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Chen Y, Bao Z, Yao F, Liu Y, Zhao B, Wu X. ChIP-Seq analysis reveals PRKACB as a target gene of HOXC13 involved in rabbit hair follicle development. Gene 2024; 893:147946. [PMID: 38381512 DOI: 10.1016/j.gene.2023.147946] [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] [Received: 09/02/2023] [Revised: 10/09/2023] [Accepted: 10/27/2023] [Indexed: 02/22/2024]
Abstract
Dermal papilla cells (DPCs) are key regulators of hair follicle (HF) development and growth, which not only regulate HF growth and cycling but play a role in the pathogenesis of hair loss. The transcription factor Homeobox C13 (HOXC13) can modulate the growth and development of HFs. Nevertheless, the specific genes and pathways regulated by HOXC13 in DPCs have yet to be determined. Thus, to gain a better understanding of genomic binding sites involved in HOXC13-regulated HF development, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) was performed on rabbit DPCs with pcDNA3.1-3 × Flag-HOXC13 overexpression. A complete set of 9670 enrichment peaks was acquired by applying HOXC13-Flag ChIP. Subsequently, the peak sequence was annotated to the rabbit genome, revealing that 6.1 % of the peaks were identified within in the promoter region. Thereafter, five annotated genes were verified using RT-qPCR. The peak-associated genes were mainly enriched in signaling pathways related to HF development, such as MAPK and PI3K-Akt. Furthermore, by using a dual-luciferase reporter assay, we found that HOXC13 can target the protein kinase cAMP‑dependent catalytic β (PRKACB) promoter region (-1596 ∼ -1107 bp) and inhibit its transcription, which was consistent with data obtained from ChIP-seq analysis. Overexpression of PRKACB gene significantly modulated the expression of BCL2, WNT2, LEF1, and SFRP2 genes related to HF development as determined by RT-qPCR (P < 0.01, P < 0.05). The CCK-8 and flow cytometry assays showed that PRKACB significantly inhibited the proliferation of DPCs and promoted apoptosis (P < 0.01). In conclusion, our research revealed that PRKACB has the potential to serve as a novel target gene of HOXC13, contributing to the regulation of the proliferation and apoptosis of DPCs. The process of identifying global target genes can contribute to the understanding of the intricate pathways that HOXC13 regulates in the growth of HFs.
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Affiliation(s)
- Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Zhiyuan Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Fan Yao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yan Liu
- Animal Husbandry and Veterinary Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
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Lv X, Li Y, Chen W, Wang S, Cao X, Yuan Z, Getachew T, Mwacharo J, Haile A, Li Y, Sun W. Association between DNA Methylation in the Core Promoter Region of the CUT-like Homeobox 1 ( CUX1) Gene and Lambskin Pattern in Hu Sheep. Genes (Basel) 2023; 14:1873. [PMID: 37895221 PMCID: PMC10606103 DOI: 10.3390/genes14101873] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/18/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
CUT-like homeobox 1 (CUX1) has been proven to be a key regulator in sheep hair follicle development. In our previous study, CUX1 was identified as a differential expressed gene between Hu sheep lambskin with small wave patterns (SM) and straight wool patterns (ST); however, the exact molecular mechanism of CUX1 expression has been obscure. As DNA methylation can regulate the gene expression, the potential association between CUX1 core promotor region methylation and lambskin pattern in Hu sheep was explored in the present study. The results show that the core promoter region of CUX1 was present at (-1601-(-1) bp) upstream of the transcription start site. A repressive region (-1151-(-751) bp) was also detected, which had a strong inhibitory effect on CUX1 promoter activity. Bisulfite amplicon sequencing revealed that no significant difference was detected between the methylation levels of CUX1 core promoter region in SM tissues and ST tissues. Although the data demonstrated the differential expression of CUX1 between SM and ST probably has no association with DNA methylation, the identification of the core region and a potential repressive region of CUX1 promoter can enrich the role of CUX1 in Hu sheep hair follicle development.
