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Ma S, Cao W, Ma X, Ye X, Qin C, Li B, Liu W, Lu Q, Wu C, Fu X. Metabolomics reveals metabolites associated with hair follicle cycle in cashmere goats. BMC Vet Res 2024; 20:208. [PMID: 38760765 PMCID: PMC11100241 DOI: 10.1186/s12917-024-04057-0] [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: 09/12/2023] [Accepted: 05/06/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND The hair follicle is a skin accessory organ that regulates hair development, and its activity varies on a regular basis. However, the significance of metabolites in the hair follicle cycle has long been unknown. RESULTS Targeted metabolomics was used in this investigation to reveal the expression patterns of 1903 metabolites in cashmere goat skin during anagen to telogen. A statistical analysis was used to investigate the potential associations between metabolites and the hair follicle cycle. The findings revealed clear changes in the expression patterns of metabolites at various phases and in various feeding models. The majority of metabolites (primarily amino acids, nucleotides, their metabolites, and lipids) showed downregulated expression from anagen (An) to telogen (Tn), which was associated with gene expression, protein synthesis and transport, and cell structure, which reflected, to some extent, that the cells associated with hair follicle development are active in An and apoptotic in An-Tn. It is worth mentioning that the expression of vitamin D3 and 3,3',5-triiodo-L-thyronine decreased and then increased, which may be related to the shorter and longer duration of outdoor light, which may stimulate the hair follicle to transition from An to catagen (Cn). In the comparison of different hair follicle development stages (An, Cn, and Tn) or feeding modes (grazing and barn feeding), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that common differentially expressed metabolites (DEMs) (2'-deoxyadenosine, L-valine, 2'-deoxyuridine, riboflavin, cytidine, deoxyguanosine, L-tryptophan, and guanosine-5'-monophosphate) were enriched in ABC transporters. This finding suggested that this pathway may be involved in the hair follicle cycle. Among these DEMs, riboflavin is absorbed from food, and the expression of riboflavin and sugars (D-glucose and glycogen) in skin tissue under grazing was greater and lower than that during barn feeding, respectively, suggesting that eating patterns may also alter the hair follicle cycle. CONCLUSIONS The expression patterns of metabolites such as sugars, lipids, amino acids, and nucleotides in skin tissue affect hair follicle growth, in which 2'-deoxyadenosine, L-valine, 2'-deoxyuridine, riboflavin, cytidine, deoxyguanosine, L-tryptophan, and guanosine-5'-monophosphate may regulate the hair follicle cycle by participating in ABC transporters. Feeding practices may regulate hair follicle cycles by influencing the amount of hormones and vitamins expressed in the skin of cashmere goats.
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Affiliation(s)
- Shengchao Ma
- Key Laboratory of Special Environments Biodiversity Application and Regulation in Xinjiang, College of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, 830017, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, 830017, China
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Xinjiang, Urumqi, 830011, China
| | - Wenzhi Cao
- Key Laboratory of Special Environments Biodiversity Application and Regulation in Xinjiang, College of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, 830017, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, 830017, China
| | - Xiaolin Ma
- Key Laboratory of Special Environments Biodiversity Application and Regulation in Xinjiang, College of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, 830017, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, 830017, China
| | - Xiaofang Ye
- Key Laboratory of Special Environments Biodiversity Application and Regulation in Xinjiang, College of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, 830017, China
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, 830017, China
| | - Chongkai Qin
- Xinjiang Aksu Prefecture Animal Husbandry Technology Extension Center, Xinjiang, Aksu, 843000, China
| | - Bin Li
- Xinjiang Aksu Prefecture Animal Husbandry Technology Extension Center, Xinjiang, Aksu, 843000, China
| | - Wenna Liu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Xinjiang, Urumqi, 830011, China
| | - Qingwei Lu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Xinjiang, Urumqi, 830011, China
| | - Cuiling Wu
- Key Laboratory of Special Environments Biodiversity Application and Regulation in Xinjiang, College of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, 830017, China.
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, 830017, China.
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Xinjiang, Urumqi, 830011, China.
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Zheng Y, Chen R, Yue C, Zhang Y, Guo S, Wang Y, Bai Z, Cai W, Hui T, Sun J, Zhang X, Wang Z. CeRNA regulates network and expression and SNP effect on NFKBIA of cashmere fineness. Anim Biotechnol 2023; 34:2863-2874. [PMID: 36165594 DOI: 10.1080/10495398.2022.2124165] [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] [Indexed: 11/01/2022]
Abstract
In this study, a total of 1140 Liaoning Cashmere Goats (LCG) were genotyped for single nucleotide polymorphism (SNP) of NFKBIA gene. There are 15 SNPs and 7 genotypes have been found, and G1547A (GG) genotype has been associated with cashmere fineness and cashmere yield. An integrated ceRNA regulatory network of NFKBIA gene was made. To prove NFKBIA and these non-coding RNAs (ncRNAs) may be related to cashmere fineness, we performed qPCR on these ncRNA in LCG coarse type skin (CT-LCG) and LCG fine type skin (FT-LCG). The result of qPCR showed lncRNA XLOC_011060 and ciRNA452 are at high expression level in CT-LCG, all miRNAs appear high expressed in FT-LCG, and mir-93 was the most significant difference between CT-LCG and FT-LCG. In addition, five miRNAs were selected for qPCR in different genotypes. The qPCR results showed that mir-93 might negatively regulate cashmere fineness and mir-17-5p may play a positive role in regulating cashmere fineness of individuals with G1355A (AG) genotype. These results demonstrated that NFKBIA gene is associated with cashmere fineness of LCG and G1547A (GG) genotype is the preferred marker genotype for cashmere fineness.
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Affiliation(s)
- Yuanyuan Zheng
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Rui Chen
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chang Yue
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yingchun Zhang
- Wenhua Road Primary School, Shenhe District, Shenyang, China
| | - Suping Guo
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanru Wang
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhixian Bai
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Weidong Cai
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Taiyu Hui
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jiaming Sun
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xinjiang Zhang
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zeying Wang
- College of Animal Science &Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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Wu C, Xu Q, Li J, Qin C, Tulafu H, Liu W, Lu Q, Zheng W, Fu X. Regulation of cashmere fineness traits by noncoding RNA in Jiangnan cashmere goats. BMC Genomics 2023; 24:604. [PMID: 37821834 PMCID: PMC10566132 DOI: 10.1186/s12864-023-09531-x] [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: 01/16/2023] [Accepted: 07/24/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Cashmere has long been used as the raw material for wool textiles. The diameter of the cashmere fibre determines its quality and economic value. However, the regulatory role of noncoding RNAs (ncRNAs) in cashmere fineness remains unclear, especially regarding the interaction between ncRNAs and coding RNAs. RESULTS Transcriptome sequencing was used to identify the expression profiles of long noncoding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs) in the skin tissues of Jiangnan cashmere goats with different cashmere fineness levels. Integration analysis of ncRNA and coding RNA was performed in combination with previous research results. The results showed that 16,437 lncRNAs, 2234 circRNAs, and 1322 miRNAs were identified in 8 skin samples of cashmere goats. A total of 403 differentially expressed (DE) lncRNAs, 62 DE circRNAs and 30 DE miRNAs were identified in the skin tissues of the fine groups (Fe) and coarse groups (Ce). We predicted the target gene of DE lncRNA, the target gene of DE miRNA and the host gene of DE circRNA. Based on functional annotation and enrichment analysis of target genes, we found that DE lncRNAs could be involved in regulating the fineness traits of cashmere. The most potential lncRNAs were MSTRG.42054.1, MSTRG.18602.3, and MSTRG.2199.13. CONCLUSIONS The data from this study enriched the cashmere goat noncoding RNA database and helped to supplement the annotation of the goat genome. The results provided a new direction for the breeding of cashmere characters.
