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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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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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Mabrouk I, Zhou Y, Wang S, Song Y, Fu X, Xu X, Liu T, Wang Y, Feng Z, Fu J, Ma J, Zhuang F, Cao H, Jin H, Wang J, Sun Y. Transcriptional Characteristics Showed That miR-144-y/FOXO3 Participates in Embryonic Skin and Feather Follicle Development in Zhedong White Goose. Animals (Basel) 2022; 12:ani12162099. [PMID: 36009690 PMCID: PMC9405214 DOI: 10.3390/ani12162099] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/08/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Simple Summary Feather is one of the most valuable and economical products in goose farming and plays a crucial physiological role in birds. For avian biology and the poultry industry, it is essential to comprehend and regulate how skin and feather follicles develop during embryogenesis. This study showed that several key regulatory genes (FOXO3, CTGF, and PTCH1, among others) and miRNAs (miR-144-y) participated in the developmental process of the skin and feather follicles in Zhedong white goose. Our findings are particularly important because they will serve as a valuable resource for upcoming studies on down feathers in agricultural economic growth regarding complex molecular mechanisms and breeding techniques. Abstract Skin and feather follicle development are essential processes for goose embryonic growth. Transcriptome and next-generation sequencing (NGS) network analyses were performed to improve the genome of Zhedong White goose and discover the critical genes, miRNAs, and pathways involved in goose skin and feather follicle morphogenesis. Sequencing output generated 6,002,591,668 to 8,675,720,319 clean reads from fifteen libraries. There were 1234, 3024, 4416, and 5326 different genes showing differential expression in four stages, E10 vs. E13, E10 vs. E18, E10 vs. E23, and E10 vs. E28, respectively. The differentially expressed genes (DEGs) were found to be implicated in multiple biological processes and pathways associated with feather growth and development, such as the Wnt signaling pathway, cell adhesion molecules, ECM–receptor interaction signaling pathways, and cell cycle and DNA replication pathways, according to functional analysis. In total, 8276 DEGs were assembled into twenty gene profiles with diverse expression patterns. The reliability of transcriptome results was verified by real-time quantitative PCR by selecting seven DEGs and five miRNAs. The localization of forkhead box O3 (FOXO3), connective tissue growth factor (CTGF), protein parched homolog1 (PTCH1), and miR-144-y by in situ hybridization showed spatial-temporal expression patterns and that FOXO3 and miR-144-y have an antagonistic targeting relationship. The correlation coefficient of FOXO3 and miR-144-y was -0.948, showing a strong negative correlation. Dual-luciferase reporter assay results demonstrated that miR-144-y could bind to the expected location to suppress the expression of FOXO3, which supports that there is a targeting relationship between them. The detections in this report will provide critical insight into the complex molecular mechanisms and breeding practices underlying the developmental characteristics of skin and feather follicles in Zhedong white geese.
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Affiliation(s)
- Ichraf Mabrouk
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yuxuan Zhou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Sihui Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yupu Song
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Xianou Fu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Xiaohui Xu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Tuoya Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yudong Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Ziqiang Feng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Jinhong Fu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Jingyun Ma
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Fangming Zhuang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Heng Cao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Honglei Jin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Jingbo Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yongfeng Sun
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Key Laboratory of Animal Production, Product Quality and Security, Jilin Agricultural University, Ministry of Education, Changchun 130118, China
- Correspondence:
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Wu L, Jiao X, Zhang D, Cheng Y, Song G, Qu Y, Lei F. Comparative Genomics and Evolution of Avian Specialized Traits. Curr Genomics 2021; 22:496-511. [PMID: 35386431 PMCID: PMC8905638 DOI: 10.2174/1389202923666211227143952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 11/25/2022] Open
Abstract
Genomic data are important for understanding the origin and evolution of traits. Under the context of rapidly developing of sequencing technologies and more widely available genome sequences, researchers are able to study evolutionary mechanisms of traits via comparative genomic methods. Compared with other vertebrates, bird genomes are relatively small and exhibit conserved synteny with few repetitive elements, which makes them suitable for evolutionary studies. Increasing genomic progress has been reported on the evolution of powered flight, body size variation, beak morphology, plumage colouration, high-elevation colonization, migration, and vocalization. By summarizing previous studies, we demonstrate the genetic bases of trait evolution, highlighting the roles of small-scale sequence variation, genomic structural variation, and changes in gene interaction networks. We suggest that future studies should focus on improving the quality of reference genomes, exploring the evolution of regulatory elements and networks, and combining genomic data with morphological, ecological, behavioural, and developmental biology data.