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Affiliation(s)
- Xiaoyang Lv
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Yue Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Animal Husbandry and Veterinary Station, Zhuba Street, Hongze District, Huai’an 223100, China
| | - Weihao Chen
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Shanhe Wang
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
| | - Tesfaye Getachew
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Joram Mwacharo
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Aynalem Haile
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- International Centre for Agricultural Research in the Dry Areas, Addis Ababa 999047, Ethiopia
| | - Yutao Li
- CSIRO Agriculture and Food, 306 Carmody Rd., Saint Lucia, QLD 4067, Australia;
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- “Innovative China” “Belt and Road” International Agricultural Technology Innovation Institute for Evaluation, Protection, and Improvement on Sheep Genetic Resource, Yangzhou 225009, China
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Integrated Analysis of lncRNA and mRNA Reveals Novel Insights into Wool Bending in Zhongwei Goat. Animals (Basel) 2021; 11:ani11113326. [PMID: 34828057 PMCID: PMC8614501 DOI: 10.3390/ani11113326] [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: 09/18/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary The high-quality lambskin of the Chinese Zhongwei goat has a high economic value. The quality of lamb skin is mainly affected by the curvature of the wool, which is regulated by the growth and development of hair follicles. In this study, the expression profiles of long non-coding RNAs (lncRNAs) of 45-day-old and 108-day-old Zhongwei goats were constructed by the Ribo Zero RNA sequencing. A total of 60 differential lncRNAs and 352 differential mRNAs were identified. The functional annotation of differential lncRNAs target genes showed that they were mainly enriched in PI3K-Akt and Arachidonic acid metabolic signaling pathways. In combination with qRT-PCR and WGCNA results, we speculate that LOC102172600 and LOC102191729 might affect hair follicle development and wool curvature by regulating the target genes. These results provide new insights into the potential role of lncRNA in regulating wool bending. Abstract Chinese Zhongwei goat is a rare and precious fur breed as its lamb fur is a well-known fur product. Wool bending of lamb fur of the Zhongwei goat is its most striking feature. However, the curvature of the wool decreases gradually with growth, which significantly affects its quality and economic value. The mechanism regulating the phenotypic changes of hair bending is still unclear. In the present study, the skin tissues of Zhongwei goats at 45 days (curving wool) and 108 days (slight-curving wool) after birth were taken as the research objects, and the expression profiling of long non-coding RNAs (lncRNAs) and mRNAs were analyzed based on the Ribo Zero RNA sequencing (RNA-seq) method. In total, 46,013 mRNAs and 13,549 lncRNAs were identified, of which 352 were differentially expressed mRNAs and 60 were. lncRNAs. Functional enrichment analysis of the target genes of lncRNAs were mainly enriched in PI3K-Akt, Arachidonic acid metabolic, cAMP, Wnt, and other signaling pathways. The qRT-PCR results of eight selected lncRNAs and target genes were consistent with the sequencing result, which indicated our data were reliable. Through the analysis of the weighted gene co-expression network, 13 co-expression modules were identified. The turquoise module contained a large number of differential expressed lncRNAs, which were mainly enriched in the PI3K-Akt signaling pathway and cAMP signaling pathway. The predicted LOC102172600 and LOC102191729 might affect the development of hair follicles and the curvature of wool by regulating the target genes. Our study provides novel insights into the potential roles of lncRNAs in the regulation of wool bending. In addition, the study offers a theoretical basis for further study of goat wool growth, so as to be a guidance and reference for breeding and improvement in the future.
