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Liu MM, Feng XL, Qi C, Zhang SE, Zhang GL. The significance of single-cell transcriptome analysis in epididymis research. Front Cell Dev Biol 2024; 12:1357370. [PMID: 38577504 PMCID: PMC10991796 DOI: 10.3389/fcell.2024.1357370] [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: 01/10/2024] [Accepted: 03/12/2024] [Indexed: 04/06/2024] Open
Abstract
As a crucial component of the male reproductive system, the epididymis plays multiple roles, including sperm storage and secretion of nutritive fluids for sperm development and maturation. The acquisition of fertilization capacity by sperm occurs during their transport through the epididymis. Compared with the testis, little has been realized about the importance of the epididymis. However, with the development of molecular biology and single-cell sequencing technology, the importance of the epididymis for male fertility should be reconsidered. Recent studies have revealed that different regions of the epididymis exhibit distinct functions and cell type compositions, which are likely determined by variations in gene expression patterns. In this research, we primarily focused on elucidating the cellular composition and region-specific gene expression patterns within different segments of the epididymis and provided detailed insights into epididymal function in male fertility.
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Affiliation(s)
- Meng-Meng Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Xin-Lei Feng
- Animal Products Quality and Safety Center of Shandong Province, Jinan, Shandong, China
| | - Chao Qi
- Provincial Animal Husbandry Station of Shandong Province, Jinan, Shandong, China
| | - Shu-Er Zhang
- Provincial Animal Husbandry Station of Shandong Province, Jinan, Shandong, China
| | - Guo-Liang Zhang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, China
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Jaglan K, Dhaka SS, Magotra A, Patil CS, Ghanghas A. Exploring MicroRNA biogenesis, applications and bioinformatics analysis in livestock: A comprehensive review. Reprod Domest Anim 2024; 59:e14529. [PMID: 38268204 DOI: 10.1111/rda.14529] [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: 08/29/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Small non-coding RNAs called microRNAs (miRNAs) control the expression of genes post-transcriptionally. Their correlation with commercial economic traits including milk, meat and egg production, as well as their effective role in animal productivity, fertility, embryo survival and disease resistance, make them significant in livestock research. The miRNAs exhibit distinct spatial and temporal expression patterns, offering insights into their functional roles within cells and tissues. Aberrant miRNA production can disrupt vital cellular processes and genetic networks, contributing to conditions like metabolic disorders and viral diseases. These short RNA molecules are present in extracellular fluids, displaying remarkable stability against RNA degradation enzymes and extreme environmental conditions. miRNAs preservation is facilitated through packaging in lipid vesicles or complex formation with RNA-binding proteins. Numerous studies have illuminated the roles of miRNAs in diverse physiological processes, including embryonic stem cell differentiation, haematopoietic stem cell proliferation and differentiation and the coordinated development of organ systems. The integration of miRNA profiling, next-generation sequencing and bioinformatics analysis paves the way for transformative advancements in livestock research and industry. The present review underscores the applications of miRNAs in livestock, showcasing their potential to improve breeding strategies, diagnose diseases and enhance our understanding of fundamental biological processes.
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Affiliation(s)
- Komal Jaglan
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - S S Dhaka
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Ankit Magotra
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - C S Patil
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Amandeep Ghanghas
- Department of Livestock Production Management, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
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Song T, Liu Y, Cuomu R, Tan Y, A Wang C, De J, Cao X, Zeng X. Polymorphisms Analysis of BMP15, GDF9 and BMPR1B in Tibetan Cashmere Goat ( Capra hircus). Genes (Basel) 2023; 14:genes14051102. [PMID: 37239462 DOI: 10.3390/genes14051102] [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: 04/06/2023] [Revised: 05/10/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The Tibetan cashmere goat is a prolific goat breed in China. In sheep breeds, natural mutations have demonstrated that the transforming growth factor beta (TGF-β) super family ligands, such as growth differentiation factor 9 (GDF9), bone morphogenetic protein 15 (BMP15) and their type I receptor (bone morphogenetic protein receptor (BMPR1B), are essential for ovulation and increasing litter size. In this study, 216 female Tibetan cashmere goats were sampled, and candidate genes with fecundity traits were detected via restriction fragment length polymorphism (RFLP) and sequenced. Four polymorphic loci were found in specific amplification fragments of BMP15 and GDF9. Two SNP sites of the BMP15 gene were discovered, namely G732A and C805G. The G732A mutation did not cause the change in amino acids, and the frequencies of each genotype were 0.695 for the GG type, 0.282 for the GA type and 0.023 for the AA type. The C805G mutation caused amino acids to change from glutamine to glutamate. The genotype frequencies were 0.620 for the CC type, 0.320 for the CG type and 0.320 for the CG type. For the GG type 0.060, the G3 and G4 mutations of the GDF9 gene were all homozygous mutations. Two known SNP sites, C719T and G1189A, were detected in the Tibetan cashmere goat GDF9 gene, of which the C719T mutation caused a change of alanine to valine, with a genotype frequency of 0.944 for the CC type and 0.056 for the CT type, whereas no TT type was found. The G1189A mutation caused valine to become isoleucine, and the frequencies of each genotype were 0.579 for the GG type, 0.305 for the GA type and 0.116 for the AA type; G1, B2, B3, B4, FecXH, FecXI, FecXL, G2, G5, G6, G7, G8, FecGE, FecTT and FecB mutations were not found in Tibetan cashmere goats. The results of this study provide a data basis for future studies of BMP15, GDF9 and BMPR1B gene mutations in goats.
