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Cao M, Xiong L, Wang X, Guo S, Hu L, Kang Y, Wu X, Bao P, Chu M, Liang C, Pei J, Guo X. Comprehensive analysis of differentially expressed mRNAs, circRNAs, and miRNAs and their ceRNA network in the testis of cattle-yak, yak, and cattle. Genomics 2024; 116:110872. [PMID: 38849017 DOI: 10.1016/j.ygeno.2024.110872] [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: 03/06/2024] [Revised: 05/14/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024]
Abstract
Cattle-yak is a hybrid offspring resulting from the crossbreeding of yak and cattle, and it exhibits substantial heterosis in production performance. However, male sterility in cattle-yak remains a concern. Reports suggest that noncoding RNAs are involved in the regulation of spermatogenesis. Therefore, in this study, we comprehensively compared testicular transcription profiles among cattle, yak, and cattle-yak. Numerous differentially expressed genes (DEGs), differentially expressed circRNAs (DECs), and differentially expressed miRNAs (DEMs) were identified in the intersection of two comparison groups, namely cattle versus cattle-yak and yak versus cattle-yak, with the number of DEGs, DECs, and DEMs being 4968, 360, and 59, respectively. The DEGs in cattle-yaks, cattle, and yaks were mainly associated with spermatogenesis, male gamete generation, and sexual reproduction. Concurrently, GO and KEGG analyses indicated that DEC host genes and DEM source genes were involved in the regulation of spermatogenesis. The construction of a potential competing endogenous RNA network revealed that some differentially expressed noncoding RNAs may be involved in regulating the expression of genes related to testicular spermatogenesis, including miR-423-5p, miR-449b, miR-34b/c, and miR-15b, as well as previously unreported miR-6123 and miR-1306, along with various miRNA-circRNA interaction pairs. This study serves as a valuable reference for further investigations into the mechanisms underlying male sterility in cattle-yaks.
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Affiliation(s)
- Mengli Cao
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Lin Xiong
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xingdong Wang
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Shaoke Guo
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Liyan Hu
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yandong Kang
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xiaoyu Wu
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Min Chu
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jie Pei
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China.
| | - Xian Guo
- Key Laboratory of Yak Breeding in Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China.
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Wang X, Guo S, Xiong L, Wu X, Bao P, Kang Y, Cao M, Ding Z, Liang C, Pei J, Guo X. Complete characterization of the yak testicular development using accurate full-length transcriptome sequencing. Int J Biol Macromol 2024; 271:132400. [PMID: 38759851 DOI: 10.1016/j.ijbiomac.2024.132400] [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: 02/21/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Alternative splicing is a prevalent phenomenon in testicular tissues. Due to the low assembly accuracy of short-read RNA sequencing technology in analyzing post-transcriptional regulatory events, full-length (FL) transcript sequencing is highly demanded to accurately determine FL splicing variants. In this study, we performed FL transcriptome sequencing of testicular tissues from 0.5, 1.5, 2.5, and 4-year-old yaks and 4-year-old cattle-yaks using Oxford Nanopore Technologies. The obtained sequencing data were predicted to have 47,185 open reading frames (ORFs), including 26,630 complete ORFs, detected 7645 fusion transcripts, 15,355 alternative splicing events, 25,798 simple sequence repeats, 7628 transcription factors, and 35,503 long non-coding RNAs. A total of 40,038 novel transcripts were obtained from the sequencing data, and the proportion was almost close to the number of known transcripts identified. Structural analysis and functional annotation of these novel transcripts resulted in the successful annotation of 9568 transcripts, with the highest and lowest annotation numbers in the Nr and KOG databases, respectively. Weighted gene co-expression network analysis revealed the key regulatory pathways and hub genes at various stages of yak testicular development. Our findings enhance our comprehension of transcriptome complexity, contribute to genome annotation refinement, and provide foundational data for further investigations into male sterility in cattle-yaks.