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Affiliation(s)
- Cuiling Wu
- School of Life Sciences, Xinjiang Normal University, Urumqi, China
| | - Qin Xu
- Key Laboratory of Special Environmental Medicine, Xinjiang Military General Hospital, Urumqi, China
| | - Jianying Li
- Key Laboratory of Special Environmental Medicine, Xinjiang Military General Hospital, Urumqi, China
| | - Chongkai Qin
- Aksu Prefecture Animal Husbandry Technology Extension Center, Aksu, China
| | - Hanikezi Tulafu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Wenna Liu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Qingwei Lu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Wenxin Zheng
- Xinjiang Uygur Autonomous Region Breeding sheep and wool Cashmere Quality Safety Supervision and Inspection Center, Institute of Animal Husbandry Quality Standard, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China.
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China.
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Sun H, Meng K, Wang Y, Wang Y, Yuan X, Li X. LncRNAs regulate the cyclic growth and development of hair follicles in Dorper sheep. Front Vet Sci 2023; 10:1186294. [PMID: 37583467 PMCID: PMC10423938 DOI: 10.3389/fvets.2023.1186294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/11/2023] [Indexed: 08/17/2023] Open
Abstract
Introduction Hair follicles in Dorper sheep are characterized by seasonal cyclic growth and development, consequently resulting in hair shedding during spring. The cyclic growth and development of hair follicles are regulated by several influencing factors such as photoperiods, hormones, age of the animal, genes, long non-coding RNAs (lncRNAs), and signaling pathways. Methods In the present study, skin samples of five shedding sheep (S), used as experimental animals, and three non-shedding sheep (N), used as controls, were collected at three time points (September 27, 2019; January 3, 2020; and March 17, 2020) for RNA sequencing (RNA-seq) technology. Nine different groups (S1-vs-S2, S1-vs-S3, S2-vs-S3, N1- vs-N2, N1-vs-N3, N2-vs-N3, S1-vs-N1, S2-vs-N2, and S3-vs-N3) were compared using FDR < 0.05 and log 21 FC >as thresholds to assess the differences in the expression of lncRNAs. Results and discussion In total, 395 differentially expressed (DE) lncRNAs were screened. Cluster heatmap analysis identified two types of expression patterns, namely, high expression during the anagen phase (A pattern) and high expression during the telogen phase (T pattern). Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the target genes were largely enriched in the Estrogen signaling pathway, PI3K-Akt signaling pathway, Fc gamma R-mediated phagocytosis, and cell adhesion molecules (CAMs), which are associated with hair follicle cyclic growth and development-related pathways. In addition, 17 pairs of lncRNAs-target genes related to hair follicle cyclic growth and development were screened, and a regulatory network was constructed. Altogether, candidate lncRNAs and their regulated target genes were screened that contributed to sheep hair follicle cyclic growth and development. We believe these findings will provide useful insights into the underlying regulatory mechanisms.
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Affiliation(s)
| | | | | | | | | | - Xinhai Li
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
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Khaveh N, Schachler K, Berghöfer J, Jung K, Metzger J. Altered hair root gene expression profiles highlight calcium signaling and lipid metabolism pathways to be associated with curly hair initiation and maintenance in Mangalitza pigs. Front Genet 2023; 14:1184015. [PMID: 37351343 PMCID: PMC10282778 DOI: 10.3389/fgene.2023.1184015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Hair types have been under strong targeted selection in domestic animals for their impact on skin protection, thermoregulation and exterior morphology, and subsequent economic importance. In pigs, a very special hair phenotype was observed in Mangalitza, who expresses a thick coat of curly bristles and downy hair. Two breed-specific missense variants in TRPM2 and CYP4F3 were suggested to be associated with the Mangalitza pig's hair shape due to their role in hair follicle morphogenesis reported for human and mice. However, the mechanism behind this expression of a curly hair type is still unclear and needs to be explored. In our study, hair shafts were measured and investigated for the curvature of the hair in Mangalitza and crossbreeds in comparison to straight-coated pigs. For molecular studies, hair roots underwent RNA sequencing for a differential gene expression analysis using DESeq2. The output matrix of normalized counts was then used to construct weighted gene co-expression networks. The resulting hair root gene expression profiles highlighted 454 genes to be significantly differentially expressed for initiation of curly hair phenotype in newborn Mangalitza piglets versus post-initiation in later development. Furthermore, 2,554 genes showed a significant differential gene expression in curly hair in comparison to straight hair. Neither TRPM2 nor CYP4F3 were identified as differentially expressed. Incidence of the genes in weighted co-expression networks associated with TRPM2 and CYP4F3, and prominent interactions of subsequent proteins with lipids and calcium-related pathways suggested calcium signaling and/or lipid metabolism as essential players in the induction of the curly hair as well as an ionic calcium-dependency to be a prominent factor for the maintenance of this phenotype. Subsequently, our study highlights the complex interrelations and dependencies of mutant genes TRPM2 and CYP4F3 and associated gene expression patterns, allowing the initiation of curly hair type during the development of a piglet as well as the maintenance in adult individuals.
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Affiliation(s)
- Nadia Khaveh
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Kathrin Schachler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Jan Berghöfer
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Klaus Jung
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Julia Metzger
- Research Group Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
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Wang J, Fan H, Li M, Zhao K, Xia S, Chen Y, Shao J, Tang T, Bai X, Liu Z, Lu Y, Chen X, Sun W, Jia X, Lai S. Integration of Non-Coding RNA and mRNA Profiles Reveals the Mechanisms of Rumen Development Induced by Different Types of Diet in Calves. Genes (Basel) 2023; 14:genes14051093. [PMID: 37239453 DOI: 10.3390/genes14051093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Selecting suitable feed types and understanding the gastrointestinal digestive mechanism are helpful for the growth and health of calves in intensive dairy farming. However, the effects on rumen development of changing the molecular genetic basis and the regulatory mechanism by using different feed types are still unclear. Nine 7-day-old Holstein bull calves were randomly divided into GF (concentrate), GFF (alfalfa: oat grass = 3:2) and TMR (concentrate: alfalfa grass: oat grass: water = 0.30:0.12:0.08:0.50) diet experiment groups. Rumen tissue and serum samples were collected for physiological and transcriptomic analysis after 80 days. The results showed that serum α-amylase content and ceruloplasmin activity were significantly higher in the TMR group, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis ncRNAs and mRNAs were significantly enriched in the pathways of rumen epithelial development and stimulated rumen cell growth, including the Hippo signaling pathway, Wnt signaling pathway, thyroid hormone signaling pathway, ECM-receptor interaction and the absorption of protein and fat. The circRNAs/lncRNA-miRNAs-mRNA networks constructed, including novel_circ_0002471, novel_circ_0012104, TCONS_00946152, TCONS_00960915, bta-miR-11975, bta-miR-2890, PADI3 and CLEC6A, participated in metabolic pathways of lipid, immune system, oxidative stress and muscle development. In conclusion, the TMR diet could improve rumen digestive enzyme activities, stimulate rumen nutrient absorption and stimulate the DEGs related to energy homeostasis and microenvironment balance, and is thus better than the GF and GFF diets for promoting rumen growth and development.
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Affiliation(s)
- Jie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Huimei Fan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mianying Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Kaisen Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Siqi Xia
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiahao Shao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xue Bai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zheliang Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yusheng Lu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiangrui Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenqiang Sun
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xianbo Jia
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Songjia Lai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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RNA-Seq Reveals the Roles of Long Non-Coding RNAs (lncRNAs) in Cashmere Fiber Production Performance of Cashmere Goats in China. Genes (Basel) 2023; 14:genes14020384. [PMID: 36833312 PMCID: PMC9956036 DOI: 10.3390/genes14020384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/17/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are a kind of non-coding RNA being >200 nucleotides in length, and they are found to participate in hair follicle growth and development and wool fiber traits regulation. However, there are limited studies reporting the role of lncRNAs in cashmere fiber production in cashmere goats. In this study, Liaoning cashmere (LC) goats (n = 6) and Ziwuling black (ZB) goats (n = 6) with remarkable divergences in cashmere yield, cashmere fiber diameter, and cashmere color were selected for the construction of expression profiles of lncRNAs in skin tissue using RNA sequencing (RNA-seq). According to our previous report about the expression profiles of mRNAs originated from the same skin tissue as those used in the study, the cis and trans target genes of differentially expressed lncRNAs between the two caprine breeds were screened, resulting in a lncRNA-mRNA network. A total of 129 lncRNAs were differentially expressed in caprine skin tissue samples between LC goats and ZB goats. The presence of 2 cis target genes and 48 trans target genes for the differentially expressed lncRNAs resulted in 2 lncRNA-cis target gene pairs and 93 lncRNA-trans target gene pairs. The target genes concentrated on signaling pathways that were related to fiber follicle development, cashmere fiber diameter, and cashmere fiber color, including PPAR signaling pathway, metabolic pathways, fatty acid metabolism, fatty acid biosynthesis, tyrosine metabolism, and melanogenesis. A lncRNA-mRNA network revealed 22 lncRNA-trans target gene pairs for seven differentially expressed lncRNAs selected, of which 13 trans target genes contributed to regulation of cashmere fiber diameter, while nine trans target genes were responsible for cashmere fiber color. This study brings a clear explanation about the influences of lncRNAs over cashmere fiber traits in cashmere goats.