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Affiliation(s)
- Tianzeng Song
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China
| | - Yacheng Liu
- Isotope Research Laboratory, Sichuan Agricultural University, Ya'an 625014, China
| | - Renqing Cuomu
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China
| | - Yao Tan
- Isotope Research Laboratory, Sichuan Agricultural University, Ya'an 625014, China
| | - Cuoji A Wang
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China
| | - Ji De
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China
| | - Xiaohan Cao
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China
- Isotope Research Laboratory, Sichuan Agricultural University, Ya'an 625014, China
| | - Xianyin Zeng
- Isotope Research Laboratory, Sichuan Agricultural University, Ya'an 625014, China
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Li C, Yan Y, Pan C, Adjei M, Shahzad K, Wang P, Pan M, Li K, Wang Y, Zhao W. Identification and analysis of differentially expressed (DE) circRNA in epididymis of yak and cattleyak. Front Vet Sci 2023; 10:1040419. [PMID: 36825227 PMCID: PMC9941329 DOI: 10.3389/fvets.2023.1040419] [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: 09/13/2022] [Accepted: 01/18/2023] [Indexed: 02/09/2023] Open
Abstract
Circular RNAs (circRNAs), as endogenous non-coding RNA with unique closed ring structure, is closely related to animal reproduction, and understanding the expression of circRNA in yak and cattleyak epididymal tissues is of great significance for understanding cattleyak sterility. Based on this, we screened and identified the differentially expressed circRNA in the epididymis of three yaks and two cattleyak. A total of 1,298 circRNAs were identified in the epididymis of yak and cattleyak, of which 137 differentially expressed (DE) circRNAs and the functions of some of them were elucidated in this research, as well as qPCR verification to 6 circRNAs from the 137 DE circRNAs. Gene Ontology (GO) enrichment analysis suggested that DE circRNAs were mainly related to metabolic process, development process, immune system process, reproductive process, reproduction, biological adhesion and growth. COG classification analysis showed that the DE circRNAs derived genes were mainly related to replication, recombination and repair. KEGG pathway analysis suggested that DE circRNAs were mainly involved in RNA degradation. In addition, we also screened Bta-mir-103, which is a circRNA binding miRNA related to sperm activity.
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Affiliation(s)
- Chunhai Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Yan Yan
- College of Life Sciences, Yan'an University, Yan'An, Shaanxi, China
| | - Cheng Pan
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Michael Adjei
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Khuram Shahzad
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Peng Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Meilan Pan
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Kerui Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Ye Wang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China,*Correspondence: Ye Wang ✉
| | - Wangsheng Zhao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China,Wangsheng Zhao ✉
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Sethi S, Mehta P, Pandey A, Gupta G, Rajender S. miRNA Profiling of Major Testicular Germ Cells Identifies Stage-Specific Regulators of Spermatogenesis. Reprod Sci 2022; 29:3477-3493. [PMID: 35715552 DOI: 10.1007/s43032-022-01005-x] [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: 03/18/2022] [Accepted: 06/07/2022] [Indexed: 12/14/2022]
Abstract
Spermatogenesis is tightly controlled at transcriptional, post-transcriptional, and epigenetic levels by various regulators, including miRNAs. This study deals with the identification of miRNAs critical to the three important stages of germ cell development (spermatocytes, round spermatids, and mature sperm) during spermatogenesis. We used high-throughput transcriptome sequencing to identify the differentially expressed miRNAs in the pachytene spermatocytes, round spermatids, and mature sperm of rat. We identified 1843 miRNAs that were differentially expressed across the three stages of germ cell development. These miRNAs were further categorized into three classes according to their pattern of expression during spermatogenesis: class 1 - miRNAs found exclusively in one stage and absent in the other two stages; class 2 - miRNAs found in any two stages but absent in the third stage; class 3 - miRNAs expressed in all the three stages. Six hundred forty-six miRNAs were found to be specific to one developmental stage, 443 miRNAs were found to be common across any two stages, and 754 miRNAs were common to all the three stages. Target prediction for ten most abundant miRNAs specific to each category identified miRNA regulators of mitosis, meiosis, and cell differentiation. The expression of each miRNA is specific to a particular developmental stage, which is required to maintain a significant repertoire of target mRNAs in the respective stage. Thus, this study provided valuable data that can be used in the future to identify the miRNAs involved in spermatogenic arrest at a particular stage of the germ cell development.