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Affiliation(s)
- Xingdong Wang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Shaoke Guo
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Lin Xiong
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Yandong Kang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Mengli Cao
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Ziqiang Ding
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China
| | - Jie Pei
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China.
| | - Xian Guo
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, PR China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, PR China.
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Bai R, Chen D, Xiong H, Song H, Wang T, Yang X, Tang J, Feng Y, Li J, Li F. SPAG6 c.900 T>C affects boar semen quality and blood-testis barrier function by creating a new splice acceptor site. Anim Genet 2023. [PMID: 37211688 DOI: 10.1111/age.13330] [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: 10/08/2022] [Revised: 03/16/2023] [Accepted: 04/28/2023] [Indexed: 05/23/2023]
Abstract
Sperm associated antigen 6 (SPAG6) acts as a scaffolding protein in the center of the flagellar axoneme and has an impact on the maturation of the motility of mammalian sperm flagella and the maintenance of sperm structure. In our previous research, SPAG6 c.900 T>C in exon 7 and exon 7 skipped transcript was identified by analyzing RNA-seq data of testicular tissues from 60 day (sexually immature) and 180 day (sexually mature) Large White boars. Herein, we found porcine SPAG6 c.900 T>C to be associated with semen quality traits in Duroc, Large White and Landrace pigs. SPAG6 c.900 C can generate a new splice acceptor site, inhibit the occurrence of SPAG6 exon 7 skipping to a certain extent, thereby promote the growth of Sertoli cells and maintain the normal blood-testis barrier function. This study provides new insights into the molecular regulation of spermatogenesis and a new genetic marker for the improvement of semen quality in pigs.
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Affiliation(s)
- Rong Bai
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Dake Chen
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Hao Xiong
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Huibin Song
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Tiansu Wang
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xinpeng Yang
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Jinhua Tang
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yue Feng
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Jialian Li
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Fenge Li
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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Song H, Chen D, Bai R, Feng Y, Wu S, Wang T, Xia X, Li J, Miao YL, Zuo B, Li F. BCL2-associated athanogene 6 exon24 contributes to testosterone synthesis and male fertility in mammals. Cell Prolif 2022; 55:e13281. [PMID: 35688694 PMCID: PMC9251057 DOI: 10.1111/cpr.13281] [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: 01/12/2022] [Revised: 05/10/2022] [Accepted: 05/24/2022] [Indexed: 11/28/2022] Open
Abstract
Objectives BCL2‐associated athanogene 6 (BAG6) plays critical roles in spermatogenesis by maintaining testicular cell survival. Our previous data showed porcine BAG6 exon24‐skipped transcript is highly expressed in immature testes compared with mature testes. The objective of this study is to reveal the functional significance of BAG6 exon24 in mammalian spermatogenesis. Materials and Methods CRISPR/Cas9 system was used to generate Bag6 exon24 knockout mice. Testes and cauda epididymal sperm were collected from mice. TMT proteomics analysis was used to discover the protein differences induced by Bag6 exon24 deletion. Testosterone enanthate was injected into mice to generate a high‐testosterone mice model. H&E staining, qRT‐PCR, western blotting, vector/siRNA transfection, immunofluorescence, immunoprecipitation, transmission electron microscopy, TUNEL and ELISA were performed to investigate the phenotypes and molecular basis. Results Bag6 exon24 knockout mice show sub‐fertility along with partially impaired blood‐testis barrier, increased apoptotic testicular cell rate and abnormal sperm morphology. Endoplasmic reticulum stress occurs in Bag6 exon24‐deficient testes and sterol regulatory element‐binding transcription factor 2 is activated; as a result, cytochrome P450 family 51 subfamily A member 1 expression is up‐regulated, which causes a high serum testosterone level. Additionally, serine/arginine‐rich splicing factor 1 down‐regulates BAG6 exon24‐skipped transcripts in porcine Sertoli cells by binding to 35–51 nt on BAG6 exon24 via its N‐terminal RNA‐recognition domain. Conclusions Our findings reveal the critical roles of BAG6 exon24 in testosterone biosynthesis and male fertility, which provides new insights into the regulation of spermatogenesis and pathogenesis of subfertility in mammals.