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Wu C, Yuan L, Cao W, Ye X, Ma X, Qin C, Li B, Yu F, Fu X. Regulation of secondary hair follicle cycle in cashmere goats by miR-877-3p targeting IGFBP5 gene. J Anim Sci 2023; 101:skad314. [PMID: 37777862 PMCID: PMC10583983 DOI: 10.1093/jas/skad314] [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: 07/12/2023] [Accepted: 09/29/2023] [Indexed: 10/02/2023] Open
Abstract
Cashmere, a highly valuable animal product derived from cashmere goats, holds significant economic importance. MiRNAs serve as crucial regulators in the developmental processes of mammalian hair follicles. Understanding the regulation of miRNAs during the hair follicle cycle is essential for enhancing cashmere quality. In this investigation, we employed high-throughput sequencing technology to analyze the expression profiles of miRNAs in the secondary hair follicles of Jiangnan cashmere goats at different stages. Through bioinformatics analysis, we identified differentially expressed miRNAs (DE miRNAs). The regulatory relationships between miRNAs and their target genes were verified using multiple techniques, including RT-qPCR, western blot, Dual-Luciferase Reporter, and CKK-8 assays. Our findings revealed the presence of 193 DE miRNAs during various stages of the hair follicle cycle in Jiangnan cashmere goats. Based on the previously obtained mRNA data, the target genes of DE miRNA were predicted, and 1,472 negative regulatory relationships between DE miRNAs and target genes were obtained. Notably, the expression of chi-miR-877-3p was down-regulated during the telogen (Tn) phase compared to the anagen (An) and catagen (Cn) phases, while the IGFBP5 gene exhibited up-regulation. Further validation experiments confirmed that overexpression of chi-miR-877-3p in dermal papilla cells suppressed IGFBP5 gene expression and facilitated cell proliferation. The results of this study provide novel insights for analyzing the hair follicle cycle.
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Affiliation(s)
- Cuiling Wu
- Key Laboratory of Special Environments Biodiversity Application and Regulation in Xinjiang, School of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, China
| | - Liang Yuan
- Key Laboratory of Special Environments Biodiversity Application and Regulation in Xinjiang, School of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, China
| | - Wenzhi Cao
- Key Laboratory of Special Environments Biodiversity Application and Regulation in Xinjiang, School of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, China
| | - Xiaofang Ye
- Key Laboratory of Special Environments Biodiversity Application and Regulation in Xinjiang, School of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, China
| | - Xiaolin Ma
- Key Laboratory of Special Environments Biodiversity Application and Regulation in Xinjiang, School of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, China
| | - Chongkai Qin
- Xinjiang Aksu Prefecture Animal Husbandry Technology Extension Center, Aksu, China
| | - Bin Li
- Xinjiang Aksu Prefecture Animal Husbandry Technology Extension Center, Aksu, China
| | - Fei Yu
- Key Laboratory of Special Environments Biodiversity Application and Regulation in Xinjiang, School of Life Sciences, Xinjiang Normal University, Xinjiang, Urumqi, China
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Xinjiang Urumqi, China
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Zhang C, Qin Q, Liu Z, Xu X, Lan M, Xie Y, Wang Z, Li J, Liu Z. Identification of the key proteins associated with different hair types in sheep and goats. Front Genet 2022; 13:993192. [PMID: 36212123 PMCID: PMC9539809 DOI: 10.3389/fgene.2022.993192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Animal-derived fiber has the characteristics of being light, soft, strong, elastic and a good thermal insulator, and it is widely used in many industries and traditional products, so it plays an important role in the economy of some countries. Variations in phenotypes of wool fibers among different species and breeds are important for industry. We found that the mean fiber diameter of cashmere was significantly smaller than that of sheep wool (p < 0.01), and sheep wool was significantly smaller than goat wool (p < 0.01). Compared with traditional proteomics technology, we analyzed cashmere, guard hair, and wool by Laber-free proteomics technology and detected 159, 204, and 70 proteins, respectively. Through the sequential windowed acquisition of all theoretical fragmentations (SWATH), 41 and 54 differentially expressed proteins were successfully detected in the cashmere vs. wool group and guard hair vs. wool group. Protein‒protein interaction network analysis of differentially expressed proteins revealed many strong interactions related to KRT85, KRTAP15-1 and KRTAP3-1. The final analysis showed that the proportion of KRT85, KRTAP15-1 and KRTAP3-1 might be the key to the difference in fiber diameter and could be used as a potential molecular marker for distinguishing different fiber types.
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Affiliation(s)
- Chongyan Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Qing Qin
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhichen Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaolong Xu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingxi Lan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yuchun Xie
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhixin Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding of Ministry of Agriculture, Hohhot, China
- The Inner Mongolia Autonomous Region Goat Genetics and Breeding Engineering Technology Research Center, Hohhot, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding of Ministry of Agriculture, Hohhot, China
- The Inner Mongolia Autonomous Region Goat Genetics and Breeding Engineering Technology Research Center, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction in Inner Mongolia Autonomous Region, Hohhot, China
| | - Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding of Ministry of Agriculture, Hohhot, China
- The Inner Mongolia Autonomous Region Goat Genetics and Breeding Engineering Technology Research Center, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction in Inner Mongolia Autonomous Region, Hohhot, China
- *Correspondence: Zhihong Liu,
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10
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Comprehensive Transcriptome Analysis of Hair Follicle Morphogenesis Reveals That lncRNA-H19 Promotes Dermal Papilla Cell Proliferation through the Chi-miR-214-3p/β-Catenin Axis in Cashmere Goats. Int J Mol Sci 2022; 23:ijms231710006. [PMID: 36077403 PMCID: PMC9456307 DOI: 10.3390/ijms231710006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/22/2022] Open
Abstract
Cashmere is initiated and develops in the fetal stages and the number and density of secondary hair follicles (SHFs) determine cashmere production and quality. Growing evidence indicates that both microRNA (miRNA) and long non-coding RNA (lncRNA) play an indispensable role in hair follicle (HF) growth and development. However, little is known about miRNAs, lncRNAs, and their functions as well as their interactions during cashmere initiation and development. Here, based on lncRNA and miRNA high-throughput sequencing and bioinformatics analysis, we identified 10,485 lncRNAs, 40,639 mRNAs, and 605 miRNAs in cashmere goat skin during HF induction, organogenesis, and cytodifferentiation stages. Among them, 521 lncRNAs, 5976 genes, and 204 miRNAs were differentially expressed (DE). KEGG analysis of DE genes indicated that ECM–receptor interaction and biosynthesis of amino acids were crucial for HF development. Notch, TGF-beta, and Wnt signaling pathways were also identified, which are conventional pathways associated with HF growth and development. Then, the ceRNA regulatory network was constructed, and the impact of lncRNA H19 was investigated in dermal papilla (DP) cells. The MTT, CCK-8, and EdU assays showed that the viability and proliferation of DP cells were promoted by H19, and mechanistic studies suggested that H19 performed its function through the chi-miR-214-3p/β-catenin axis. The present study created a resource for lncRNA, miRNA, and mRNA studies in cashmere morphogenesis. It could contribute to a better understanding of the molecular mechanism of ncRNAs involved in the regulation of HF growth and development.
