Hair follicle transcriptome profiles during the transition from anagen to catagen in Cashmere goat (Capra hircus)

Metabolomics reveals metabolites associated with hair follicle cycle in cashmere goats

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.

CeRNA regulates network and expression and SNP effect on NFKBIA of cashmere fineness

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.

Analysis of m6A methylation in skin tissues of different sex Liaoning cashmere goats

N⁶-methyladenosine (m⁶A) is the most frequent internal modification of mRNA and lncRNA in eukaryotes. We used two high-throughput sequencing method, m⁶A-seq and RNA-seq to identify pivotal m⁶A-modified genes in cashmere fineness and fiber growth. 8062 m⁶A peaks were detected by m⁶A-seq, including 2157 upregulated and 6445 downregulated. Furthermore, by comparing m⁶A-modified genes of the male Liaoning Cashmere Goat (M-LCG) and female Liaoning Cashmere Goat (F-LCG) skin tissues, we get 862 differentially expressed m⁶A-modified genes. To identify differently expressed m⁶A genes associated with cashmere fineness, 11 genes were selected for validation using real time fluorescent quantitative PCR in M-LCG and F-LCG. This study provides an acadamic basis on the molecular regulation mechanism of m⁶A modification in cashmere growth process.

The Dynamic Change of Gene-Regulated Networks in Cashmere Goat Skin with Seasonal Variation

The Cashmere goat (Capra hircus) is renowned for its high-quality fiber production trait. The hair cycle in Cashmere goat has an annual rhythm. To deepen the understanding of the molecular foundation of annual rhythm in the skin of Cashmere goat, we did a comparative analysis of the Cashmere goat skin transcriptome all year round. 4002 Differentially expressed genes (DEGs) were identified with seasonal variations. 12 months transcriptome were divided into four developmental stages: Jan-Mar, Apr-Jul, Aug-Oct, and Nov-Dec based on gene expression patterns. 13 modules of highly correlated genes in skin were identified using WGCNA. Ten of these modules were consistent with the development stages. The gene function of those genes in each module was analyzed by functional enrichment. The results indicated that Wnt and Hedgehog signaling pathways were inhibited from January to March and activated from April to July. The cutaneous immune system of Cashmere goats has high activity from August to October. Fatty acid metabolism dominates goat skin from November to December. This study provides new information related to the annual skin development cycle, which could provide molecular biological significance for understanding the seasonal development and response to the annual rhythm of skin.

Inner Mongolian Cashmere Goat Secondary Follicle Development Regulation Research Based on mRNA-miRNA Co-analysis

Inner Mongolia cashmere goats, as an important part of animal husbandry production, play an important role in animal fiber industry. In recent years, scientific research has made a lot of explorations on the molecular regulation mechanism of hair follicle cycle growth, but few studies have been reported on the development of cashmere hair in fetal period. This study was based on the completion of 21 skin samples of mRNA and miRNA sequencing in 7 fetal periods (45 days, 55 days,65 days,75 days,95 days,115 days and 135 days) of the Inner Mongolia Cashmere goat. The target genes of miRNA associated with the development of secondary hair follicles in the cashmere goats were selected through the combination analysis of mRNA and miRNA data. Then the overexpression vector was constructed and the interaction between the miRNA and the target gene was identified by Dual-Luciferase Reporter Gene System. The function and interaction relationship of chi-miR-199a-5p and TGF-β2 were verified by RT-qPCR and western blot at the level of the fibroblasts in Inner Mongolia Cashmere goat. It provides a theoretical basis for further study of miRNA and its target genes regulating the occurrence and development of skin hair follicles. As the result shows, the expression trends of 7 genes (BAMBI, SMAD1, LTBP1, PPP2R1B, ID4, BMP8B and PITX2) and 7 miRNA (chi-miR-17-5p, chi-miR-125b-3p, chi-miR-21-5p, chi-miR-143-5p and chi-miR-106b-5p) in the skin samples for the seven stages of the fetus were shown to be consistent with the sequencing results. the results of sequencing are reliable. The correlation coefficient of TGF-β2 and chi-miR-199a-5p in fetal 45d-135d expression is −0.84, showing a strong negative correlation, The target relationship was preliminarily judged. The results of double luciferase vector report showed that chi-miR-199a-5p significantly decreased the expression of luciferase in TGF-β2 3′UTR, It is determined that there is a reciprocal relationship between them at a specific time. We transfected chi-miR199a-5p-FAM mimics into fibroblasts cultured in vitro from Inner Mongolia cashmere goats. After transfection, the cells were harvested to extract total RNA and protein. The mRNA and protein expression levels of TGF-β2 in fibroblasts were detected by RT-qPCR and western blot. It was verified that chi-miR-199a-5p inhibited TGF-β2 expression at both mRNA and protein translation levels in fibroblasts. At the same time, it was again proved that the TGF-β2 gene is a target gene of chi-miR199a-5p.

