scholarly journals Screening and Identification of LncRNAs Related to Villus Growth of Liaoning Cashmere Goats and Their Effects on Growth after FGF5 Treatment

2020 ◽  
Author(s):  
Mei Jin ◽  
Qin Feng Zhao ◽  
Ping Ni ◽  
Jun Piao ◽  
Ai Jing Piao
Keyword(s):  
Target Genes ◽  
Economic Value ◽  
Growth Cycle ◽  
Cashmere Goat ◽  
Lncrna Gene ◽  
Skin Cells ◽  
Non Coding Rna ◽  
Screening And Identification ◽  
Cashmere Goats ◽  
Long Non Coding Rna

Abstract (Background)Liaoning Cashmere Goat cashmere has high economic value FGF5 is an important factor regulating its growth. The role of long non-coding RNA (LncRNA) in the mammalian villus growth cycle has still not been studied in detail.(Results)We demonstrated that treatment of skin cells with FGF5 inhibited the expression of LncRNA in cells, down-regulated the expression of the target genes CBS and CTH, and promoted the expression of related keratin genes k26, kap11.1. Overexpressing LncRNA reversed the inhibiting effect of FGF5 on the target genes CBS and CTH. (Conclusions)we believe that FGF5 can regulate the growth and development of Cashmere Goat hair by promoting the expression of related keratin and keratin-associated protein genes. This mechanism is achieved by inhibiting the expression of the LncRNA gene and then down-regulating the expression of the target genes CBS and CTH.

scholarly journals Screening and Identification of LncRNAs Related to Villus Growth of Liaoning Cashmere Goats and Their Effects on Growth after FGF5 Treatment

2020 ◽  
Author(s):  
Mei Jin ◽  
Qin Feng Zhao ◽  
Ping Ni ◽  
Jun Piao ◽  
Ai Jing Piao
Keyword(s):  
Target Genes ◽  
Economic Value ◽  
Growth Cycle ◽  
Cashmere Goat ◽  
Lncrna Gene ◽  
Skin Cells ◽  
Non Coding Rna ◽  
Screening And Identification ◽  
Cashmere Goats ◽  
Long Non Coding Rna

Abstract (Background) Liaoning Cashmere Goat cashmere has high economic value FGF5 is an important factor regulating its growth. The role of long non-coding RNA (LncRNA) in the mammalian villus growth cycle has still not been studied in detail.(Results) We demonstrated that treatment of skin cells with FGF5 inhibited the expression of LncRNA in cells, down-regulated the expression of the target genes CBS and CTH, and promoted the expression of related keratin genes k26, kap11.1. Overexpressing LncRNA reversed the inhibiting effect of FGF5 on the target genes CBS and CTH. (Conclusions) we believe that FGF5 can regulate the growth and development of Cashmere Goat hair by promoting the expression of related keratin and keratin-associated protein genes. This mechanism is achieved by inhibiting the expression of the LncRNA gene and then down-regulating the expression of the target genes CBS and CTH.

scholarly journals Screening and Identification of LncRNAs Related to Villus Growth of Liaoning Cashmere Goats and Their Effects on Growth after FGF5 Treatment

2020 ◽  
Author(s):  
Mei Jin ◽  
Qin Feng Zhao ◽  
Ping Ni ◽  
Jun Piao ◽  
Ai Jing Piao
Keyword(s):  
Target Genes ◽  
Economic Value ◽  
Growth Cycle ◽  
Cashmere Goat ◽  
Lncrna Gene ◽  
Over Expression ◽  
Skin Cells ◽  
Non Coding Rna ◽  
Screening And Identification ◽  
Cashmere Goats

Abstract (Background)Liaoning cashmere goat cashmere has high economic value FGF5 is an important factor regulating its growth. The role of long non-coding RNA (LncRNA) in the mammalian villus growth cycle has still not been studied in detail.(Results)This study investigated how LncRNA mediates the effects of FGF5 on the growth of Liaoning cashmere goats. By using RNA-seq sequencing technology, over-expression and interference lentiviral technology and qPCR, we demonstrated that treatment of skin cells with FGF5 inhibited the expression of LncRNA in cells, down-regulated the expression of the target genes CBS and CTH, and promoted the expression of related keratin genes k26, kap11.1. Then, overexpressing LncRNA in skin cells reversed the inhibiting effect of FGF5 on the target genes CBS and CTH which further inhibited the expression of k26, kap11.1. Finally, we demonstrated the inhibition of CBS and CTH and elevation k26 and kap11.1 genes when the expression level of LncRNA gene is downregulated using RNA interference. (Conclusions)Therefore, we believe that FGF5 can regulate the growth and development of cashmere goat hair by promoting the expression of related keratin and keratin-associated protein genes. This mechanism is achieved by inhibiting the expression of the LncRNA gene and then down-regulating the expression of the target genes CBS and CTH.