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11
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Zhao B, Li J, Liu M, Hu S, Yang N, Liang S, Zhang X, Dai Y, Bao Z, Chen Y, Wu X. lncRNA2919 Suppresses Rabbit Dermal Papilla Cell Proliferation via trans-Regulatory Actions. Cells 2022; 11:2443. [PMID: 35954286 PMCID: PMC9368379 DOI: 10.3390/cells11152443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
Hair follicles (HFs) are complex organs that grow cyclically during mammals' growth and development. Long non-coding RNAs (lncRNAs) cannot be translated into proteins and play crucial roles in many biological processes. In our previous study, candidate lncRNAs associated with HF cyclic regeneration were screened, and we identified that the novel lncRNA, lncRNA2919, was significantly expressed during catagen. Here, we identified that lncRNA2919 has no coding potentiality and is highly expressed in the cell nucleus, and downregulates HF growth and development-related genes, inhibits cell proliferation, and promotes cell apoptosis in rabbit dermal papilla cells. lncRNA2919 recruits STAT1 to form a compound. As a key transcription factor, STAT1 regulates the transcriptional expression of KRTAP11-1. Our study revealed that lncRNA2919 is involved in HF cyclic regeneration through the trans-regulatory lncRNA2919-STAT1-KRTAP11-1 axis. This study elucidates the mechanism through which lncRNA2919 regulates HF growth and development and the role of lncRNA2919 as a new therapeutic target in animal wool production and human hair-related disease treatment.
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Affiliation(s)
- Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jiali Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Ming Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Shuaishuai Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Naisu Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Shuang Liang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiyu Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yingying Dai
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhiyuan Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
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12
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Wu C, Li J, Xu X, Xu Q, Qin C, Liu G, Wei C, Zhang G, Tian K, Fu X. Effect of the FA2H Gene on cashmere fineness of Jiangnan cashmere goats based on transcriptome sequencing. BMC Genomics 2022; 23:527. [PMID: 35864447 PMCID: PMC9306159 DOI: 10.1186/s12864-022-08763-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/13/2022] [Indexed: 11/17/2022] Open
Abstract
Background Cashmere goats are a heterogeneous hairy mammal. The fineness of cashmere can affect its economic value. Therefore, in this study, we used transcriptome sequencing techniques to analyze the gene expression profiles of the skin tissues of cashmere goats with different cashmere fineness. The selected candidate genes were functionally verified with the secondary hair follicle hair papillary cells of cashmere goats. Results We identified 479 DEGs, of which 238 mRNAs were up-regulated in the fine velvet group and 241 mRNA were down-regulated. Based on functional annotation and protein interaction network analysis, we found some genes that may affect the fineness of cashmere, including SOX18, SOX4, WNT5A, IGFBP4, KAP8, KRT36, and FA2H. Using qRT-PCR, Western blot, CCK-8 cell viability detection, EDU cell proliferation detection, and flow cytometry, we found that overexpression of the FA2H gene could promote the proliferation of secondary hair follicle DPCs in cashmere goats. At the same time, we proved that FA2H could regulate the expression levels of the FGF5 and BMP2 genes in DPCs. Conclusion The results of this study provide a useful reference for the genetics and breeding of Jiangnan cashmere goats and goat genome annotation, and provide an experimental basis for improving cashmere quality of the cashmere goat. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08763-7.
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Affiliation(s)
- Cuiling Wu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.,College of Animal Science, Xinjiang Agricultural University, Urumqi, 830052, China.,Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool Sheep and Cashmere-Goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, 830011, China
| | - Jianying Li
- Key Laboratory of Special Environmental Medicine, Xinjiang Military General Hospital, Urumqi, 830000, China
| | - Xinming Xu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool Sheep and Cashmere-Goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, 830011, China
| | - Qi Xu
- Key Laboratory of Special Environmental Medicine, Xinjiang Military General Hospital, Urumqi, 830000, China
| | - Chongkai Qin
- Xinjiang Aksu Prefecture Animal Husbandry Technology Extension Center, Aksu, 843000, China
| | - Guifen Liu
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Chen Wei
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Guoping Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool Sheep and Cashmere-Goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, 830011, China.
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13
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Wu C, Qin C, Fu X, Huang X, Tian K. Integrated analysis of lncRNAs and mRNAs by RNA-Seq in secondary hair follicle development and cycling (anagen, catagen and telogen) of Jiangnan cashmere goat (Capra hircus). BMC Vet Res 2022; 18:167. [PMID: 35524260 PMCID: PMC9074311 DOI: 10.1186/s12917-022-03253-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/18/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Among the world's finest natural fiber composites is derived from the secondary hair follicles (SHFs) of cashmere goats yield one of the world's best natural fibres. Their development and cycling are characterized by photoperiodism with diverse, well-orchestrated stimulatory and inhibitory signals. Long non-coding RNA (lncRNAs) and mRNAs play important roles in hair follicle (HF) development. However, not many studies have explored their specific functions in cashmere development and cycling. This study detected mRNAs and lncRNAs with their candidate genes and related pathways in SHF development and cycling of cashmere goat. We utilized RNA sequencing (RNA-Seq) and bioinformatics analysis on lncRNA and mRNA expressions in goat hair follicles to discover candidate genes and metabolic pathways that could affect development and cycling (anagen, catagen, and telogen). RESULTS We identified 228 differentially expressed (DE) mRNAs and 256 DE lncRNA. For mRNAs, catagen and anagen had 16 upregulated and 35 downregulated DEGs, catagen and telogen had 18 upregulated and 9 downregulated DEGs and telogen and anagen had 52 upregulated and 98 downregulated DEGs. LncRNA witnessed 22 upregulated and 39 downregulated DEGs for catagen and anagen, 36 upregulated and 29 downregulated DEGs for catagen and telogen as well as 66 upregulated and 97 downregulated DEGs for telogen and anagen. Several key genes, including MSTRG.5451.2, MSTRG.45465.3, MSTRG.11609.2, CHST1, SH3BP4, CDKN1A, GAREM1, GSK-3β, DEFB103A KRTAP9-2, YAP1, S100A7A, FA2H, LOC102190037, LOC102179090, LOC102173866, KRT2, KRT39, FAM167A, FAT4 and EGFL6 were shown to be potentially important in hair follicle development and cycling. They were related to, WNT/β-catenin, mTORC1, ERK/MAPK, Hedgehog, TGFβ, NFkB/p38MAPK, caspase-1, and interleukin (IL)-1a signaling pathways. CONCLUSION This work adds to existing understanding of the regulation of HF development and cycling in cashmere goats via lncRNAs and mRNAs. It also serves as theoretical foundation for future SHF research in cashmere goats.
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Affiliation(s)
- Cuiling Wu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, 830052, China.,Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.,Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool sheep & Cashmere-goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, 830011, China
| | - Chongkai Qin
- Xinjiang Aksu Prefecture Animal Husbandry Technology Extension Center, Aksu, 843000, China
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool sheep & Cashmere-goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, 830011, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, 830052, China.
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China. .,Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool sheep & Cashmere-goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, 830011, China.