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Affiliation(s)
- Lei Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaolu Jiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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5
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Charton C, Youm DJ, Ko BJ, Seol D, Kim B, Chai HH, Lim D, Kim H. The transcriptomic blueprint of molt in rooster using various tissues from Ginkkoridak (Korean long-tailed chicken). BMC Genomics 2021; 22:594. [PMID: 34348642 PMCID: PMC8340483 DOI: 10.1186/s12864-021-07903-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/13/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Annual molt is a critical stage in the life cycle of birds. Although the most extensively documented aspects of molt are the renewing of plumage and the remodeling of the reproductive tract in laying hens, in chicken, molt deeply affects various tissues and physiological functions. However, with exception of the reproductive tract, the effect of molt on gene expression across the tissues known to be affected by molt has to date never been investigated. The present study aimed to decipher the transcriptomic effects of molt in Ginkkoridak, a Korean long-tailed chicken. Messenger RNA data available across 24 types of tissue samples (9 males) and a combination of mRNA and miRNA data on 10 males and 10 females blood were used. RESULTS The impact of molt on gene expression and gene transcript usage appeared to vary substantially across tissues types in terms of histological entities or physiological functions particularly related to nervous system. Blood was the tissue most affected by molt in terms of differentially expressed genes in both sexes, closely followed by meninges, bone marrow and heart. The effect of molt in blood appeared to differ between males and females, with a more than fivefold difference in the number of down-regulated genes between both sexes. The blueprint of molt in roosters appeared to be specific to tissues or group of tissues, with relatively few genes replicating extensively across tissues, excepted for the spliceosome genes (U1, U4) and the ribosomal proteins (RPL21, RPL23). By integrating miRNA and mRNA data, when chickens molt, potential roles of miRNA were discovered such as regulation of neurogenesis, regulation of immunity and development of various organs. Furthermore, reliable candidate biomarkers of molt were found, which are related to cell dynamics, nervous system or immunity, processes or functions that have been shown to be extensively modulated in response to molt. CONCLUSIONS Our results provide a comprehensive description at the scale of the whole organism deciphering the effects of molt on the transcriptome in chicken. Also, the conclusion of this study can be used as a valuable resource in transcriptome analyses of chicken in the future and provide new insights related to molt.
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Affiliation(s)
- Clémentine Charton
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dong-Jae Youm
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc, Seoul, Republic of Korea
| | - Bongsang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc, Seoul, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, 1500, Wanju, Republic of Korea
| | - Dajeong Lim
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, 1500, Wanju, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
- eGnome, Inc, Seoul, Republic of Korea.
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6
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Saranathan V, Finet C. Cellular and developmental basis of avian structural coloration. Curr Opin Genet Dev 2021; 69:56-64. [PMID: 33684846 DOI: 10.1016/j.gde.2021.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
Vivid structural colors in birds are a conspicuous and vital part of their phenotype. They are produced by a rich diversity of integumentary photonic nanostructures in skin and feathers. Unlike pigmentary coloration, whose genetic basis is being elucidated, little is known regarding the pathways underpinning organismal structural coloration. Here, we review available data on the development of avian structural colors. In particular, feather photonic nanostructures are understood to be intracellularly self-assembled by physicochemical forces typically seen in soft colloidal systems. We identify promising avenues for future research that can address current knowledge gaps, which are also highly relevant for the sustainable engineering of advanced bioinspired and biomimetic materials.