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Affiliation(s)
- Huibin Song
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Dake Chen
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Rong Bai
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yue Feng
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shang Wu
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Tiansu Wang
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xuanyan Xia
- College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jialian Li
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yi-Liang Miao
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Bo Zuo
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
| | - Fenge Li
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
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Xu H, Sun W, Pei S, Li W, Li F, Yue X. Identification of Key Genes Related to Postnatal Testicular Development Based on Transcriptomic Data of Testis in Hu Sheep. Front Genet 2022; 12:773695. [PMID: 35145544 PMCID: PMC8822165 DOI: 10.3389/fgene.2021.773695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
The selection of testis size can improve the reproductive capacity of livestock used for artificial insemination and has been considered as an important strategy for accelerating the breeding process. Although much work has been done to investigate the mechanisms of testis development in various species, there is little information available in regard to the differences in transcriptomic profiling of sheep testes at different developmental stages. In this work, we aimed to identify differentially expressed genes (DEGs) by RNA-Seq in sheep during different growth stages, including 0 month old (infant, M0), 3 months old (puberty, M3), 6 months old (sexual maturity, M6) and 12 months old (body maturity, M12). A total of 4,606 (2,381 up and 2,225 down), 7,500 (4,368 up and 3,132 down), 15 (8 up and seven down) DEGs were identified in M3_vs_M0, M6_vs_M3, and M12_vs_M6 comparison, respectively. Of which, a number of genes were continuously up-regulated and down-regulated with testicular development, including ODF3, ZPBP1, PKDREJ, MYBL1, PDGFA, IGF1, LH, INSL3, VIM, AMH, INHBA, COL1A1, COL1A2, and INHA. GO analysis illustrated that DEGs were mainly involved in testis development and spermatogenesis. KEGG analysis identified several important pathways and verified several reproduction-associated DEGs such as COL1A1, COL1A2, PDGFA, and IGF1. In addition, two gene modules highly associated with testis development and core genes with testis size were identified using weighted gene co-expression network analysis (WGCNA), including hub genes positively associated with testis size such as RANBP9, DNAH17, SPATA4, CIB4 and SPEM1, and those negatively associated with testis size such as CD81, CSK, PDGFA, VIM, and INHBA. This study comprehensively identified key genes related to sheep testicular development, which may provide potential insights for understanding male fertility and better guide in animal breeding.
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Khan IM, Liu H, Zhuang J, Khan NM, Zhang D, Chen J, Xu T, Avalos LFC, Zhou X, Zhang Y. Circular RNA Expression and Regulation Profiling in Testicular Tissues of Immature and Mature Wandong Cattle ( Bos taurus). Front Genet 2021; 12:685541. [PMID: 34880896 PMCID: PMC8647812 DOI: 10.3389/fgene.2021.685541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
Wandong cattle are an autochthonous Chinese breed used extensively for beef production. The breed tolerates extreme weather conditions and raw feed and is resistant to tick-borne diseases. However, the genetic basis of testis development and sperm production as well as breeding management is not well established in local cattle. Therefore, improving the reproductive efficiency of bulls via genetic selection is crucial as a single bull can breed thousands of cows through artificial insemination (AI). Testis development and spermatogenesis are regulated by hundreds of genes and transcriptomes. However, circular RNAs (circRNAs) are the key players in many biological developmental processes that have not been methodically described and compared between immature and mature stages in Bovine testes. In this study, we performed total RNA-seq and comprehensively analyzed the circRNA expression profiling of the testis samples of six bulls at 3 years and 3 months of developmental age. In total, 17,013 circRNAs were identified, of which 681 circRNAs (p-adjust < 0.05) were differentially expressed (DE). Among these DE circRNAs, 579 were upregulated and 103 were downregulated in calf and bull testes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the identified target genes were classified into three broad functional categories, including biological process, cellular component, and molecular function, and were enriched in the lysine degradation, cell cycle, and cell adhesion molecule pathways. The binding interactions between DE circRNAs and microRNAs (miRNAs) were subsequently constructed using bioinformatics approaches. The source genes ATM, CCNA1, GSK3B, KMT2C, KMT2E, NSD2, SUCLG2, QKI, HOMER1, and SNAP91 were found to be actively associated with bull sexual maturity and spermatogenesis. In addition, a real-time quantitative polymerase chain reaction (RT-qPCR) analysis showed a strong correlation with the sequencing data. Moreover, the developed model of Bovine testes in the current study provides a suitable framework for understanding the mechanism of circRNAs in the development of testes and spermatogenesis.