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14
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Identification and Molecular Analysis of m6A-circRNAs from Cashmere Goat Reveal Their Integrated Regulatory Network and Putative Functions in Secondary Hair Follicle during Anagen Stage. Animals (Basel) 2022; 12:ani12060694. [PMID: 35327094 PMCID: PMC8944478 DOI: 10.3390/ani12060694] [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: 12/17/2021] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Cashmere is a natural, high-end textile material. It is derived from the secondary hair follicle (SHFs) tissue in the skin of cashmere goats. Previous studies have indicated that m6A modifications in circRNA molecules play important roles in a variety of cells through multiple mechanisms. However, little information is available on the expression profile and functional regulatory characteristics of m6A-modified circRNA (m6A-circRNA) in SHFs of cashmere goats. In this study, a total of 15 m6A-circRNAs were identified. Six of these m6A-circRNAs were revealed to have significantly higher expression in skin at anagen than at telogen. To gain insight into the potential regulatory mechanisms of the anagen up-regulated m6A-circRNAs, we constructed the regulatory networks along with related pathways in SHFs of cashmere goats. In addition, we found that the expression trends of four m6A-circRNAs in the SHFs during SHF cycles were highly similar to their host genes. However, the expression patterns of two m6A-circRNAs were inconsistent with the linear RNAs from their host genes in the SHFs of cashmere goats. These results will provide new insights to elucidate the biological functions and regulatory features of m6A-circRNA in SHF development and cashmere growth in goats. Abstract N6-methyladenosine (m6A) is the most abundant modification in linear RNA molecules. Over the last few years, interestingly, many circRNA molecules are also found to have extensive m6A modification sites with temporal and spatial specific expression patterns. To date, however, little information is available concerning the expression profiling and functional regulatory characteristics of m6A modified circRNAs (m6A-circRNAs) in secondary hair follicles (SHFs) of cashmere goats. In this study, a total of fifteen m6A-circRNAs were identified and characterized in the skin tissue of cashmere goats. Of these, six m6A-circRNAs were revealed to have significantly higher expression in skin at anagen compared with those at telogen. The constructed ceRNA network indicated a complicated regulatory relationship of the six anagen up-regulated m6A-circRNAs through miRNA mediated pathways. Several signaling pathways implicated in the physiological processes of hair follicles were enriched based on the potential regulatory genes of the six anagen up-regulated m6A-circRNAs, such as TGF-beta, axon guidance, ribosome, and stem cell pluripotency regulatory pathways, suggesting the analyzed m6A-circRNAs might be essentially involved in SHF development and cashmere growth in cashmere goats. Further, we showed that four m6A-circRNAs had highly similar expression trends to their host genes in SHFs of cashmere goats including m6A-circRNA-ZNF638, -TULP4, -DNAJB6, and -CAT. However, the expression patterns of two m6A-circRNAs (m6A-circRNA-STAM2 and -CAAP1) were inconsistent with the linear RNAs from their host genes in the SHFs of cashmere goats. These results provide novel information for eluci-dating the biological function and regulatory characteristics of the m6A-circRNAs in SHF development and cashmere growth in goats.
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15
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Yan H, Jin M, Li Y, Gao Y, Ding Q, Wang X, Zeng W, Chen Y. miR-1 Regulates Differentiation and Proliferation of Goat Hair Follicle Stem Cells by Targeting IGF1R and LEF1 Genes. DNA Cell Biol 2022; 41:190-201. [PMID: 35007429 DOI: 10.1089/dna.2021.0288] [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] [Indexed: 11/12/2022] Open
Abstract
Hair follicle stem cells (HFSCs) play a significant role in hair development. miR-1 has been reported as an important regulatory factor that affects hair follicle growth and development, but its regulatory mechanism on HFSC development remains unknown. In this study, the molecular mechanism of miR-1 in regulating HFSC proliferation and differentiation was investigated. High-throughput RNA-seq and integrated analysis were performed to identify differentially transcribed mRNAs and microRNAs (miRNAs) in HFSCs co-cultured with dermal papilla cells (named dHFSCs) and control HFSCs. We then determined the molecular function of miR-1 in HFSCs. Compared with HFSCs, 13 differentially transcribed miRNAs were identified in dHFSCs. The in vitro results indicated that the overtranscription of miR-1 inhibited HFSC proliferation, but enhanced HFSC differentiation by targeting IGF1R and LEF1 genes. This study provides new insights into the molecular mechanisms of HFSC development. Approval ID (2014ZX08008-002).
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Affiliation(s)
- Hailong Yan
- Department of Neurology, Institute of Brain Science, Medical School, Shanxi Datong University, Datong, China
- Shanxi key Laboratory of Inflammatory Neurodegenerative Disease, Institute of Brain Science, Shanxi Datong University, Datong, China
| | - Miaohan Jin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yan Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ye Gao
- Department of Neurology, Institute of Brain Science, Medical School, Shanxi Datong University, Datong, China
- Shanxi key Laboratory of Inflammatory Neurodegenerative Disease, Institute of Brain Science, Shanxi Datong University, Datong, China
| | - Qiang Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wenxian Zeng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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16
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Gao WZ, Xue HL, Yang JC. Proteomics analysis of the secondary hair follicle cycle in Liaoning cashmere goat. Small Rumin Res 2021. [DOI: 10.1016/j.smallrumres.2021.106408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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17
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Shang F, Wang Y, Ma R, Di Z, Wu Z, Hai E, Rong Y, Pan J, Liang L, Wang Z, Wang R, Liu Z, Zhao Y, Wang Z, Li J, Zhang Y. Expression Profiling and Functional Analysis of Circular RNAs in Inner Mongolian Cashmere Goat Hair Follicles. Front Genet 2021; 12:678825. [PMID: 34178035 PMCID: PMC8226234 DOI: 10.3389/fgene.2021.678825] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/29/2021] [Indexed: 11/23/2022] Open
Abstract
Background Inner Mongolian cashmere goats have hair of excellent quality and high economic value, and the skin hair follicle traits of cashmere goats have a direct and important effect on cashmere yield and quality. Circular RNA has been studied in a variety of tissues and cells. Result In this study, high-throughput sequencing was used to obtain the expression profiles of circular RNA (circRNA) in the hair follicles of Inner Mongolian cashmere goats at different embryonic stages (45, 55, 65, and 75 days). A total of 21,784 circRNAs were identified. At the same time, the differentially expressed circRNA in the six comparison groups formed in the four stages were: d75vsd45, 59 upregulated and 33 downregulated DE circRNAs; d75vsd55, 61 upregulated and 102 downregulated DE circRNAs; d75vsd65, 32 upregulated and 33 downregulated DE circRNAs; d65vsd55, 67 upregulated and 169 downregulated DE circRNAs; d65vsd45, 96 upregulated and 63 downregulated DE circRNAs; and d55vsd45, 76 upregulated and 42 downregulated DE circRNAs. Six DE circRNA were randomly selected to verify the reliability of the sequencing results by quantitative RT-PCR. Subsequently, the circRNA corresponding host genes were analyzed by the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The results showed that the biological processes related to hair follicle growth and development enriched by GO mainly included hair follicle morphogenesis and cell development, and the signaling pathways related to hair follicle development included the Notch signaling pathway and NF-κB signaling pathway. We combined the DE circRNA of d75vsd45 with miRNA and mRNA databases (unpublished) to construct the regulatory network of circRNA–miRNA–mRNA, and formed a total of 102 pairs of circRNA–miRNA and 126 pairs of miRNA–mRNA interactions. The binding relationship of circRNA3236–chi-miR-27b-3p and circRNA3236–chi-miR-16b-3p was further verified by dual-luciferase reporter assays, and the results showed that circRNA3236 and chi-miR-27b-3p, and circRNA3236 and chi-miR-16b-3p have a targeted binding relationship. Conclusion To summarize, we established the expression profiling of circRNA in the fetal skin hair follicles of cashmere goats, and found that the host gene of circRNA may be involved in the development of hair follicles of cashmere goats. The regulatory network of circRNA–miRNA–mRNA was constructed and preliminarily verified using DE circRNAs.
