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Li Y, Song S, Zhang Z, Liu X, Zhang Y, E G, Ma Y, Jiang L. A deletion variant within the FGF5 gene in goats is associated with gene expression levels and cashmere growth. Anim Genet 2022; 53:657-664. [PMID: 35843706 DOI: 10.1111/age.13239] [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: 03/22/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 11/01/2022]
Abstract
The FGF5 gene has been associated with the regulation of fibre length in mammals, including cashmere goats. A deletion variant at ~14 kb downstream of the FGF5 gene showed significant divergence between cashmere and non-cashmere goats in previous studies. In this study, we designed specific primers to genotype the deletion variant. The results of gel electrophoresis and Sanger sequencing revealed that a 507-bp deletion mutation is located at 95 454 685-95 455 191 of chromosome 6 in goats. Genotyping data from a large panel of 288 goats showed that the deletion at the FGF5 gene locus appeared to be associated with cashmere length. The deletion variant was close to fixation (frequency 0.97) in cashmere goats. Furthermore, electrophoretic mobility shift assays for evaluating DNA-protein interaction and mRNA expression levels of FGF5 suggested that the deletion variant may serve as a cis-acting element by specifically binding transcription factors to mediate quantitative changes in FGF5 mRNA expression. Our study illustrates how a structural mutation of the FGF5 gene has contributed to the cashmere growth phenotype in domestic goats. The deletion mutation within the FGF5 gene could potentially serve as a molecular marker of cashmere growth in cashmere goat breeding.
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Affiliation(s)
- Yefang Li
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Shen Song
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,State Key Laboratory of Cardiovascular Disease Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhengkai Zhang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xuexue Liu
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,Centre d'Anthropobiologie et de Genomique de Toulouse, Universite Paul Sabatier, Toulouse, France
| | - Yanli Zhang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Guangxin E
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Yuehui Ma
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lin Jiang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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2
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Gong G, Fan Y, Yan X, Li W, Yan X, Liu H, Zhang L, Su Y, Zhang J, Jiang W, Liu Z, Wang Z, Wang R, Zhang Y, Lv Q, Li J, Su R. Identification of Genes Related to Hair Follicle Cycle Development in Inner Mongolia Cashmere Goat by WGCNA. Front Vet Sci 2022; 9:894380. [PMID: 35774980 PMCID: PMC9237575 DOI: 10.3389/fvets.2022.894380] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Cashmere goat from Inner Mongolia is an excellent local breed in China, and the related cashmere product is a kind of precious textile raw material with high price. Cashmere is generated from secondary hair follicles, which has obvious annual periodicity and includes three different stages: anagen, catagen, and telogen. Therefore, we investigated skin transcriptome data for 12 months using weighted gene co-expression network analysis (WGCNA) to explore essential modules, pathways, and genes responsible for the periodic growth and development of secondary hair follicles. A total of 17 co-expression modules were discovered by WGCNA, and there is a strong correlation between steelblue module and month (0.65, p = 3E−09), anagen (0.52, p = 1E−05), telogen (−0.6, p = 8E−08). Gene expression was generally high during late anagen to catagen (June to December), while expression was downregulated from telogen to early anagen (January–May), which is similar to the growth rule of hair follicle cycle. KEGG pathway enrichment analyses of the genes of steelblue module indicated that genes are mainly enriched in Cell cycle, Wnt signaling pathway, p53 signaling pathway and other important signal pathways. These genes were also significantly enriched in GO functional annotation of the cell cycle, microtubule movement, microtubule binding, tubulin binding, and so on. Ten genes (WIF1, WNT11, BAMBI, FZD10, NKD1, LEF1, CCND3, E2F3, CDC6, and CDC25A) were selected from these modules, and further identified as candidate biomarkers to regulate periodic development of hair follicles using qRT-PCR. The Wnt signaling pathway and Cell cycle play an important role in the periodic development of hair follicles. Ten genes were identified as essential functional molecules related to periodic development of hair follicle. These findings laid a foundation for understanding molecular mechanisms in biological functions such as hair follicle development and hair growth in cashmere goats.