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Affiliation(s)
- Vinodkumar Saranathan
- Division of Science, Yale-NUS College, 10 College Avenue West, 138609, Singapore; NUS Nanotechnology and Nanoscience Initiative, National University of Singapore, 117581, Singapore.
| | - Cédric Finet
- Division of Science, Yale-NUS College, 10 College Avenue West, 138609, Singapore
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Wang F, Chen M, Cai F, Li P, Yan J, Zhou K. Expression of specific corneous beta proteins in the developing digits of the Japanese gecko (Gekko japonicus) reveals their role in the growth of adhesive setae. Comp Biochem Physiol B Biochem Mol Biol 2020; 240:110370. [DOI: 10.1016/j.cbpb.2019.110370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/05/2019] [Accepted: 10/14/2019] [Indexed: 01/03/2023]
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8
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Soliman SA. Morphological and Histochemical Description of Quail Feather Development. Anat Rec (Hoboken) 2019; 303:1865-1883. [DOI: 10.1002/ar.24276] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 08/03/2019] [Accepted: 08/09/2019] [Indexed: 12/28/2022]
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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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10
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Cogburn LA, Trakooljul N, Chen C, Huang H, Wu CH, Carré W, Wang X, White HB. Transcriptional profiling of liver during the critical embryo-to-hatchling transition period in the chicken (Gallus gallus). BMC Genomics 2018; 19:695. [PMID: 30241500 PMCID: PMC6151027 DOI: 10.1186/s12864-018-5080-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 09/14/2018] [Indexed: 11/30/2022] Open
Abstract
Background Although hatching is perhaps the most abrupt and profound metabolic challenge that a chicken must undergo; there have been no attempts to functionally map the metabolic pathways induced in liver during the embryo-to-hatchling transition. Furthermore, we know very little about the metabolic and regulatory factors that regulate lipid metabolism in late embryos or newly-hatched chicks. In the present study, we examined hepatic transcriptomes of 12 embryos and 12 hatchling chicks during the peri-hatch period—or the metabolic switch from chorioallantoic to pulmonary respiration. Results Initial hierarchical clustering revealed two distinct, albeit opposing, patterns of hepatic gene expression. Cluster A genes are largely lipolytic and highly expressed in embryos. While, Cluster B genes are lipogenic/thermogenic and mainly controlled by the lipogenic transcription factor THRSPA. Using pairwise comparisons of embryo and hatchling ages, we found 1272 genes that were differentially expressed between embryos and hatchling chicks, including 24 transcription factors and 284 genes that regulate lipid metabolism. The three most differentially-expressed transcripts found in liver of embryos were MOGAT1, DIO3 and PDK4, whereas THRSPA, FASN and DIO2 were highest in hatchlings. An unusual finding was the “ectopic” and extremely high differentially expression of seven feather keratin transcripts in liver of 16 day embryos, which coincides with engorgement of liver with yolk lipids. Gene interaction networks show several transcription factors, transcriptional co-activators/co-inhibitors and their downstream genes that exert a ‘ying-yang’ action on lipid metabolism during the embryo-to-hatching transition. These upstream regulators include ligand-activated transcription factors, sirtuins and Kruppel-like factors. Conclusions Our genome-wide transcriptional analysis has greatly expanded the hepatic repertoire of regulatory and metabolic genes involved in the embryo-to-hatchling transition. New knowledge was gained on interactive transcriptional networks and metabolic pathways that enable the abrupt switch from ectothermy (embryo) to endothermy (hatchling) in the chicken. Several transcription factors and their coactivators/co-inhibitors appear to exert opposing actions on lipid metabolism, leading to the predominance of lipolysis in embryos and lipogenesis in hatchlings. Our analysis of hepatic transcriptomes has enabled discovery of opposing, interconnected and interdependent transcriptional regulators that provide precise ying-yang or homeorhetic regulation of lipid metabolism during the critical embryo-to-hatchling transition. Electronic supplementary material The online version of this article (10.1186/s12864-018-5080-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Larry A Cogburn
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA.
| | - Nares Trakooljul
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA.,Present Address: Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, 18196, Dummerstorf, Germany
| | - Chuming Chen
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Cathy H Wu
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Wilfrid Carré
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA.,Laboratoire de Génétique Moléculaire et Génomique, CHU Pontchaillou, 35033, Rennes, France
| | - Xiaofei Wang
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA.,Department of Biological Sciences, Tennessee State University, Nashville, TN, 37209, USA
| | - Harold B White
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
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