scholarly journals Screening of cashmere fineness-related genes and their ceRNA network construction in cashmere goats

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Taiyu Hui ◽  
Yuanyuan Zheng ◽  
Chang Yue ◽  
Yanru Wang ◽  
Zhixian Bai ◽  
...  
Keyword(s):  
Circular Rna ◽  
Differentially Expressed ◽  
Transcriptional Level ◽  
Cashmere Goat ◽  
Cerna Network ◽  
Non Coding Rna ◽  
Potential Basis ◽  
Cashmere Goats ◽  
Regulatory Effects ◽  
Long Non Coding Rna

AbstractCompetitive endogenous RNA (ceRNA) is a transcript that can be mutually regulated at the post-transcriptional level by competing shared miRNAs. The ceRNA network connects the function of protein-encoded mRNA with the function of non-coding RNA, such as microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). However, compared with the ceRNA, the identification and combined analysis of lncRNAs, mRNAs, miRNAs, and circRNAs in the cashmere fineness have not been completed. Using RNA-seq technology, we first identified the miRNAs presented in Liaoning Cashmere Goat (LCG) skin, and then analyzed the mRNAs, lncRNAs, circRNAs expressed in LCG and Inner Mongolia cashmere goat (MCG) skin. As a result, 464 known and 45 new miRNAs were identified in LCG skin. In LCG and MCG skin, 1222 differentially expressed mRNAs were identified, 170 differentially expressed lncRNAs and 32 differentially expressed circRNAs were obtained. Then, qRT-PCR was used to confirm further the representative lncRNAs, mRNAs, circRNAs and miRNAs. In addition, miRanda predicted the relationships of ceRNA regulatory network among lncRNAs, circRNAs, miRNAs and mRNAs, the potential regulatory effects were investigated by Go and KEGG analysis. Through the screening and analysis of the results, the ceRNA network regulating cashmere fineness was constructed. LncRNA MSTRG14109.1 and circRNA452 were competed with miRNA-2330 to regulated the expression of TCHH, KRT35 and JUNB, which may provide a potential basis for further research on the process of regulating the cashmere fineness.

scholarly journals Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaolan Zhang ◽  
Qi Bao ◽  
Congjun Jia ◽  
Chen Li ◽  
Yongfang Chang ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Expression Profile ◽  
Target Genes ◽  
Differential Expression Analysis ◽  
Wnt Signaling Pathway ◽  
Hair Follicles ◽  
Sequence Conservation ◽  
Cashmere Goat ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Abstract Background Long non-coding RNA (lncRNA) as an important regulator has been demonstrated playing an indispensable role in the biological process of hair follicles (HFs) growth. However, their function and expression profile in the HFs cycle of yak are yet unknown. Only a few functional lncRNAs have been identified, partly due to the low sequence conservation and lack of identified conserved properties in lncRNAs. Here, lncRNA-seq was employed to detect the expression profile of lncRNAs during the HFs cycle of yak, and the sequence conservation of two datasets between yak and cashmere goat during the HFs cycle was analyzed. Results A total of 2884 lncRNAs were identified in 5 phases (Jan., Mar., Jun., Aug., and Oct.) during the HFs cycle of yak. Then, differential expression analysis between 3 phases (Jan., Mar., and Oct.) was performed, revealing that 198 differentially expressed lncRNAs (DELs) were obtained in the Oct.-vs-Jan. group, 280 DELs were obtained in the Jan.-vs-Mar. group, and 340 DELs were obtained in the Mar.-vs-Oct. group. Subsequently, the nearest genes of lncRNAs were searched as the potential target genes and used to explore the function of DELs by GO and KEGG enrichment analysis. Several critical pathways involved in HFs development such as Wnt signaling pathway, VEGF signaling pathway, and signaling pathways regulating pluripotency of stem cells, were enriched. To further screen key lncRNAs influencing the HFs cycle, 24 DELs with differ degree of sequence conservation were obtained via a comparative analysis of partial DELs with previously published lncRNA-seq data of cashmere goat in the HFs cycle using NCBI BLAST-2.9.0+, and 3 DELs of them were randomly selected for further detailed analysis of the sequence conservation properties. Conclusions This study revealed the expression pattern and potential function of lncRNAs during HFs cycle of yak, which would expand the knowledge about the role of lncRNAs in the HFs cycle. The findings related to sequence conservation properties of lncRNAs in the HFs cycle between the two species may provide valuable insights into the study of lncRNA functionality and mechanism.

