can act on core branching modules to topologically tune the dimension of each parameter during morphogenesis and regeneration. Here, we explore the involvement of hormones in generating sexual dimorphisms using exogenously delivered hormones. Our strategy is to mimic male androgen levels by applying exogenous dihydrotestosterone and aromatase inhibitors to adult females and to mimic female estradiol levels by injecting exogenous estradiol to adult males. We also examine differentially expressed genes in the feathers of wildtype male and female chickens to identify potential downstream modifiers of feather morphogenesis. The data show male and female feather morphology and their color patterns can be modified extrinsically through molting and resetting the stem cell niche during regeneration.
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Affiliation(s)
- Randall B Widelitz
- Department of Pathology, University of Southern California, Los Angeles, California
| | - Gee-Way Lin
- Department of Pathology, University of Southern California, Los Angeles, California.,Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yung-Chih Lai
- Department of Pathology, University of Southern California, Los Angeles, California.,Integrative Stem Cell Center, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Julie A Mayer
- Department of Pathology, University of Southern California, Los Angeles, California.,Biocept Inc., San Diego, California
| | - Pin-Chi Tang
- Department of Pathology, University of Southern California, Los Angeles, California.,Department of Animal Science, National Chung Hsing University, Taichung, Taiwan.,The IEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Hsu-Chen Cheng
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan.,The IEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Ting-Xin Jiang
- Department of Pathology, University of Southern California, Los Angeles, California
| | - Chih-Feng Chen
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan.,The IEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, California.,Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Integrative Stem Cell Center, China Medical University Hospital, China Medical University, Taichung, Taiwan.,The IEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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24
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Ng CS, Li WH. Genetic and Molecular Basis of Feather Diversity in Birds. Genome Biol Evol 2018; 10:2572-2586. [PMID: 30169786 PMCID: PMC6171735 DOI: 10.1093/gbe/evy180] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2018] [Indexed: 12/16/2022] Open
Abstract
Feather diversity is striking in many aspects. Although the development of feather has been studied for decades, genetic and genomic studies of feather diversity have begun only recently. Many questions remain to be answered by multidisciplinary approaches. In this review, we discuss three levels of feather diversity: Feather morphotypes, intraspecific variations, and interspecific variations. We summarize recent studies of feather evolution in terms of genetics, genomics, and developmental biology and provide perspectives for future research. Specifically, this review includes the following topics: 1) Diversity of feather morphotype; 2) feather diversity among different breeds of domesticated birds, including variations in pigmentation pattern, in feather length or regional identity, in feather orientation, in feather distribution, and in feather structure; and 3) diversity of feathers among avian species, including plumage color and morph differences between species and the regulatory differences in downy feather development between altricial and precocial birds. Finally, we discussed future research directions.
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Affiliation(s)
- Chen Siang Ng
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan.,The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Hsiung Li
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Department of Ecology and Evolution, University of Chicago
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25
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Transmission electron microscopic and immunohistochemical observations of resting follicles of feathers in chicken show massive cell degeneration. Anat Sci Int 2018; 93:548-558. [PMID: 29931653 DOI: 10.1007/s12565-018-0449-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 06/07/2018] [Indexed: 10/28/2022]
Abstract
The molting cycle of feathers includes an anagen (growth) stage, a likely catagen stage where the feather follicles degenerate, and a resting stage where fully grown feathers remain in their follicles and are functional before molting. However, the cytological changes involved in the resting and molting stages are poorly known, so the results of an ultrastructural analysis of these processes in adult chick feathers are presented here. The study showed that the dermal papilla shrinks, and numerous cells present increased heterochromatin and free collagen fibrils in the extracellular matrix. Degeneration of the germinal epithelium of the follicle-the papillary collar-occurs with an initial substantial contraction of cells followed by an increase in heterochromatin, vesicle and lipid accumulation, and membrane and organelle degeneration. Desmosomes are still present between degenerating epithelial cells, but ribosomes and tonofilaments disappear. This suggests that cell necrosis initially proceeds as a major contraction resembling apoptosis-a process termed necroptosis, which was previously also shown to occur during the formation of barbs and barbules in mature down and pennaceous feathers. This study suggests that, aside from apoptosis, the collar epithelium degenerates due to external factors, in particular the retraction of blood vessels supplying the dermal papilla. In contrast, revascularization of the dermal papilla triggers a new phase of feather growth (anagen).