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Affiliation(s)
- Ibrar Muhammad Khan
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Hongyu Liu
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Jingyi Zhuang
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Nazir Muhammad Khan
- Department of Zoology, University of Science and Technology, Bannu, Pakistan
| | - Dandan Zhang
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Jingmeng Chen
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Tengteng Xu
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Lourdes Felicidad Córdova Avalos
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xinqi Zhou
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yunhai Zhang
- Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
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Zinovieva NA, Dotsev AV, Sermyagin AA, Deniskova TE, Abdelmanova AS, Kharzinova VR, Sölkner J, Reyer H, Wimmers K, Brem G. Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis. PLoS One 2020; 15:e0242200. [PMID: 33196682 PMCID: PMC7668599 DOI: 10.1371/journal.pone.0242200] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.
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Affiliation(s)
- Natalia Anatolievna Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
- * E-mail:
| | - Arsen Vladimirovich Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Alexander Alexandrovich Sermyagin
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Tatiana Evgenievna Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Alexandra Sergeevna Abdelmanova
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Veronika Ruslanovna Kharzinova
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology [FBN], Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology [FBN], Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Federal Agency of Scientific Organizations, settl. Dubrovitzy, Podolsk Region, Moscow Province, Russia
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine [VMU], Vienna, Austria
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8
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Tian F, Wang J, Li Y, Yang C, Zhang R, Wang X, Ju Z, Jiang Q, Huang J, Wang C, Chen J, Sun Y. Integrated analysis of mRNA and miRNA in testis and cauda epididymidis reveals candidate molecular markers associated with reproduction in Dezhou donkey. Livest Sci 2020. [DOI: 10.1016/j.livsci.2019.103885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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9
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Song H, Wang L, Chen D, Li F. The Function of Pre-mRNA Alternative Splicing in Mammal Spermatogenesis. Int J Biol Sci 2020; 16:38-48. [PMID: 31892844 PMCID: PMC6930371 DOI: 10.7150/ijbs.34422] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/20/2019] [Indexed: 01/05/2023] Open
Abstract
Alternative pre-mRNA splicing plays important roles in co-transcriptional and post-transcriptional regulation of gene expression functioned during many developmental processes, such as spermatogenesis. The studies focusing on alternative splicing on spermatogenesis supported the notion that the development of testis is regulated by a higher level of alternative splicing than other tissues. Here, we aim to review the mechanisms underlying alternative splicing, particularly the splicing variants functioned in the process of spermatogenesis and the male infertility. There are five points regarding the alternative splicing including ⅰ) a brief introduction of alternative pre-mRNA splicing; ⅱ) the alternative splicing events in spermatogenesis-associated genes enriched in different stages of spermatogenesis; ⅲ) the mechanisms of alternative splicing regulation, such as splicing factors and m6A demethylation; ⅳ) the splice site recognition and alternative splicing, including the production and degradation of abnormal transcripts caused by gene variations and nonsense-mediated mRNA decay, respectively; ⅴ) abnormal alternative splicing correlated with male infertility. Taking together, this review highlights the impacts of alternative splicing and splicing variants in mammal spermatogenesis and provides new insights of the potential application of the alternative splicing into the therapy of male infertility.