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Affiliation(s)
- Gao Gong
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yixing Fan
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xiaochun Yan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Wenze Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaomin Yan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Hongfu Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Ludan Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yixing Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Jiaxin Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Wei Jiang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Qi Lv
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
- *Correspondence: Qi Lv
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
- Jinquan Li
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
- Rui Su
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3
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Qin Y, Xu Y, Zhang Y, Gu M, Cai W, Bai Z, Zhang X, Chen R, Sun Y, Wu Y, Wang Z. Transcriptomics analysis of cashmere fineness functional genes. Anim Biotechnol 2022:1-11. [PMID: 35253626 DOI: 10.1080/10495398.2022.2042306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Liaoning cashmere goat (LCG) is a famous cashmere goat breed in China. Cashmere fineness, as an important index to evaluate cashmere quality, is also one of the problems to be improved for Liaoning cashmere goats. Transcriptome studies all mRNA transcribed by a specific tissue or cell in a certain period. It is a key link in the study of gene expression regulation. It plays an important role in the analysis of biological growth and disease. Transcriptome is spatio-temporal specific, that is, gene expression varies in different tissues or at different times. Three coarser and three fine LCG skin samples were sequenced by RNA-seq technology, and a total of 427 differentially expressed genes were obtained, including 291 up-regulated genes and 136 down-regulated genes. In the experiment, we screened out 16 genes that had significant differences in the expression of coarse and fine cashmere of Liaoning cashmere goats, so it was inferred that these 16 genes might have regulatory effects on cashmere fineness. Moreover, GO gene set enrichment analysis revealed that differential genes mainly consist of immune response, MHC protein complex, Heme binding and other pathways. KEGG analysis showed that transplant-versus-host disease and allograft rejection were the main pathways of differential genes.
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Affiliation(s)
- Yuting Qin
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanan Xu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yu Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ming Gu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Weidong Cai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhixian Bai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xinjiang Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Rui Chen
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yinggang Sun
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanzhi Wu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zeying Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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Wang D, Pu Y, Li Y, Pan D, Wang S, Tian W, Ma Y, Jiang L. Comprehensive analysis of lncRNAs involved in skeletal muscle development in ZBED6-knockout Bama pigs. BMC Genomics 2021; 22:593. [PMID: 34348644 PMCID: PMC8340374 DOI: 10.1186/s12864-021-07881-y] [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: 01/28/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The mutation of insulin-like growth factor 2 (IGF2 mutation) that a single-nucleotide substitution (G→A) in the third intron of IGF2 abrogates the interaction with zinc finger BED-type containing 6 (ZBED6) and leads to increased muscle mass in pigs. IGF2 mutation knock-in (IGF2 KI) and ZBED6 knockout (ZBED6 KO) lead to changes in IGF2 expression and increase muscle mass in mice and pigs. Long noncoding RNAs (lncRNAs) may participate in numerous biological processes, including skeletal muscle development. However, the role of the ZBED6-lncRNA axis in skeletal muscle development is poorly characterized. RESULTS In this study, we assembled transcriptomes using RNA-seq data published in previous studies by our group and identified 11,408 known lncRNAs and 2269 potential lncRNAs in seven tissues, heart, longissimus dorsi, gastrocnemius muscle, liver, spleen, lung and kidney, of ZBED6 KO (lean mass model) and WT Bama pigs. ZBED6 affected the expression of 1570 lncRNAs (differentially expressed lncRNAs [DE-lncRNAs]; log2-fold change ≥ 1, nominal p-value ≤ 0.05) in the seven examined tissues. The expressed lncRNAs (FPKM > 0.1) exhibited tissue-specific patterns in WT pigs. Specifically, 3410 lncRNAs were expressed exclusively in only one tissue. Potential functions of lncRNAs were indirectly predicted by searching their target cis- and trans-regulated protein-coding genes. LncRNAs with tissue-specific expression influence numerous genes related to tissue functions. Weighted gene coexpression network analysis (WGCNA) of 1570 DE-lncRNAs between WT and ZBED6 KO pigs was used to define the following six lncRNA modules specific to different tissues: skeletal muscle, heart, lung, spleen, kidney and liver modules. Furthermore, by conjoint analysis of longissimus dorsi data (tissue-specific expression, muscle module and DE-lncRNAs) and ChIP-PCR revealed NONSUSG002145.1 (adjusted p-values = 0.044), which is coexpressed with the IGF2 gene and binding with ZBED6, may play important roles in ZBED6 KO pig skeletal muscle development. CONCLUSIONS These findings indicate that the identified lncRNAs may play essential roles in tissue function and regulate the mechanism of ZBED6 action in skeletal muscle development in pigs. To our knowledge, this is the first study describing lncRNAs in ZBED6 KO pigs. These results may open new research directions leading to a better understanding of the global functions of ZBED6 and of lncRNA functions in skeletal muscle development in pigs.