m6A Methylation Analysis of Differentially Expressed Genes in Skin Tissues of Coarse and Fine Type Liaoning Cashmere Goats

N6-methyladenosine (m6A) is the most common internal modification in mRNAs of all higher eukaryotes. Here we perform two high-throughput sequencing methods, m6A-modified RNA immunoprecipitation sequence (MeRIP-seq) and RNA sequence (RNA-seq) to identify key genes with m6A modification in cashmere fiber growth. A total of 9,085 m6A sites were differentially RNA m6A methylated as reported from by MeRIP-seq, including 7,170 upregulated and 1,915 downregulated. In addition, by comparing m6A-modified genes between the fine-type Liaoning cashmere goat (FT-LCG) and coarse-type Liaoning Cashmere Goat (CT-LCG) skin samples, we obtain 1,170 differentially expressed genes. In order to identify the differently methylated genes related to cashmere fiber growth, 19 genes were selected to validate by performing qRT-PCR in FT-LCG and CT-LCG. In addition, GO enrichment analysis shows that differently methylated genes are mainly involved in keratin filament and intermediate filament. These findings provide a theoretical basis for future research on the function of m6A modification during the growth of cashmere fiber.

Integrated Analysis of Methylome and Transcriptome Changes Reveals the Underlying Regulatory Signatures Driving Curly Wool Transformation in Chinese Zhongwei Goats

The Zhongwei goat is kept primarily for its beautiful white, curly pelt that appears when the kid is approximately 1 month old; however, this representative phenotype often changes to a less curly phenotype during postnatal development in a process that may be mediated by multiple molecular signals. DNA methylation plays important roles in mammalian cellular processes and is essential for the initiation of hair follicle (HF) development. Here, we sought to investigate the effects of genome-wide DNA methylation by combining expression profiles of the underlying curly fleece dynamics. Genome-wide DNA methylation maps and transcriptomes of skin tissues collected from 45- to 108-day-old goats were used for whole-genome bisulfite sequencing (WGBS) and RNA sequencing, respectively. Between the two developmental stages, 1,250 of 3,379 differentially methylated regions (DMRs) were annotated in differentially methylated genes (DMGs), and these regions were mainly related to intercellular communication and the cytoskeleton. Integrated analysis of the methylome and transcriptome data led to the identification of 14 overlapping genes that encode crucial factors for wool fiber development through epigenetic mechanisms. Furthermore, a functional study using human hair inner root sheath cells (HHIRSCs) revealed that, one of the overlapping genes, platelet-derived growth factor C (PDGFC) had a significant effect on the messenger RNA expression of several key HF-related genes that promote cell migration and proliferation. Our study presents an unprecedented analysis that was used to explore the enigma of fleece morphological changes by combining methylome maps and transcriptional expression, and these data revealed stage-specific epigenetic changes that potentially affect fiber development. Furthermore, our functional study highlights a possible role for the overlapping gene PDGFC in HF cell growth, which may be a predictable biomarker for fur goat selection.

Transcriptomic Analysis of Coding Genes and Non-Coding RNAs Reveals Complex Regulatory Networks Underlying the Black Back and White Belly Coat Phenotype in Chinese Wuzhishan Pigs

Coat color is one of the most important characteristics for distinguishing Chinese indigenous pig breeds. In Wuzhishan pigs, the animals have black on the back and white on the abdomen. However, the molecular genetic basis of this phenotype is unclear. In this study, we used high-throughput RNA sequencing to compare expression profiles of coding and non-coding RNAs from white and black skin samples obtained from individual Wuzhishan pigs. The expression profiling revealed that 194 lncRNAs (long non-coding RNAs), 189 mRNAs (messenger RNAs), and 162 miRNAs (microRNAs) had significantly different levels of expression (|log₂ fold change| > 1, p-value < 0.05) in white and black skin. Compared to RNA levels in black skin, white skin had higher levels of expression of 185 lncRNAs, 181 mRNAs, and 23 miRNAs and lower levels of expression of 9 lncRNAs, 8 mRNAs, and 139 miRNAs. Functional analysis suggested that the differentially expressed transcripts are involved in biological processes such as melanin biosynthesis, pigmentation and tyrosine metabolism. Several key genes involved in melanogenesis, including MLANA, PMEL, TYR, TYRP1, DTC, TRPM1 and CAMK2A, had significantly different levels of expression in the two skin tissues. Potential lncRNA–miRNA–gene interactions were also examined. A total of 15 lncRNAs, 11 miRNAs and 7 genes formed 23 lncRNA–miRNA–gene pairs, suggesting that complex regulatory networks of coding and non-coding genes underlie the coat color trait in Wuzhishan pigs. Our study provides a foundation for understanding how lncRNA, miRNA and genes interact to regulate coat color in black-back/white-belly pigs. We also constructed lncRNA–miRNA–gene interaction networks to elucidate the complex molecular mechanisms underlying skin physiology and melanogenesis. The results extend our knowledge about the diversity of coat color among different domestic animals and provide a foundation for studying novel mechanisms that control coat color in Chinese indigenous pigs.