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26
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Yang J, Qu Y, Huang Y, Lei F. Dynamic transcriptome profiling towards understanding the morphogenesis and development of diverse feather in domestic duck. BMC Genomics 2018; 19:391. [PMID: 29793441 PMCID: PMC5968480 DOI: 10.1186/s12864-018-4778-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 05/10/2018] [Indexed: 11/14/2022] Open
Abstract
Background Feathers with complex and fine structure are hallmark avian integument appendages, which have contributed significantly to the survival and breeding for birds. Here, we aimed to explore the differentiation, morphogenesis and development of diverse feathers in the domestic duck. Results Transcriptome profiles of skin owing feather follicle from two body parts at three physiological stages were constructed to understand the molecular network and excavate the candidate genes associated with the development of plumulaceous and flight feather structures. The venn analysis of differentially expressed genes (DEGs) between abdomen and wing skin tissues at three developmental stages showed that 38 genes owing identical differentially expression pattern. Together, our data suggest that feather morphological and structural diversity can be possibly related to the homeobox proteins. The key series-clusters, many candidate biological processes and genes were identified for the morphogenesis, growth and development of two feather types. Through comparing the results of developmental transcriptomes from plumulaceous and flight feather, we found that DEGs belonging to the family of WNT, FGF and BMP have certain differences; even the consistent DEGs of skin and feather follicle transcriptomes from abdomen and wing have the different expression patterns. Conclusions Overall, this study detected many functional genes and showed differences in the molecular mechanisms of diverse feather developments. The findings in WNT, FGF and BMP, which were consistent with biological experiments, showed more possible complex modulations. A correlative role of HOX genes was also suggested but future biological verification experiments are required. This work provided valuable information for subsequent research on the morphogenesis of feathers. Electronic supplementary material The online version of this article (10.1186/s12864-018-4778-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing Yang
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, the Chinese Academy of Sciences, Beijing, 100101, China.,School of Environmental Science and Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.,Co-Innovation Center for Qinba Regions' Sustainable Development, School of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Yanhua Qu
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuan Huang
- Co-Innovation Center for Qinba Regions' Sustainable Development, School of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China.
| | - Fumin Lei
- Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, the Chinese Academy of Sciences, Beijing, 100101, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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27
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Cheng D, Yan X, Qiu G, Zhang J, Wang H, Feng T, Tian Y, Xu H, Wang M, He W, Wu P, Widelitz RB, Chuong CM, Yue Z. Contraction of basal filopodia controls periodic feather branching via Notch and FGF signaling. Nat Commun 2018; 9:1345. [PMID: 29632339 PMCID: PMC5890251 DOI: 10.1038/s41467-018-03801-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/13/2018] [Indexed: 11/21/2022] Open
Abstract
Branching morphogenesis is a general mechanism that increases the surface area of an organ. In chicken feathers, the flat epithelial sheath at the base of the follicle is transformed into periodic branches. How exactly the keratinocytes are organized into this pattern remains unclear. Here we show that in the feather follicle, the pre-branch basal keratinocytes have extensive filopodia, which contract and smooth out after branching. Manipulating the filopodia via small GTPases RhoA/Cdc42 also regulates branch formation. These basal filopodia help interpret the proximal-distal FGF gradient in the follicle. Furthermore, the topological arrangement of cell adhesion via E-Cadherin re-distribution controls the branching process. Periodic activation of Notch signaling drives the differential cell adhesion and contraction of basal filopodia, which occurs only below an FGF signaling threshold. Our results suggest a coordinated adjustment of cell shape and adhesion orchestrates feather branching, which is regulated by Notch and FGF signaling. Keratinocytes are organised into a periodic pattern in feather branching, but how this is regulated is unclear. Here, the authors show that there is a coordinated change in cell shape and adherence, mediated by Notch, FGF signalling and Rho GTPases, which in turn regulates feather branching.
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Affiliation(s)
- Dongyang Cheng
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Xiaoli Yan
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Guofu Qiu
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Juan Zhang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Hanwei Wang
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Tingting Feng
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Yarong Tian
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Haiping Xu
- Department of Mathematics, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Meiqing Wang
- Department of Mathematics, Fuzhou University, Fuzhou, Fujian, 350116, China
| | - Wanzhong He
- National Institute of Biological Sciences (NIBS), Beijing, 102206, China
| | - Ping Wu
- Department of Pathology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Randall B Widelitz
- Department of Pathology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CA, 90033, USA
| | - Zhicao Yue
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, 350116, China.