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Affiliation(s)
- Dandan Wang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P. R. China.,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China
| | - Yabin Pu
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P. R. China.,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China
| | - Yefang Li
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P. R. China.,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China
| | - Dengke Pan
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China.,Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, 610072, Chengdu, China
| | - Shengnan Wang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P. R. China.,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China
| | - Wenjie Tian
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Yuehui Ma
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P. R. China. .,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China.
| | - Lin Jiang
- Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P. R. China. .,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, P.R. China.
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5
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Hu S, Li C, Wu D, Huo H, Bai H, Wu J. The Dynamic Change of Gene-Regulated Networks in Cashmere Goat Skin with Seasonal Variation. Biochem Genet 2021; 60:527-542. [PMID: 34304316 DOI: 10.1007/s10528-021-10114-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/13/2021] [Indexed: 11/26/2022]
Abstract
The Cashmere goat (Capra hircus) is renowned for its high-quality fiber production trait. The hair cycle in Cashmere goat has an annual rhythm. To deepen the understanding of the molecular foundation of annual rhythm in the skin of Cashmere goat, we did a comparative analysis of the Cashmere goat skin transcriptome all year round. 4002 Differentially expressed genes (DEGs) were identified with seasonal variations. 12 months transcriptome were divided into four developmental stages: Jan-Mar, Apr-Jul, Aug-Oct, and Nov-Dec based on gene expression patterns. 13 modules of highly correlated genes in skin were identified using WGCNA. Ten of these modules were consistent with the development stages. The gene function of those genes in each module was analyzed by functional enrichment. The results indicated that Wnt and Hedgehog signaling pathways were inhibited from January to March and activated from April to July. The cutaneous immune system of Cashmere goats has high activity from August to October. Fatty acid metabolism dominates goat skin from November to December. This study provides new information related to the annual skin development cycle, which could provide molecular biological significance for understanding the seasonal development and response to the annual rhythm of skin.
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Affiliation(s)
- Sile Hu
- College of Life Science and Food Engineering, Inner Mongolia University for Nationalities, Tongliao, 028000, China
- Key Laboratory of Bioinformatics of Inner Mongolia University for Nationalities, Tongliao, 028000, China
- Inner Mongolia Engineering and Technical Research Center for Personalized Medicine, Tongliao, 028000, China
- Institute of Resource Biology and Ecology, College of Life Science and Food Engineering, Inner Mongolia University for Nationalities, Tongliao, 028000, China
| | - Chun Li
- Key Laboratory of Bioinformatics of Inner Mongolia University for Nationalities, Tongliao, 028000, China
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, 028000, China
| | - Dubala Wu
- Key Laboratory of Bioinformatics of Inner Mongolia University for Nationalities, Tongliao, 028000, China
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, 028000, China
| | - Hongyan Huo
- College of Life Science and Food Engineering, Inner Mongolia University for Nationalities, Tongliao, 028000, China
| | - Haihua Bai
- College of Life Science and Food Engineering, Inner Mongolia University for Nationalities, Tongliao, 028000, China
- Inner Mongolia Engineering and Technical Research Center for Personalized Medicine, Tongliao, 028000, China
- Institute of Resource Biology and Ecology, College of Life Science and Food Engineering, Inner Mongolia University for Nationalities, Tongliao, 028000, China
| | - Jianghong Wu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, 028000, China.
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, 010031, China.