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Affiliation(s)
- Fangzheng Shang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yu Wang
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
| | - Rong Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
| | - Zhengyang Di
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhihong Wu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Erhan Hai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Youjun Rong
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Jianfeng Pan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Lili Liang
- 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
| | - Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanhong Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhixin Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Jinquan Li
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China.,Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
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18
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Wang J, Sui J, Mao C, Li X, Chen X, Liang C, Wang X, Wang SH, Jia C. Identification of Key Pathways and Genes Related to the Development of Hair Follicle Cycle in Cashmere Goats. Genes (Basel) 2021; 12:genes12020180. [PMID: 33513983 PMCID: PMC7911279 DOI: 10.3390/genes12020180] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 12/13/2022] Open
Abstract
The development of hair follicle in cashmere goats shows significant periodic change, as with mice and humans. However, for cashmere goat with double-coat, the periodic change may be due to other regulatory molecules and signal pathways. To understand the mechanism of periodic development of hair follicle, we performed a weighted gene coexpression network analysis (WGCNA) to mine key genes and establish an interaction network by utilizing the NCBI public dataset. Ten coexpression modules, including 7689 protein-coding genes, were constructed by WGCNA, six of which are considered to be significantly related to the development of the hair follicle cycle. A functional enrichment analysis for each model showed that they are closely related to ECM- receptor interaction, focal adhesion, PI3K-Akt signaling pathway, estrogen signaling pathway, and so on. Combined with the analysis of differential expressed genes, 12 hub genes from coexpression modules were selected as candidate markers, i.e., COL1A1, C1QTNF6, COL1A2, AQP3, KRTAP3-1, KRTAP11-1, FA2H, NDUFS5, DERL2, MRPL14, ANTKMT and XAB2, which might be applied to improve cashmere production.
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19
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CircRNA-1926 Promotes the Differentiation of Goat SHF Stem Cells into Hair Follicle Lineage by miR-148a/b-3p/ CDK19 Axis. Animals (Basel) 2020; 10:ani10091552. [PMID: 32887226 PMCID: PMC7552268 DOI: 10.3390/ani10091552] [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: 07/31/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 12/22/2022] Open
Abstract
Simple Summary Cashmere is the fiber derived from cashmere goats. Its textiles have been favored by consumers due to their typical features, like fine, light, softness, and comfort. Circular RNAs (circRNAs) are thought to play roles in cashmere growth of cashmere goats. CircRNA-1926 was previously identified in cashmere goats, but its functional roles are unclear. In this study, we firstly confirmed the expression of circRNA-1926 in secondary hair follicle bulge of cashmere goats with a significantly higher level at anagen than the counterpart of telogen. Next, we showed that circRNA-1926 promotes the differentiation of hair follicle stem cell into hair follicle lineage in cashmere goats. Mechanistically, we found that circRNA-1926 regulated the CDK19 expression via sponging miR-148a/b-3p. Our results have demonstrated that circRNA-1926 promotes the differentiation of secondary hair follicle stem cells into hair follicle lineages in cashmere goats through sponging miR-148a/b-3p to promote the expression of the CDK19 gene. The results from this study provided novel insight into the functional roles of circRNA-1926 in hair follicle regeneration and cashmere growth. Abstract Circular RNAs (CircRNAs) are a type of non-coding RNAs, which contain a covalently closed loop structure without 5′ to 3′ free ends. CircRNAs play essential roles in the regeneration of secondary hair follicle (SHF) and cashmere growth in goats. CircRNA-1926 was previously identified in SHF of cashmere goats, but its potential roles are unclear. In this study, we confirmed the expression of circRNA-1926 in SHF bulge of nine cashmere goats with a significantly higher level at anagen than that of telogen. Through the use of both overexpression and siRNA interference, we showed that circRNA-1926 promoted the differentiation of SHF stem cell into hair follicle lineage in cashmere goats which was evaluated via indictor genes Keratin 7 and Keratin 17. Using RNA pull-down, we found that circRNA-1926 bound with miR-148a/b-3p. Additionally, our data indicated that circRNA-1926 promoted the expression of the CDK19 gene. Using dual-luciferase reporter assays, it was revealed that circRNA-1926 positively regulated the CDK19 expression through miR-148a/b-3p. The results from this study demonstrated that circRNA-1926 contributes the differentiation of SHF stem cells into hair follicle lineages in cashmere goats via sponging miR-148a/b-3p to enhance CDK19 expression.
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20
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Yin RH, Zhao SJ, Wang ZY, Zhu YB, Yin RL, Bai M, Fan YX, Wang W, Bai WL. LncRNA-599547 contributes the inductive property of dermal papilla cells in cashmere goat through miR-15b-5p/Wnt10b axis. Anim Biotechnol 2020; 33:493-507. [PMID: 32808845 DOI: 10.1080/10495398.2020.1806860] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The lncRNA-599547 (619-nt in length) is identified in secondary hair follicle (SHF) of cashmere goat, but its functional roles in regulating the inductive property of dermal papilla cells (DPCs) remains unknown. We found that lncRNA-599547 had significantly higher expression in dermal papilla of cashmere goat SHF at anagen than its counterpart at telogen. The overexpression of lncRNA-599547 led to a significant increase of ALP and LEF1 expression in DPCs (p < 0.05), whereas, the siLncRNA-1 mediated silencing of lncRNA-599547 significantly down-regulated the expression of ALP and LEF1 in DPCs (p < 0.05). Based on biotin-labeled RNA pull-down assay, we found that lncRNA-599547 directly interacted with chi-miR-15b-5p in DPCs. Based on both overexpression and silencing analysis of lncRNA-599547, our results indicate that lncRNA-599547 promotes the expression of Wnt10b in DPCs but without modulating its promoter methylation level. Using the mRNA-3'UTR fragments of goat Wnt10b containing the predicted binding sites of chi-miR-15b-5p in Dual-luciferase Reporter Assays, we show that lncRNA-599547 modulates the expression of Wnt10b at the chi-miR-15b-5p mediated post-transcriptional level. Taken together, our results indicate that lncRNA-599547 sponges miR-15b-5p to positively regulate the expression of Wnt10 gene, and thereby contributes the inductive property of DPCs in cashmere goat.
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Affiliation(s)
- Rong H Yin
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Su J Zhao
- Sichuan Animal Science Academy, Chengdu, Sichuan, China.,Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Ze Y Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Yu B Zhu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Rong L Yin
- Research Academy of Animal Husbandry and Veterinary Medicine Sciences of Jilin Province, Changchun, China
| | - Man Bai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Yi X Fan
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Wei Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
| | - Wen L Bai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, P. R. China
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21
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Cultivation of Hair Matrix Cells from Cashmere Goat Skins and Exemplified Applications. Animals (Basel) 2020; 10:ani10081400. [PMID: 32806500 PMCID: PMC7460477 DOI: 10.3390/ani10081400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 11/17/2022] Open
Abstract
Simple Summary A large scale of sequencing data pertaining to cashmere growth on cashmere goats have not been cost-effectively used due to the lack of in vitro cellular models, especially for hair matrix cells (HMCs)—the precursors of hair-forming keratinocytes, causing an enormous waste of data resources. Herein, we successfully isolated and cultivated previously unreported HMCs from cashmere goat skins and identified them morphologically and molecularly via their distinct appearance and signature genes’ expression from spatially adjacent dermal papilla cells. Through monitoring the effects of calcium and all-trans retinoic acid on HMCs using various biological techniques, we displayed that the cells are useful models to explore unsolved issues in hair fiber growth on goats. Therefore, our present success paves the road for further utilizing currently deposited data to unveil the secrets of cashmere growth and, ultimately, improve the quantity and quality of animal fibers. Abstract A functional interpretation of filtered candidates and predicted regulatory pathways related to cashmere growth from sequencing trials needs available cell models, especially for hair matrix cells (HMCs), whose continual proliferation and differentiation result in rapid hair growth. To fulfill such goals, we herein obtained primary goat HMCs via a microdissection-based method; optimized the selection of the culture medium and coating substances for better cell maintenance; and exemplified their usefulness through examining the effects of calcium and all-trans retinoic acid (ATRA) on cells using immunoblotting, flow cytometry, and other techniques. As a result, we successfully acquired primary and passaged goat HMCs with typical keratinocyte morphology. Calcium-free RPMI (Roswell Park Memorial Institute) 1640 and MEM (minimum Eagle’s medium) outperformed normal DMEM/F12 (Dulbecco’s modified Eagle’s medium/Nutrient Mixture F-12) on long-term cell maintenance, whereas serum-free media K-SFM and EpiLife failed to support cell growth. HMCs differed molecularly and morphologically from their neighbor dermal papilla cells on expressions of feature genes, such as HOXC13, and on characteristic keratinocyte-like appearances versus fibroblast shapes, respectively. Higher calcium concentrations significantly stimulated the expression of the genes (e.g., KRT1 and IVL) involved in keratinocyte differentiation and, promoted cell proliferation. Moreover, 10−5 M ATRA obviously boosted goat HMC expansions and changed their cell cycle distributions compared to the controls. Our study shines a light on researches exploring the mechanisms underlying the growth of cashmere.