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Ouyang J, Hou Q, Wang M, Zhao W, Feng D, Pi Y, Sun X. Effects of dietary mulberry leaf powder on growth performance, blood metabolites, meat quality, and antioxidant enzyme-related gene expression of fattening Hu lambs. CANADIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1139/cjas-2019-0119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This study was conducted to investigate the effects of the mulberry [Morus alba var. multicaulis (Perrott.) Loud.] leaf powder (MLP) supplementation in dietary concentrates on growth performance, blood metabolites, meat quality, and antioxidant enzyme (AOE) gene expression in fattening Hu lambs. Forty approximately 3-mo-old Hu lambs (16.5 ± 0.6 kg) were randomly allocated to five groups and fed with concentrates containing 0%, 15%, 30%, 45%, or 60% MLP (control, T15, T30, T45, and T60, respectively). The results showed that 15%–30% MLP supplementation maintained growth and carcass performance, and the weight of total stomach, especially of rumen in T15 and T30, were higher than those of the control. Dietary MLP supplementation decreased serum aspartate aminotransferase, alanine aminotransferase, lactate dehydrogenase, cholesterol, and triglyceride levels, but increased the high-density lipoprotein levels. Moreover, MLP supplementation improved the longissimus lumborum muscle color (redness), tenderness, and water-holding capacity. It was further observed that 15% MLP supplementation enhanced all AOE mRNA levels apart from that of EPHX1. In summary, dietary MLP supplementation could partially improve the blood metabolites, meat quality, and AOE mRNA levels in the liver of fattening Hu lamb, and the level of 15% supplementation was the most promising.
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Affiliation(s)
- Jialiang Ouyang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, People’s Republic of China
| | - Qirui Hou
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, People’s Republic of China
| | - Mengzhi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, People’s Republic of China
| | - Weiguo Zhao
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, People’s Republic of China
| | - Dan Feng
- Department of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Yu Pi
- Department of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Xuezhao Sun
- The Centre for Ruminant Precision Nutrition and Smart Farming, Jilin Agricultural Science and Technology University, Jilin 132101, People’s Republic of China
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Lv X, Chen W, Sun W, Hussain Z, Wang S, Wang J. Analysis of lncRNAs Expression Profiles in Hair Follicle of Hu Sheep Lambskin. Animals (Basel) 2020; 10:ani10061035. [PMID: 32549352 PMCID: PMC7341247 DOI: 10.3390/ani10061035] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
Lambskin of the Hu sheep exhibits high economic value due to its water-wave pattern. Wool curvature is the key factor of the pattern types and quality of lambskin, and it is formed by the interaction between dermal papilla cells and hair matrix cells in the hair follicle, which is regulated by various genes and signaling pathways. Herein, three full-sibling pairs of two-day-old healthy lambs (n = 6) were divided into a straight wool group (ST) and small waves group (SM) with three repetitions. RNA-seq was applied to determine the expression profile of mRNAs and lncRNAs in Hu sheep hair follicles. 25 differentially expressed mRNAs and 75 differentially expressed lncRNAs were found between SM and ST. FGF12, ATP1B4, and TCONS_00279168 were probably associated with hair follicle development. Then, Gene Ontology (GO) and KEGG enrichment analysis were implemented for the functional annotation of target genes of differentially expressed lncRNAs. The results showed that many genes, such as FGF12 and ATP1B4, were found enriched in PI3K-Akt signaling, MAPK signaling, and Ras signaling pathway associated with hair follicle growth and development. In addition, the interaction network of differentially expressed lncRNAs and mRNAs showed that a total of 6 differentially expressed lncRNAs were associated with 12 differentially expressed mRNAs, which may be as candidate mRNAs and lncRNAs. TCONS_00279168 may target ATP1B4 and FGF12 to regulate MAPK, PI3K-Akt, Ras signaling pathways involved in the sheep hair follicle development process. These results will provide the basis for exploring hair follicle development.
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Affiliation(s)
- Xiaoyang Lv
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.L.); (W.C.); (Z.H.); (S.W.)
| | - Weihao Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.L.); (W.C.); (Z.H.); (S.W.)
| | - Wei Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.L.); (W.C.); (Z.H.); (S.W.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Correspondence: (W.S.); (J.W.); Tel.: +86-0514-87979213 (W.S.)
| | - Zahid Hussain
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.L.); (W.C.); (Z.H.); (S.W.)
| | - Shanhe Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.L.); (W.C.); (Z.H.); (S.W.)
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.L.); (W.C.); (Z.H.); (S.W.)
- Correspondence: (W.S.); (J.W.); Tel.: +86-0514-87979213 (W.S.)
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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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