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6
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Ding H, Zhao H, Zhao X, Qi Y, Wang X, Huang D. Analysis of histology and long noncoding RNAs involved in the rabbit hair follicle density using RNA sequencing. BMC Genomics 2021; 22:89. [PMID: 33509078 PMCID: PMC7845105 DOI: 10.1186/s12864-021-07398-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/19/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Hair follicle density influences wool fibre production, which is one of the most important traits of the Wan Strain Angora rabbit. However, molecular mechanisms regulating hair follicle density have remained elusive. RESULTS In this study, hair follicle density at different body sites of Wan Strain Angora rabbits with high and low wool production (HWP and LWP) was investigated by histological analysis. Haematoxylin-eosin staining showed a higher hair follicle density in the skin of the HWP rabbits. The long noncoding RNA (lncRNA) profile was investigated by RNA sequencing, and 50 and 38 differentially expressed (DE) lncRNAs and genes, respectively, were screened between the HWP and LWP groups. A gene ontology analysis revealed that phospholipid, lipid metabolic, apoptotic, lipid biosynthetic, and lipid and fatty acid transport processes were significantly enriched. Potential functional lncRNAs that regulate lipid metabolism, amino acid synthesis, as well as the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) and hedgehog signalling pathways, were identified. Consequently, five lncRNAs (LNC_002171, LNC_000797, LNC_005567, LNC_013595, and LNC_020367) were considered to be potential regulators of hair follicle density and development. Three DE lncRNAs and genes were validated by quantitative real-time polymerase chain reaction (q-PCR). CONCLUSIONS LncRNA profiles provide information on lncRNA expression to improve the understanding of molecular mechanisms involved in the regulation of hair follicle density.
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Affiliation(s)
- Haisheng Ding
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, People's Republic of China
| | - Huiling Zhao
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, People's Republic of China
| | - Xiaowei Zhao
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, People's Republic of China
| | - Yunxia Qi
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, People's Republic of China
| | - Xiaofei Wang
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, People's Republic of China
| | - Dongwei Huang
- Anhui Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, People's Republic of China.
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Jiao Q, Wang YR, Zhao JY, Wang ZY, Guo D, Bai WL. Identification and molecular analysis of cashmere goat lncRNAs reveal their integrated regulatory network and potential roles in secondary hair follicle. Anim Biotechnol 2020; 32:719-732. [PMID: 32233965 DOI: 10.1080/10495398.2020.1747477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Long non-coding RNAs (lncRNAs) is a class of eukaryotic transcripts with length of more than 200 bp. They contribute to the regulation of gene expressions involved in multiple processes including the skin cell proliferation, differentiation, and reconstruction of the secondary hair follicles (SHFs). In this study, firstly, we identified 16 putative lncRNAs from SHFs of cashmere goat based on the EST sequences from NCBI database. Secondly, we investigated their transcriptional pattern in SHFs of cashmere goat, and constructed their ceRNA regulatory networks. The RT-qPCR results showed four lncRNAs (lncRNA-475074, -052149, -052140, and -051789) were significantly up-regulated, and nine lncRNAs (lncRNA-711032, -475083, -475070, -052139, -052127, -052037, -051903, -051847, and -051804) were significantly down-regulatd in anagen SHFs of cashmere goat. CeRNA networks analysis revealed complex interactional relationship among lncRNAs, miRNAs and mRNAs. Further, the KEGG pathway enrichment was performed for the potential target genes of the identified lncRNAs based on bioinformatics technique, and the results indicated that differentially expressed lncRNAs directly or indirectly might regulate potential target genes. Our results from this study will provide a significant information for further exploring the functions and possible mechanisms of the identified lncRNAs in SHFs of cashmere goat.