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28
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Chokeshaiusaha K, Puthier D, Nguyen C, Sananmuang T. A demonstration of the H3 trimethylation ChIP-seq analysis of galline follicular mesenchymal cells and male germ cells. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 31:791-797. [PMID: 29381903 PMCID: PMC5933975 DOI: 10.5713/ajas.17.0744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/23/2017] [Accepted: 01/10/2018] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Trimethylation of histone 3 (H3) at 4th lysine N-termini (H3K4me3) in gene promoter region was the universal marker of active genes specific to cell lineage. On the contrary, coexistence of trimethylation at 27th lysine (H3K27me3) in the same loci-the bivalent H3K4m3/H3K27me3 was known to suspend the gene transcription in germ cells, and could also be inherited to the developed stem cell. In galline species, throughout example of H3K4m3 and H3K27me3 ChIP-seq analysis was still not provided. We therefore designed and demonstrated such procedures using ChIP-seq and mRNA-seq data of chicken follicular mesenchymal cells and male germ cells. METHODS Analytical workflow was designed and provided in this study. ChIP-seq and RNA-seq datasets of follicular mesenchymal cells and male germ cells were acquired and properly preprocessed. Peak calling by Model-based analysis of ChIP-seq 2 was performed to identify H3K4m3 or H3K27me3 enriched regions (Fold-change≥2, FDR≤0.01) in gene promoter regions. Integrative genomics viewer was utilized for cellular retinoic acid binding protein 1 (CRABP1), growth differentiation factor 10 (GDF10), and gremlin 1 (GREM1) gene explorations. RESULTS The acquired results indicated that follicular mesenchymal cells and germ cells shared several unique gene promoter regions enriched with H3K4me3 (5,704 peaks) and also unique regions of bivalent H3K4m3/H3K27me3 shared between all cell types and germ cells (1,909 peaks). Subsequent observation of follicular mesenchyme-specific genes-CRABP1, GDF10, and GREM1 correctly revealed vigorous transcriptions of these genes in follicular mesenchymal cells. As expected, bivalent H3K4m3/H3K27me3 pattern was manifested in gene promoter regions of germ cells, and thus suspended their transcriptions. CONCLUSION According the results, an example of chicken H3K4m3/H3K27me3 ChIP-seq data analysis was successfully demonstrated in this study. Hopefully, the provided methodology should hereby be useful for galline ChIP-seq data analysis in the future.
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Affiliation(s)
- Kaj Chokeshaiusaha
- Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK 43 Moo 6 Bangpra, Sriracha Chonburi 20110, Thailand
| | - Denis Puthier
- Laboratoire TAGC/INSERM U1090, Parc Scientifique de Luminy case 928, 163, avenue de Luminy, Marseille cedex 09 13288, France
| | - Catherine Nguyen
- Laboratoire TAGC/INSERM U1090, Parc Scientifique de Luminy case 928, 163, avenue de Luminy, Marseille cedex 09 13288, France
| | - Thanida Sananmuang
- Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK 43 Moo 6 Bangpra, Sriracha Chonburi 20110, Thailand
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29
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Kondo M, Sekine T, Miyakoshi T, Kitajima K, Egawa S, Seki R, Abe G, Tamura K. Flight feather development: its early specialization during embryogenesis. ZOOLOGICAL LETTERS 2018; 4:2. [PMID: 29372073 PMCID: PMC5771061 DOI: 10.1186/s40851-017-0085-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/29/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Flight feathers, a type of feather that is unique to extant/extinct birds and some non-avian dinosaurs, are the most evolutionally advanced type of feather. In general, feather types are formed in the second or later generation of feathers at the first and following molting, and the first molting begins at around two weeks post hatching in chicken. However, it has been stated in some previous reports that the first molting from the natal down feathers to the flight feathers is much earlier than that for other feather types, suggesting that flight feather formation starts as an embryonic event. The aim of this study was to determine the inception of flight feather morphogenesis and to identify embryological processes specific to flight feathers in contrast to those of down feathers. RESULTS We found that the second generation of feather that shows a flight feather-type arrangement has already started developing by chick embryonic day 18, deep in the skin of the flight feather-forming region. This was confirmed by shh gene expression that shows barb pattern, and the expression pattern revealed that the second generation of feather development in the flight feather-forming region seems to start by embryonic day 14. The first stage at which we detected a specific morphology of the feather bud in the flight feather-forming region was embryonic day 11, when internal invagination of the feather bud starts, while the external morphology of the feather bud is radial down-type. CONCLUSION The morphogenesis for the flight feather, the most advanced type of feather, has been drastically modified from the beginning of feather morphogenesis, suggesting that early modification of the embryonic morphogenetic process may have played a crucial role in the morphological evolution of this key innovation. Co-optation of molecular cues for axial morphogenesis in limb skeletal development may be able to modify morphogenesis of the feather bud, giving rise to flight feather-specific morphogenesis of traits.