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22
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Yin RH, Wang YR, Zhao SJ, Yin RL, Bai M, Wang ZY, Zhu YB, Cong YY, Liu HY, Bai WL. LncRNA-599554 sponges miR-15a-5p to contribute inductive ability of dermal papilla cells through positive regulation of the expression of Wnt3a in cashmere goat. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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23
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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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24
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Comprehensive analysis of circRNAs from cashmere goat skin by next generation RNA sequencing (RNA-seq). Sci Rep 2020; 10:516. [PMID: 31949277 PMCID: PMC6965140 DOI: 10.1038/s41598-019-57404-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
Circular RNA (circRNA) is endogenous non-coding RNA (ncRNA) with a covalently closed circular structure. It is mainly generated through RNA alternative splicing or back-splicing. CircRNA is known in the majority of eukaryotes and very stable. However, knowledge of the circRNA involved in regulating cashmere fineness is limited. Skin samples were collected from Liaoning cashmere goats (LCG) and Inner Mongolia cashmere goats (MCG) during the anagen period. For differentially expressed circRNAs, RNA sequencing was performed, and the analysis led to an identification of 17 up-regulated circRNAs and 15 down-regulated circRNAs in LCG compared with MCG skin samples. In order to find the differentially expressed circRNAs in LCG, we carried out qPCRs on 10 candidate circRNAs in coarse type skin of LCG (CT-LCG) and fine type skin of LCG (FT-LCG). Four circRNAs: ciRNA128, circRNA6854, circRNA4154 and circRNA3620 were confirmed to be significantly differential expression in LCG. Also, a regulatory network of circRNAs-miRNAs was bioinformatically deduced and may help to understand molecular mechanisms of potential circRNA involvement in regulating cashmere fineness.
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25
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Huang J, Zheng Q, Wang S, Wei X, Li F, Ma Y. High-Throughput RNA Sequencing Reveals NDUFC2-AS lncRNA Promotes Adipogenic Differentiation in Chinese Buffalo ( Bubalus bubalis L). Genes (Basel) 2019; 10:genes10090689. [PMID: 31500202 PMCID: PMC6770997 DOI: 10.3390/genes10090689] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/02/2019] [Accepted: 09/05/2019] [Indexed: 12/21/2022] Open
Abstract
The buffalo (Bubalus bubalis L.) is prevalent in China and the increasing demand for meat production has changed its role from being a beast of burden to a meat source. The low fat deposition level has become one of the main barriers for its use in meat production. It is urgent to reveal factors involved in fat deposition in buffalo. This study performed RNA sequencing to investigate both long noncoding RNAs (lncRNAs) and mRNAs of adipose tissues in young and adult buffalos. A total of 124 lncRNAs and 2008 mRNAs showed differential expression patterns between young and adult samples. Coexpression analysis and functional enrichment revealed 585 mRNA–lncRNA pairs with potential function in fat deposition. After validation by qRT-PCR, we focused on a lncRNA transcribed from the ubiquinone oxidoreductase subunit C2 (NDUFC2) antisense (AS) strand which showed high correlation with thyroid hormone responsive protein (THRSP). NDUFC2-AS lncRNA is highly expressed in adipose tissue and maturation adipocytes and mainly exists in the nucleus. Functional assays demonstrated that NDUFC2-AS lncRNA promotes adipogenic differentiation by upregulating the expression levels of THRSP and CCAAT enhancer binding protein alpha (C/EBPα) in buffalo. These results indicate that NDUFC2-AS lncRNA promotes fat deposition in buffalo.
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Affiliation(s)
- Jieping Huang
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Qiuzhi Zheng
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Shuzhe Wang
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Xuefeng Wei
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Fen Li
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
- School of Agriculture, Ningxia University, Yinchuan, Ningxia 750021, China.
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26
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Discovery and molecular analysis of conserved circRNAs from cashmere goat reveal their integrated regulatory network and potential roles in secondary hair follicle. ELECTRON J BIOTECHN 2019. [DOI: 10.1016/j.ejbt.2019.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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27
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Ma S, Wang Y, Zhou G, Ding Y, Yang Y, Wang X, Zhang E, Chen Y. Synchronous profiling and analysis of mRNAs and ncRNAs in the dermal papilla cells from cashmere goats. BMC Genomics 2019; 20:512. [PMID: 31221080 PMCID: PMC6587304 DOI: 10.1186/s12864-019-5861-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 05/29/2019] [Indexed: 12/14/2022] Open
Abstract
Background Dermal papilla cells (DPCs), the “signaling center” of hair follicle (HF), delicately master continual growth of hair in mammals including cashmere, the fine fiber annually produced by secondary HF embedded in cashmere goat skins. Such unparalleled capacity bases on their exquisite character in instructing the cellular activity of hair-forming keratinocytes via secreting numerous molecular signals. Past studies suggested microRNA (miRNAs) and long non-coding RNAs (lncRNAs) play essential roles in a wide variety of biological process, including HF cycling. However, their roles and related molecular mechanisms in modulating DPCs secretory activities are still poorly understood. Results Here, we separately cultivated DPCs and their functionally and morphologically distinct dermal fibroblasts (DFs) from cashmere goat skins at anagen. With the advantage of high throughput RNA-seq, we synchronously identified 2540 lncRNAs and 536 miRNAs from two types of cellular samples at 4th passages. Compared with DFs, 1286 mRNAs, 18 lncRNAs, and 42 miRNAs were upregulated, while 1254 mRNAs, 53 lncRNAs and 44 miRNAs were downregulated in DPCs. Through overlapping with mice data, we ultimately defined 25 core signatures of DPCs, including HOXC8 and RSPO1, two crucial activators for hair follicle stem cells (HFSCs). Subsequently, we emphatically investigated the impacts of miRNAs and lncRNAs (cis- and trans- acting) on the genes, indicating that ncRNAs extensively exert negative and positive effects on their expressions. Furthermore, we screened lncRNAs acting as competing endogenous RNAs (ceRNAs) to sponge miRNAs and relief their repressive effects on targeted genes, and constructed related lncRNAs-miRNAs-HOXC8/RSPO1 interactive lines using bioinformatic tools. As a result, XR_310320.3-chi-miR-144-5p-HOXC8, XR_311077.2-novel_624-RSPO1 and others lines appeared, displaying that lncRNAs might serve as ceRNAs to indirectly adjust HFSCs status in hair growth. Conclusion The present study provides an unprecedented inventory of lncRNAs, miRNAs and mRNAs in goat DPCs and DFs. We also exhibit some miRNAs and lncRNAs potentially participate in the modulation of HFSCs activation via delicately adjusting core signatures of DPCs. Our report shines new light on the latent roles and underlying molecular mechanisms of ncRNAs on hair growth. Electronic supplementary material The online version of this article (10.1186/s12864-019-5861-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sen Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ying Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Guangxian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.,Department of Animal Science, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, China
| | - Yi Ding
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yuxin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Enping Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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28
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Yan H, Gao Y, Ding Q, Liu J, Li Y, Jin M, Xu H, Ma S, Wang X, Zeng W, Chen Y. Exosomal Micro RNAs Derived from Dermal Papilla Cells Mediate Hair Follicle Stem Cell Proliferation and Differentiation. Int J Biol Sci 2019; 15:1368-1382. [PMID: 31337968 PMCID: PMC6643152 DOI: 10.7150/ijbs.33233] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/24/2019] [Indexed: 12/17/2022] Open
Abstract
Recent studies have demonstrated that dermal papilla cell-derived exosomes (DPC-Exos) promote the anagen stage of hair follicle (HF) growth and delay the catagen stage. However, the roles of DPC-Exos in regulating hair follicle stem cell (HFSC) quiescence and activation remain unknown. Here, we found that HFSC differentiation was induced by co-culture with DPCs, and that DPC-Exos attached to the surface of HFSCs. Using micro RNA (miRNA) high-throughput sequencing, we identified 111 miRNAs that were significantly differentially expressed between DPC-Exos and DPCs, and the predicted target genes of the top 34 differentially expressed miRNAs indicated that DPC-Exos regulate HFSCs proliferation and differentiation via genes involved in cellular signal transduction, fatty acid expression regulation, and cellular communication. The overexpression of miR-22-5p indicated that it negatively regulates HFSC proliferation and LEF1 was revealed as the direct target gene of miR-22-5p. We therefore propose the miR-22-5p-LEF1 axis as a novel pathway regulating HFSC proliferation.