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Affiliation(s)
- Qian Jiao
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
| | - Yan R Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
| | - Jun Y Zhao
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
| | - Ze Y Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
| | - Dan Guo
- Academy of Animal Husbandry Science of Liaoning Province, Liaoyang, P.R. China
| | - Wen L Bai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
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8
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Thymosin β4 Identified by Transcriptomic Analysis from HF Anagen to Telogen Promotes Proliferation of SHF-DPCs in Albas Cashmere Goat. Int J Mol Sci 2020; 21:ijms21072268. [PMID: 32218218 PMCID: PMC7177334 DOI: 10.3390/ijms21072268] [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: 02/21/2020] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 01/09/2023] Open
Abstract
Increasing cashmere yield is one of the important goals of cashmere goat breeding. To achieve this goal, we screened the key genes that can improve cashmere performance. In this study, we used the RNA raw datasets of the skin and dermal papilla cells of secondary hair follicle (SHF-DPCs) samples of hair follicle (HF) anagen and telogen of Albas cashmere goats and identified a set of significant differentially expressed genes (DEGs). To explore potential associations between gene sets and SHF growth features and to identify candidate genes, we detected functional enrichment and constructed protein-protein interaction (PPI) networks. Through comprehensive analysis, we selected Thymosin β4 (Tβ4), Rho GTPase activating protein 6 (ARHGAP6), ADAM metallopeptidase with thrombospondin type 1 motif 15, (ADAMTS15), Chordin (CHRD), and SPARC (Osteonectin), cwcv and kazal-like domains proteoglycan 1 (SPOCK1) as candidate genes. Gene set enrichment analysis (GSEA) for these genes revealed Tβ4 and ARHGAP6 have a close association with the growth and development of SHF-DPCs. However, the expression of Tβ4 in the anagen was higher than that in the telogen, so we finally chose Tβ4 as the ultimate research object. Overexpressing Tβ4 promoted and silencing Tβ4 inhibited the proliferation of SHF-DPCs. These findings suggest that Tβ4 can promote the growth and development of SHF-DPCs and indicate that this molecule may be a valuable target for increasing cashmere production.
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9
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Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats. BMC Genomics 2020; 21:254. [PMID: 32293242 PMCID: PMC7092584 DOI: 10.1186/s12864-020-6656-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 03/05/2020] [Indexed: 02/08/2023] Open
Abstract
Background The mammary gland is a unique organ for milk synthesis, secretion and storage, and it undergoes cyclical processes of development, differentiation, lactation and degeneration. At different developmental periods, the biological processes governing mammary gland physiology and internal environmental homeostasis depend on a complex network of genes and regulatory factors. Emerging evidence indicates that lncRNAs have arbitrarily critical functions in regulating gene expression in many organisms; however, the systematic characteristics, expression, and regulatory roles of lncRNAs in the mammary gland tissues of dairy goats have not been determined. Result In the present study, we profiled long noncoding RNA (lncRNA) expression in the mammary gland tissues of Laoshan dairy goats (Capra hircus) from different lactation periods at the whole-genome level, to identify, characterize and explore the regulatory functions of lncRNAs. A total of 37,249 transcripts were obtained, of which 2381 lncRNAs and 37,249 mRNAs were identified, 22,488 transcripts, including 800 noncoding transcripts and 21,688 coding transcripts, differed significantly (p ≤ 0.01) among the different lactation stages. The results of lncRNA-RNA interaction analysis showed that six known lncRNAs belonging to four families were identified as the precursors of 67 known microRNAs; 1478 and 573 mRNAs were predicted as hypothetical cis-regulation elements and antisense mRNAs, respectively. GO annotation and KEGG analysis indicated that the coexpressed mRNAs were largely enriched in biological processes related to such activities as metabolism, immune activation, and stress,., and most genes were involved in pathways related to such phenomena as inflammation, cancer, signal transduction, and metabolism. Conclusions Our results clearly indicated that lncRNAs involved in responses to stimuli, multiorganism processes, development, reproductive processes and growth, are closely related to mammary gland development and lactation.
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Zhao B, Chen Y, Hu S, Yang N, Wang M, Liu M, Li J, Xiao Y, Wu X. Systematic Analysis of Non-coding RNAs Involved in the Angora Rabbit ( Oryctolagus cuniculus) Hair Follicle Cycle by RNA Sequencing. Front Genet 2019; 10:407. [PMID: 31130985 PMCID: PMC6509560 DOI: 10.3389/fgene.2019.00407] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 04/12/2019] [Indexed: 12/12/2022] Open
Abstract
The hair follicle (HF) cycle is a complicated and dynamic process in mammals, associated with various signaling pathways and gene expression patterns. Non-coding RNAs (ncRNAs) are RNA molecules that are not translated into proteins but are involved in the regulation of various cellular and biological processes. This study explored the relationship between ncRNAs and the HF cycle by developing a synchronization model in Angora rabbits. Transcriptome analysis was performed to investigate ncRNAs and mRNAs associated with the various stages of the HF cycle. One hundred and eleven long non-coding RNAs (lncRNAs), 247 circular RNAs (circRNAs), 97 microRNAs (miRNAs), and 1,168 mRNAs were differentially expressed during the three HF growth stages. Quantitative real-time PCR was used to validate the ncRNA transcriptome analysis results. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses provided information on the possible roles of ncRNAs and mRNAs during the HF cycle. In addition, lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA ceRNA networks were constructed to investigate the underlying relationships between ncRNAs and mRNAs. LNC_002919 and novel_circ_0026326 were found to act as ceRNAs and participated in the regulation of the HF cycle as miR-320-3p sponges. This research comprehensively identified candidate regulatory ncRNAs during the HF cycle by transcriptome analysis, highlighting the possible association between ncRNAs and the regulation of hair growth. This study provides a basis for systematic further research and new insights on the regulation of the HF cycle.