scholarly journals Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak

2020 ◽  
Author(s):  
Xiaolan Zhang ◽  
Qi Bao ◽  
Congjun Jia ◽  
Chen Li ◽  
Yongfang Chang ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Expression Profile ◽  
Target Genes ◽  
Differential Expression Analysis ◽  
Wnt Signaling Pathway ◽  
Hair Follicles ◽  
Sequence Conservation ◽  
Cashmere Goat ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Abstract Background: Long non-coding RNA (lncRNA) as an important regulator has been demonstrated playing an indispensable role in the biological process of hair follicles (HFs) growth. However, their function and expression profile in the HFs cycle of yak are yet unknown. Only a few functional lncRNAs have been identified, partly due to the low sequence conservation and lack of identified conserved properties in lncRNAs. Here, lncRNA-seq was employed to detect the expression profile of lncRNAs during the HFs cycle of yak, and the sequence conservation of two datasets between yak and cashmere goat during the HFs cycle was analyzed. Results: A total of 2884 lncRNAs were identified in 5 phases (Jan., Mar., Jun., Aug., and Oct.) during the HFs cycle of yak. Then, differential expression analysis between 3 phases (Jan., Mar., and Oct.) was performed, revealing that 198 differentially expressed lncRNAs (DELs) were obtained in the Oct.-vs-Jan. group, 280 DELs were obtained in the Jan.-vs-Mar. group, and 340 DELs were obtained in the Mar.-vs-Oct. group. Subsequently, the nearest genes of lncRNAs were searched as the potential target genes and used to explore the function of DELs by GO and KEGG enrichment analysis. Several critical pathways involved in HFs development such as Wnt signaling pathway, VEGF signaling pathway, and signaling pathways regulating pluripotency of stem cells, were enriched. To further screen key lncRNAs influencing the HFs cycle, 24 DELs with differ degree of sequence conservation were obtained via a comparative analysis of partial DELs with previously published lncRNA-seq data of cashmere goat in the HFs cycle using NCBI BLAST-2.9.0+, and 3 DELs of them were randomly selected for further detailed analysis of the sequence conservation properties.Conclusions: This study revealed the expression pattern and potential function of lncRNAs during HFs cycle of yak, which would expand the knowledge about the role of lncRNAs in the HFs cycle. The findings related to sequence conservation properties of lncRNAs in the HFs cycle between the two species may provide valuable insights into the study of lncRNA functionality and mechanism.

scholarly journals Screening and Identification of LncRNAs Related to Villus Growth of Liaoning Cashmere Goats and Their Effects on Growth after FGF5 Treatment

2019 ◽  
Author(s):  
Mei Jin ◽  
Qin Feng Zhao ◽  
Ping Ni ◽  
Jun Piao ◽  
Ai Jing Piao
Keyword(s):  
Hair Follicle ◽  
Target Genes ◽  
Economic Value ◽  
Research Direction ◽  
Growth Cycle ◽  
Follicle Development ◽  
Keratin Gene ◽  
Cashmere Goats ◽  
Hair Follicle Development ◽  
New Research

Abstract Abstract : (Background)Liaoning cashmere goat cashmere has high economic value FGF5 is an important factor regulating its growth. The role of long non-coding RNA (LncRNA) in the mammalian villus growth cycle has still not been studied in detail.(Results)This study investigated how LncRNA mediates the effects of FGF5 on the growth of Liaoning cashmere goats. We screened for LncRNA related to hair follicle development and villus growth by RNA-seq sequencing. GO and pathway analysis determined that the optimal treatment conditions for FGF5 drugs are 10 -4 g/L for 72h (F4_72h). The expression levels of CBS, CTH, keratin gene K26, KAP11.1 were studied when overexpressing and interfering with LncRNA. (Conclusions)To our knowledge, this is the first study on how LncRNA regulates villi growth by regulating target genes and keratin genes in the amino acid metabolic pathway; it is also the first to open a new research direction for studying the mechanism of FGF5 in regulating hair follicle development and villus growth.