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Affiliation(s)
- Shruti Sethi
- CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research [AcSIR], Ghaziabad, India
| | - Poonam Mehta
- CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research [AcSIR], Ghaziabad, India
| | - Aastha Pandey
- CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research [AcSIR], Ghaziabad, India
| | - Gopal Gupta
- CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research [AcSIR], Ghaziabad, India
| | - Singh Rajender
- CSIR-Central Drug Research Institute, Lucknow, India.
- Academy of Scientific and Innovative Research [AcSIR], Ghaziabad, India.
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Adjei M, Yan Y, Li C, Pan C, Pan M, Wang P, Li K, Shahzad K, Chen X, Zhao W. Comparative transcriptome analysis in the caput segment of yak and cattleyak epididymis. Theriogenology 2022; 195:217-228. [DOI: 10.1016/j.theriogenology.2022.10.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 10/14/2022] [Accepted: 10/30/2022] [Indexed: 11/05/2022]
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Lang X, Adjei M, Wang C, Chen X, Li C, Wang P, Pan M, Li K, Shahzad K, Zhao W. RNA-Seq reveals the functional specificity of epididymal caput, corpus, and cauda genes of cattleyak. Anim Sci J 2022; 93:e13732. [PMID: 35543176 DOI: 10.1111/asj.13732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/05/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022]
Abstract
The first filial generation of the cattleyaks demonstrates hybrid vigor; however, the male cattleyaks are infertile and restrict productivity and breeding. The discovery of genes in a segment-specific approach offers valuable information and understanding concerning fertility status, yet the biology of cattleyak epididymis is still progressing. Comparative transcriptome analysis was performed on segment pairs of cattleyak epididymis. The caput versus corpus epididymis provided the highest (57.8%) differentially expressed genes (DEGs), corpus versus cauda (25.1%) followed, whereas caput versus cauda pair (17.1%) had the least DEGs. The expression levels of genes coding EPHB6, TLR1, MUC20, MT3, INHBB, TRPV5, EI24, PAOX, KIF12, DEPDC5, and KRT25, which might have the potentials to regulate the homeostasis, innate immunity, differentiation, motility, transport, and sperm maturation-related function in epididymal cells, were downregulated in the distal segment of epididymis. Top enriched KEGG pathways included mTOR, axon guidance, and taste transduction signaling pathways. EIF4B, EPHB6, and TAS2R42 were enriched in the pathways, respectively. Identifying key, new, and unexplored DEGs among the epididymal segments and further analyzing them could boost cattleyak fertility by maximizing sperm quality from genetically better sires and also facilitate better understanding of the epididymal biology.
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Affiliation(s)
- Xia Lang
- Institute of Animal & Pasture Science and Green Agricultural, Key laboratory for sheep, goat and cattle germplasm and straw feed in Gansu Province, Gansu Academy of Agricultural Science, Lanzhou, China
| | - Michael Adjei
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Cailian Wang
- Institute of Animal & Pasture Science and Green Agricultural, Key laboratory for sheep, goat and cattle germplasm and straw feed in Gansu Province, Gansu Academy of Agricultural Science, Lanzhou, China
| | - Xiaoying Chen
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, China
| | - Chunhai Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Peng Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Meilan Pan
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Kerui Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Khuram Shahzad
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Wangsheng Zhao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
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Yang C, Guo X, Dong F, Meng F, Wang L, Wang P, Zhang C, Ren Y. miR-542-3p reduces antioxidant capacity in goat caput epididymal epithelial cells by targeting glutathione peroxidase 5 (GPx5). Theriogenology 2022; 186:168-174. [DOI: 10.1016/j.theriogenology.2022.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/12/2022] [Accepted: 04/16/2022] [Indexed: 11/28/2022]
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9
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Wu C, Wang C, Zhai B, Zhao Y, Zhao Z, Yuan Z, Zhang M, Tian K, Fu X. Study of microRNA Expression Profile in Different Regions of Ram Epididymis. Reprod Domest Anim 2021; 56:1209-1219. [PMID: 34169586 DOI: 10.1111/rda.13978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/01/2021] [Indexed: 11/29/2022]
Abstract
The regional expression of epididymal genes provides a guarantee for sperm maturation. As a class of endogenous non-coding small RNAs, microRNAs (miRNAs) play an important role in spermatogenesis, maturation and fertilization. Currently, the regulatory role of miRNA in the epididymis is poorly understood. Here, transcriptome sequencing was used to analyse miRNA expression profiles in three regions of the epididymis of rams, including caput, corpus and cauda. The results showed that there were 13 known miRNAs between the caput and corpus controls, 29 between the caput and cauda and 22 differences between the corpus and cauda. Based on the analysis of miRNA target genes by GO and KEGG, a negative regulation network of miRNA-mRNA was constructed in which let-7, miR-541-5p, miR-133b and miR-150 may play an important regulatory role in the maturation regulation of ram epididymal sperm. This research provides a reference for studying the regulation mechanism of sperm maturation in male epididymis and improving semen quality and male reproductive performance.
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Affiliation(s)
- Cuiling Wu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China.,Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Gongzhuling, China.,Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Chunxin Wang
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Bo Zhai
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Yunhui Zhao
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Zhuo Zhao
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Zhiyu Yuan
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Mingxin Zhang
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 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, China
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