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Affiliation(s)
- Mao Kondo
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Tomoe Sekine
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Taku Miyakoshi
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Keiichi Kitajima
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Shiro Egawa
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Ryohei Seki
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
- Mammalian Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540 Japan
| | - Gembu Abe
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Koji Tamura
- Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
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30
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Lin J, Yue Z. Coupling of apical-basal polarity and PCP to interpret the Wnt signaling gradient and orient feather branch. Development 2018; 145:dev.162792. [DOI: 10.1242/dev.162792] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 07/31/2018] [Indexed: 12/31/2022]
Abstract
To sense a global directional cue and orient cell growth is crucial in tissue morphogenesis. An anterior-posterior gradient of Wnt signaling controls the helical growth of feather branches (barbs), thus the formation of bilateral feathers. However, it remains unclear how the keratinocytes sense this gradient and orient barb growth. Here we show that due to feather branching, the global Wnt gradient is subdivided into periodic barbs. Within each barb, the anterior barbule plate cells tilt before the posterior cells. The core PCP gene Prickle1 is involved, as knockdown of its expression resulted in no cell shape change and no barb tilting. Furthermore, perturbation of the Wnt gradient leads to diffusive Prickle1 expression, and loss of barb orientation. Finally, the asymmetric distribution of Wnt6/Fzd10 is coordinated by the apical-basal polarity of the barbule plate keratinocytes, which is in turn regulated by the Par3/aPKC machinery. Our data elucidate a new mechanism through which the global Wnt signaling gradient is interpreted locally to construct complex spatial forms.
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Affiliation(s)
- Jianqiong Lin
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, China
| | - Zhicao Yue
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, China
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31
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Cooke TF, Fischer CR, Wu P, Jiang TX, Xie KT, Kuo J, Doctorov E, Zehnder A, Khosla C, Chuong CM, Bustamante CD. Genetic Mapping and Biochemical Basis of Yellow Feather Pigmentation in Budgerigars. Cell 2017; 171:427-439.e21. [PMID: 28985565 PMCID: PMC5951300 DOI: 10.1016/j.cell.2017.08.016] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/14/2017] [Accepted: 08/08/2017] [Indexed: 12/31/2022]
Abstract
Parrot feathers contain red, orange, and yellow polyene pigments called psittacofulvins. Budgerigars are parrots that have been extensively bred for plumage traits during the last century, but the underlying genes are unknown. Here we use genome-wide association mapping and gene-expression analysis to map the Mendelian blue locus, which abolishes yellow pigmentation in the budgerigar. We find that the blue trait maps to a single amino acid substitution (R644W) in an uncharacterized polyketide synthase (MuPKS). When we expressed MuPKS heterologously in yeast, yellow pigments accumulated. Mass spectrometry confirmed that these yellow pigments match those found in feathers. The R644W substitution abolished MuPKS activity. Furthermore, gene-expression data from feathers of different bird species suggest that parrots acquired their colors through regulatory changes that drive high expression of MuPKS in feather epithelia. Our data also help formulate biochemical models that may explain natural color variation in parrots. VIDEO ABSTRACT.
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Affiliation(s)
- Thomas F Cooke
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Curt R Fischer
- ChEM-H, Stanford University, Stanford, CA 94305, USA; Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
| | - Ping Wu
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA
| | - Ting-Xin Jiang
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA
| | - Kathleen T Xie
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James Kuo
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Elizabeth Doctorov
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ashley Zehnder
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chaitan Khosla
- ChEM-H, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Departments of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA; Integrative Stem Cell Center, China Medical University, Taichung 404, Taiwan; Center for the Integrative and Evolutionary Galliformes Genomics, National Chung Hsing University, Taichung 402, Taiwan
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA.
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