scholarly journals Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak

2020 ◽  
Author(s):  
Xiaolan Zhang ◽  
Qi Bao ◽  
Congjun Jia ◽  
Chen Li ◽  
Yongfang Chang ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Expression Profile ◽  
Target Genes ◽  
Differential Expression Analysis ◽  
Wnt Signaling Pathway ◽  
Hair Follicles ◽  
Sequence Conservation ◽  
Cashmere Goat ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Abstract Background: Long non-coding RNA (lncRNA) as an important regulator has been demonstrated playing an indispensable role in the biological process of hair follicles (HFs) growth. However, their function and expression profile in the HFs cycle of yak are yet unknown. Only a few functional lncRNAs have been identified, partly due to the low sequence conservation and lack of identified conserved properties in lncRNAs. Here, lncRNA-seq was employed to detect the expression profile of lncRNAs during the HFs cycle of yak, and the sequence conservation of two datasets between yak and cashmere goat during the HFs cycle was analyzed. Results: A total of 2884 lncRNAs were identified in 5 phases (Jan., Mar., Jun., Aug., and Oct.) during the HFs cycle of yak. Then, differential expression analysis between 3 phases (Jan., Mar., and Oct.) was performed, revealing that 198 differentially expressed lncRNAs (DELs) were obtained in the Oct.-vs-Jan. group, 280 DELs were obtained in the Jan.-vs-Mar. group, and 340 DELs were obtained in the Mar.-vs-Oct. group. Subsequently, the nearest genes of lncRNAs were searched as the potential target genes and used to explore the function of DELs by GO and KEGG enrichment analysis. Several critical pathways involved in HFs development such as Wnt signaling pathway, VEGF signaling pathway, and signaling pathways regulating pluripotency of stem cells, were enriched. To further screen key lncRNAs influencing the HFs cycle, 24 DELs with differ degree of sequence conservation were obtained via a comparative analysis of partial DELs with previously published lncRNA-seq data of cashmere goat in the HFs cycle using NCBI BLAST-2.9.0+, and 3 DELs of them were randomly selected for further detailed analysis of the sequence conservation properties.Conclusions: This study revealed the expression pattern and potential function of lncRNAs during HFs cycle of yak, which would expand the knowledge about the role of lncRNAs in the HFs cycle. The findings related to sequence conservation properties of lncRNAs in the HFs cycle between the two species may provide valuable insights into the study of lncRNA functionality and mechanism.

scholarly journals Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Guoning Wang ◽  
Xingfen Wang ◽  
Yan Zhang ◽  
Jun Yang ◽  
Zhikun Li ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Verticillium Wilt ◽  
Dynamic Characteristics ◽  
Target Genes ◽  
Acid Metabolism ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Alpha Linolenic Acid ◽  
Non Coding Rna ◽  
Long Non Coding Rna

Abstract Background Verticillium wilt is a widespread and destructive disease, which causes serious loss of cotton yield and quality. Long non-coding RNA (lncRNA) is involved in many biological processes, such as plant disease resistance response, through a variety of regulatory mechanisms, but their possible roles in cotton against Verticillium dahliae infection remain largely unclear. Results Here, we measured the transcriptome of resistant G. hirsutum following infection by V. dahliae and 4277 differentially expressed lncRNAs (delncRNAs) were identified. Localization and abundance analysis revealed that delncRNAs were biased distribution on chromosomes. We explored the dynamic characteristics of disease resistance related lncRNAs in chromosome distribution, induced expression profiles, biological function, and these lncRNAs were divided into three categories according to their induced expression profiles. For the delncRNAs, 687 cis-acting pairs and 14,600 trans-acting pairs of lncRNA-mRNA were identified, which indicated that trans-acting was the main way of Verticillium wilt resistance-associated lncRNAs regulating target mRNAs in cotton. Analyzing the regulation pattern of delncRNAs revealed that cis-acting and trans-acting lncRNAs had different ways to influence target genes. Gene Ontology (GO) enrichment analysis revealed that the regulatory function of delncRNAs participated significantly in stimulus response process, kinase activity and plasma membrane components. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that delncRNAs participated in some important disease resistance pathways, such as plant-pathogen interaction, alpha-linolenic acid metabolism and plant hormone signal transduction. Additionally, 21 delncRNAs and 10 target genes were identified as being involved in alpha-linolenic acid metabolism associated with the biosynthesis of jasmonic acid (JA). Subsequently, we found that GhlncLOX3 might regulate resistance to V. dahliae through modulating the expression of GhLOX3 implicated in JA biosynthesis. Further functional analysis showed that GhlncLOX3-silenced seedlings displayed a reduced resistance to V. dahliae, with down-regulated expression of GhLOX3 and decreased content of JA. Conclusion This study shows the dynamic characteristics of delncRNAs in multiaspect, and suggests that GhlncLOX3-GhLOX3-JA network participates in response to V. dahliae invasion. Our results provide novel insights for genetic improvement of Verticillium wilt resistance in cotton using lncRNAs.