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Affiliation(s)
- Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Shuaishuai Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Naisu Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Manman Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Ming Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jiali Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yeyi Xiao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
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An Integrated Analysis of Cashmere Fineness lncRNAs in Cashmere Goats. Genes (Basel) 2019; 10:genes10040266. [PMID: 30987022 PMCID: PMC6523453 DOI: 10.3390/genes10040266] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/23/2019] [Accepted: 03/28/2019] [Indexed: 02/06/2023] Open
Abstract
Animal growth and development are regulated by long non-coding RNAs (lncRNAs). However, the functions of lncRNAs in regulating cashmere fineness are poorly understood. To identify the key lncRNAs that are related to cashmere fineness in skin, we have collected skin samples of Liaoning cashmere goats (LCG) and Inner Mongolia cashmere goats (MCG) in the anagen phase, and have performed RNA sequencing (RNA-seq) approach on these samples. The high-throughput sequencing and bioinformatics analyses identified 437 novel lncRNAs, including 93 differentially expressed lncRNAs. We also identified 3084 differentially expressed messenger RNAs (mRNAs) out of 27,947 mRNAs. Gene ontology (GO) analyses of lncRNAs and target genes in cis show a predominant enrichment of targets that are related to intermediate filament and intermediate filament cytoskeleton. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, sphingolipid metabolism is a significant pathway for lncRNA targets. In addition, this is the first report to reveal the possible lncRNA–mRNA regulatory network for cashmere fineness in cashmere goats. We also found that lncRNA XLOC_008679 and its target gene, KRT35, may be related to cashmere fineness in the anagen phase. The characterization and expression analyses of lncRNAs will facilitate future studies on the potential value of fiber development in LCG.
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Zheng Y, Wang Z, Zhu Y, Wang W, Bai M, Jiao Q, Wang Y, Zhao S, Yin X, Guo D, Bai W. LncRNA-000133 from secondary hair follicle of Cashmere goat: identification, regulatory network and its effects on inductive property of dermal papilla cells. Anim Biotechnol 2019; 31:122-134. [PMID: 30632899 DOI: 10.1080/10495398.2018.1553788] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Long noncoding RNAs (lncRNAs), a class of non-protein conding RNAs > 200 nt in length, were thought to play critical roles in regulating the expression of protein-coding genes. Here, we identified and characterized a novel lncRNA-000133 from the secondary hair follicle (SHF) of cashmere goat with its ceRNA network analysis, as well as, its potential effects on inductive property of dermal papilla cells were evaluated through overexpression analysis. Expression analysis indicated that lncRNA-000133 had a significantly higher expression at anagen than that at telogen in SHF of Cashmere goat, suggesting that lncRNA-000133 might be involved in the reconstruction of SHF with the formation and growth of cashmere fiber. Taken together with methylation analysis, we showed that 5' regulatory region methylation of the lncRNA-000133 gene might be involved in its expression suppression in SHF of Cashmere goat. The ceRNA regulatory network showed that a rich and complex regulatory relationship between lncRNA-000133 and related miRNAs with their target genes. The overexpression of lncRNA-000133 led to a significant increasing in the relative expression of ET-1, SCF, ALP and LEF1 in dermal papilla cells suggesting that lncRNA-000133 appears to contribute the inductive property of dermal papilla cells.
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Affiliation(s)
- Yuanyuan Zheng
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Zeying Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Yubo Zhu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Wei Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Man Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Qian Jiao
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Yanru Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Sujun Zhao
- Sichuan Animal Science Academy, Chengdu, P. R. China
| | - Xianbo Yin
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Dan Guo
- Academy of Animal Husbandry Science of Liaoning Province, Liaoyang, P. R. China
| | - Wenlin Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
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