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Affiliation(s)
- Hailong Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Life Science Research Center, Yulin University, Yulin, China
| | - Ye Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- School of Medicine, Shanxi Datong University, Datong, China
| | - Qiang Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yan Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Miaohan Jin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Han Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Sen Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wenxian Zeng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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29
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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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30
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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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31
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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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32
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Jiao Q, Yin RH, Zhao SJ, Wang ZY, Zhu YB, Wang W, Zheng YY, Yin XB, Guo D, Wang SQ, Zhu YX, Bai WL. Identification and molecular analysis of a lncRNA-HOTAIR transcript from secondary hair follicle of cashmere goat reveal integrated regulatory network with the expression regulated potentially by its promoter methylation. Gene 2018; 688:182-192. [PMID: 30521888 DOI: 10.1016/j.gene.2018.11.084] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 11/05/2018] [Accepted: 11/22/2018] [Indexed: 01/17/2023]
Abstract
The HOTAIR transcript is transcribed from the antisense strand within the HOXC gene cluster, and it is thought to play a role in regulating the inductive capacity of dermal papilla cells during the reconstruction of hair-follicle. In the current investigation, we firstly isolated and characterized a lncRNA-HOTAIR transcript from the secondary hair follicle of cashmere goat. Also, we analyzed its transcriptional pattern and methylation level of HOTAIR gene promoter in secondary hair follicle of cashmere goat during anagen and telogen stages. Nucleotide composition analysis indicated that the contents of Adenine (A) and Thymine (T) are higher than that of Guanine (G) and Cytosine (C) in lncRNA-HOTAIR transcript of cashmere goat with the highest frequency distribution of AG nucleotide pair (8.06%). The regulatory network analysis showed a directly or indirectly complex regulatory relationships between lncRNA-HOTAIR of cashmere goat and its potential target molecules: miRNAs, mRNAs and proteins. Also, we showed that lncRNA-HOTAIR was properly transcribed at both anagen and telogen stages of secondary hair follicle of cashmere goat with the anagen being significantly higher than telogen in its expression, which suggest that lncRNA-HOTAIR transcript might be involved in the reconstruction of secondary hair follicle with the formation and growth of cashmere fiber. Taken together with methylation analysis of HOTAIR gene promoter, our data suggest that the promoter methylation of HOTAIR gene most likely is involved in its transcriptional suppression in secondary hair follicle of cashmere goat.
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Affiliation(s)
- Qian Jiao
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Rong H Yin
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Su J Zhao
- Sichuan Animal Science Academy, Chengdu 610066, PR China
| | - Ze Y Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Yu B Zhu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Wei Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Yuan Y Zheng
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Xian B Yin
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Dan Guo
- Academy of Animal Husbandry Science of Liaoning Province, Liaoyang 111000, PR China
| | - Shi Q Wang
- Academy of Animal Husbandry Science of Liaoning Province, Liaoyang 111000, PR China
| | - Yan X Zhu
- Academy of Animal Husbandry Science of Liaoning Province, Liaoyang 111000, PR China
| | - Wen L Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China.
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Su R, Fan Y, Qiao X, Li X, Zhang L, Li C, Li J. Transcriptomic analysis reveals critical genes for the hair follicle of Inner Mongolia cashmere goat from catagen to telogen. PLoS One 2018; 13:e0204404. [PMID: 30356261 PMCID: PMC6200190 DOI: 10.1371/journal.pone.0204404] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 09/07/2018] [Indexed: 12/12/2022] Open
Abstract
There are two main types of hair follicle in Inner Mongolia Cashmere goats, the primary hair follicle (PHF) producing hair fibers and the secondary hair follicle (SHF) producing cashmere fibers. Of both fibers from cashmere-bearing goats in Aerbasi, Inner Mongolia, the timing of cyclical phases for the cashmere have been well clarified but hair fibers have been less noticeable. Herein, we evaluated transcriptome of PHF and SHF from the same three goats in Aerbasi at the catagen- and telogen phase of cashmere growth. We totally found 1977 DEGs between PHFs at the telogen and catagen phases of SHF, 1199 DEGs between telogen- and catagen SHF, 2629 DEGs between PHF at the catagen phase of SHF and catagen SHF, and 755 DEGs between PHF at the telogen phase of SHF and telogen SHF. By analyzing gene functions based on GO and KEGG database, we found that the DEGs have functions in muscle contraction and muscle filament sliding between catagen- and telogen SHF, indicating that arrector pilli muscles might play a role on the transition from catagen to telogen. Moreover, considering that the enriched GO and KEGG categories of the DEGs between PHF and SHF, we suggested that part of PHF might rest in their own anagen phase when SHF are at catagen, but PHF might enter into the telogen phase at SHF’s telogen. Finally, we highly recommended the several potential genes acting as the regulators of the transition between growth phases including IL17RB and eight members of ZNF. These results provide insight into molecular mechanisms on the transition of SHF from catagen to telogen together with PHF’s growth situation at SHF’s catagen and telogen in Inner Mongolia Cashmere goats.
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Affiliation(s)
- Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, China
| | - Yixing Fan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xian Qiao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xiaokai Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Lei Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Chun Li
- College of Animal Science, Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Autonomous Region, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Inner Mongolia Autonomous Region, Hohhot, China
- * E-mail:
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Li C, Li Y, Zhou G, Gao Y, Ma S, Chen Y, Song J, Wang X. Whole-genome bisulfite sequencing of goat skins identifies signatures associated with hair cycling. BMC Genomics 2018; 19:638. [PMID: 30153818 PMCID: PMC6114738 DOI: 10.1186/s12864-018-5002-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/08/2018] [Indexed: 01/07/2023] Open
Abstract
Background Hair follicles (HFs), upon development, undergo repetitive cycles of growth (anagen), regression (catagen), and rest (telogen). The transition between the stages is determined by multiple molecular signals, including DNA methylation, which plays important roles in mammalian cellular identity and is essential for the development of HFs. Secondary hair follicles (SHFs) in cashmere goat exhibit classic cyclic hair development, and little has been done on a genome-wide scale to examine potentially methylated genes involved in the hair cyclic transition. Results Genome-wide DNA methylation profiles between skin tissues sampled during the anagen and telogen stages in cashmere goats were investigated using whole-genome bisulfite sequencing (WGBS). The methylation status was observed to be higher in the skin samples with HFs in the telogen than those in the anagen stage. A total of 1311 differentially methylated regions (DMRs) were identified between the two groups, which contained 493 fully annotated DMR-related genes (DMGs) (269 Hyper- DMGs and 224 Hypo-DMGs). Furthermore, a significant over-representation of the functional categories for DMGs related to immune response and intercellular crosstalk during hair cycling was observed. By integrating DNA methylation and mRNA expression data, we revealed that four genes (FMN1, PCOLCE, SPTLC3, and COL5A1) are crucial factors for elucidating epigenetic mechanisms contributing to the telogen-to-anagen transition. Conclusion Our study provided systematic methylome maps pertaining to the hair cycling stages (anagen vs telogen) at a single-base resolution, and revealed stage-specific methylation loci during cashmere growth or quiescence. Furthermore, we identified epigenetically regulated genes that are potentially involved in HF development and growth in cashmere goats, and likely in other mammal species. Electronic supplementary material The online version of this article (10.1186/s12864-018-5002-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yan Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Guangxian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ye Gao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Sen Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
| | - Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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