scholarly journals Integrated Analysis of Long Non-Coding RNA and mRNA Expression Profiles in Testes of Calves and Sexually Mature Wandong Bulls (Bos taurus)

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2006
Author(s):  
Hongyu Liu ◽  
Ibrar Muhammad Khan ◽  
Huiqun Yin ◽  
Xinqi Zhou ◽  
Muhammad Rizwan ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Age Groups ◽  
Adherens Junction ◽  
Integrated Analysis ◽  
Sequencing Data ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Rna Interaction ◽  
Long Non Coding Rna

The mRNAs and long non-coding RNAs axes are playing a vital role in the regulating of post-transcriptional gene expression. Thereby, elucidating the expression pattern of mRNAs and long non-coding RNAs underlying testis development is crucial. In this study, mRNA and long non-coding RNAs expression profiles were investigated in 3-month-old calves and 3-year-old mature bulls’ testes by total RNA sequencing. Additionally, during the gene level analysis, 21,250 mRNAs and 20,533 long non-coding RNAs were identified. As a result, 7908 long non-coding RNAs (p-adjust < 0.05) and 5122 mRNAs (p-adjust < 0.05) were significantly differentially expressed between the distinct age groups. In addition, gene ontology and biological pathway analyses revealed that the predicted target genes are enriched in the lysine degradation, cell cycle, propanoate metabolism, adherens junction and cell adhesion molecules pathways. Correspondingly, the RT-qPCR validation results showed a strong consistency with the sequencing data. The source genes for the mRNAs (CCDC83, DMRTC2, HSPA2, IQCG, PACRG, SPO11, EHHADH, SPP1, NSD2 and ACTN4) and the long non-coding RNAs (COX7A2, COX6B2, TRIM37, PRM2, INHBA, ERBB4, SDHA, ATP6VOA2, FGF9 and TCF21) were found to be actively associated with bull sexual maturity and spermatogenesis. This study provided a comprehensive catalog of long non-coding RNAs in the bovine testes and also offered useful resources for understanding the differences in sexual development caused by the changes in the mRNA and long non-coding RNA interaction expressions between the immature and mature stages.

scholarly journals Transcriptome Analysis of Long Non-Coding RNA in the Bovine Mammary Gland Following Dietary Supplementation with Linseed Oil and Safflower Oil

2018 ◽  
Vol 19 (11) ◽  
pp. 3610 ◽  
Author(s):  
Eveline Ibeagha-Awemu ◽  
Ran Li ◽  
Pier-Luc Dudemaine ◽  
Duy Do ◽  
Nathalie Bissonnette
Keyword(s):  
Mammary Gland ◽  
Treatment Period ◽  
Target Genes ◽  
Linseed Oil ◽  
Control Diet ◽  
Functional Enrichment ◽  
Safflower Oil ◽  
Bovine Mammary Gland ◽  
Non Coding Rna ◽  
Long Non Coding Rna

This study aimed to characterize the long non-coding RNA (lncRNA) expression in the bovine mammary gland and to infer their functions in dietary response to 5% linseed oil (LSO) or 5% safflower oil (SFO). Twelve cows (six per treatment) in mid lactation were fed a control diet for 28 days followed by a treatment period (control diet supplemented with 5% LSO or 5% SFO) of 28 days. Mammary gland biopsies were collected from each animal on day-14 (D-14, control period), D+7 (early treatment period) and D+28 (late treatment period) and were subjected to RNA-Sequencing and subsequent bioinformatics analyses. Functional enrichment of lncRNA was performed via potential cis regulated target genes located within 50 kb flanking regions of lncRNAs and having expression correlation of >0.7 with mRNAs. A total of 4955 lncRNAs (325 known and 4630 novel) were identified which potentially cis targeted 59 and 494 genes in LSO and SFO treatments, respectively. Enrichments of cis target genes of lncRNAs indicated potential roles of lncRNAs in immune function, nucleic acid metabolism and cell membrane organization processes as well as involvement in Notch, cAMP and TGF-β signaling pathways. Thirty-two and 21 lncRNAs were differentially expressed (DE) in LSO and SFO treatments, respectively. Six genes (KCNF1, STARD13, BCL6, NXPE2, HHIPL2 and MMD) were identified as potential cis target genes of six DE lncRNAs. In conclusion, this study has identified lncRNAs with potential roles in mammary gland functions and potential candidate genes and pathways via which lncRNAs might function in response to LSO and SFA.

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