Genetic effects of vascular endothelial growth factor and its receptor 2 on feather maturity in three chicken breeds

1. The goal of the current study was to evaluate the genetic effects of the vascular endothelial growth factor (VEGF) and its receptor (VEGFR-2) on feather maturity in the Qingyuan partridge chicken, Guangxi sanhuang chicken and Princess chicken. 2. Both SSCP-PCR and qPCR were employed to detect the polymorphism and gene expression of the VEGF and VEGFR-2 genes. 3. Four SNPs were identified in the VEGFR-2 gene. Exon10-A69G was associated with feather maturity (P < 0.01). Princess chickens with the genotype EF had higher feather maturity scores (P < 0.01). Higher expression levels of VEGF and VEGFR-2 were detected in the immature feather group of Qingyuan partridge chickens, especially in the skin. 4. The VEGF and VEGFR-2 genes play critical roles in feather maturity. In addition, exon10-A69G and genotype EF in the Princess chicken could potentially be utilised as genetic markers to improve efficiency in breeding.

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

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.

Transcriptomic analysis reveals critical genes for the hair follicle of Inner Mongolia cashmere goat from catagen to telogen

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.

Long noncoding RNA and gene expression analysis of melatonin-exposed Liaoning cashmere goat fibroblasts indicating cashmere growth

Cashmere produced from Liaoning cashmere goat is highly valuable. Melatonin is an important factor affecting cashmere growth and can regulate the growth cycle via effects on gene expression. Long noncoding RNAs (lncRNAs) regulate gene expression, but detailed studies of their effect on hair growth are lacking. To explore how lncRNA mediates the effects of melatonin on cashmere growth, we used RNA-Seq including a control condition (C) and three melatonin treatments (1.0 g/L 24 h (M1_24H), 0.2 g/L 24 h (M2_24H), 0.2 g/L 72 h (M2_72H)). M1_24H, M2_24H, and M2_72H had 32, 10, and 113 differentially expressed lncRNAs, respectively. Gene ontology (GO) and pathway analyses results showed that melatonin was most beneficial to cashmere growth at 0.2 g/L 72 h, and nuclear factor (NF)-κB signaling corresponding to an effect of LncRNA MTC was involved in hair follicle development. We found that melatonin upregulated XLOC_005914 lncRNA (LncRNA MTC). Proliferation increased in the 0.2 g/L 72 h condition and cells with high LncRNA MTC expression, but it was reduced in fibroblasts with knocked down LncRNA MTC expression. This is the first report that LncRNA MTC promotes fibroblast proliferation and regulates hair follicle development and cashmere growth by activating NF-κB signaling.

Transcriptomic inspection revealed a possible pathway regulating the formation of the high-quality brush hair in Chinese Haimen goat (Capra hircus)

The high-quality brush hair, or Type III brush hair, is coarse hair but with a tip and little medulla, which uniquely grows in the cervical carina of Chinese Haimen goat (Capra hircus). To unveil the mechanism of the formation of Type III brush hair in Haimen goats, transcriptomic RNAseq technology was used for screening of differentially expressed genes (DEGs) in the skin samples of the Type III and the non-Type III hair goats, and these DEGs were analysed by KEGG pathway analysis. The results showed that a total of 295 DEGs were obtained, mainly from three main functional types: cellular component, molecular function and biological process. These DEGs were mainly enriched in three KEGG pathways, such as protein processing in endoplasmic reticulum, MAPK, and complement and coagulation cascades. These DEGs gave hints to a possible mechanism, under which heat stress possibly initiated the formation. The study provided some useful biological information, which could give a new view about the roles of certain factors in hair growth and give hints on the mechanism of the formation of the Type III brush hair in Chinese Haimen goat.

Comparative Transcriptome Analysis of Mink (Neovison vison) Skin Reveals the Key Genes Involved in the Melanogenesis of Black and White Coat Colour

Farmed mink (Neovison vison) is one of the most important fur-bearing species worldwide, and coat colour is a crucial qualitative characteristic that contributes to the economic value of the fur. To identify additional genes that may play important roles in coat colour regulation, Illumina/Solexa high-throughput sequencing technology was used to catalogue the global gene expression profiles in mink skin with two different coat colours (black and white). RNA-seq analysis indicated that a total of 12,557 genes were differentially expressed in black versus white minks, with 3,530 genes up-regulated and 9,027 genes down-regulated in black minks. Significant differences were not observed in the expression of MC1R and TYR between the two different coat colours, and the expression of ASIP was not detected in the mink skin of either coat colour. The expression levels of KITLG, LEF1, DCT, TYRP1, PMEL, Myo5a, Rab27a and SLC7A11 were validated by qRT-PCR, and the results were consistent with RNA-seq analysis. This study provides several candidate genes that may be associated with the development of two coat colours in mink skin. These results will expand our understanding of the complex molecular mechanisms underlying skin physiology and melanogenesis in mink and will provide a foundation for future studies.