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Affiliation(s)
- Huibin Song
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ling Wang
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Dake Chen
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Fenge Li
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, PR China
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10
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Marques DBD, Bastiaansen JWM, Broekhuijse MLWJ, Lopes MS, Knol EF, Harlizius B, Guimarães SEF, Silva FF, Lopes PS. Weighted single-step GWAS and gene network analysis reveal new candidate genes for semen traits in pigs. Genet Sel Evol 2018; 50:40. [PMID: 30081822 PMCID: PMC6080523 DOI: 10.1186/s12711-018-0412-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 07/11/2018] [Indexed: 12/13/2022] Open
Abstract
Background In recent years, there has been increased interest in the study of the molecular processes that affect semen traits. In this study, our aim was to identify quantitative trait loci (QTL) regions associated with four semen traits (motility, progressive motility, number of sperm cells per ejaculate and total morphological defects) in two commercial pig lines (L1: Large White type and L2: Landrace type). Since the number of animals with both phenotypes and genotypes was relatively small in our dataset, we conducted a weighted single-step genome-wide association study, which also allows unequal variances for single nucleotide polymorphisms. In addition, our aim was also to identify candidate genes within QTL regions that explained the highest proportions of genetic variance. Subsequently, we performed gene network analyses to investigate the biological processes shared by genes that were identified for the same semen traits across lines. Results We identified QTL regions that explained up to 10.8% of the genetic variance of the semen traits on 12 chromosomes in L1 and 11 chromosomes in L2. Sixteen QTL regions in L1 and six QTL regions in L2 were associated with two or more traits within the population. Candidate genes SCN8A, PTGS2, PLA2G4A, DNAI2, IQCG and LOC102167830 were identified in L1 and NME5, AZIN2, SPATA7, METTL3 and HPGDS in L2. No regions overlapped between these two lines. However, the gene network analysis for progressive motility revealed two genes in L1 (PLA2G4A and PTGS2) and one gene in L2 (HPGDS) that were involved in two biological processes i.e. eicosanoid biosynthesis and arachidonic acid metabolism. PTGS2 and HPGDS were also involved in the cyclooxygenase pathway. Conclusions We identified several QTL regions associated with semen traits in two pig lines, which confirms the assumption of a complex genetic determinism for these traits. A large part of the genetic variance of the semen traits under study was explained by different genes in the two evaluated lines. Nevertheless, the gene network analysis revealed candidate genes that are involved in shared biological pathways that occur in mammalian testes, in both lines. Electronic supplementary material The online version of this article (10.1186/s12711-018-0412-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniele B D Marques
- Animal Science Department, Universidade Federal de Viçosa, Viçosa, MG, 36.570-000, Brazil
| | - John W M Bastiaansen
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.
| | | | - Marcos S Lopes
- Topigs Norsvin Research Center B.V., P.O. Box 43, 6640 AA, Beuningen, The Netherlands.,Topigs Norsvin, Curitiba, PR, 80.420-210, Brazil
| | - Egbert F Knol
- Topigs Norsvin Research Center B.V., P.O. Box 43, 6640 AA, Beuningen, The Netherlands
| | - Barbara Harlizius
- Topigs Norsvin Research Center B.V., P.O. Box 43, 6640 AA, Beuningen, The Netherlands
| | - Simone E F Guimarães
- Animal Science Department, Universidade Federal de Viçosa, Viçosa, MG, 36.570-000, Brazil
| | - Fabyano F Silva
- Animal Science Department, Universidade Federal de Viçosa, Viçosa, MG, 36.570-000, Brazil
| | - Paulo S Lopes
- Animal Science Department, Universidade Federal de Viçosa, Viçosa, MG, 36.570-000, Brazil
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11
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Gao Y, Wu M, Fan Y, Li S, Lai Z, Huang Y, Lan X, Lei C, Chen H, Dang R. Identification and characterization of circular RNAs in Qinchuan cattle testis. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180413. [PMID: 30109096 PMCID: PMC6083711 DOI: 10.1098/rsos.180413;180413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/21/2018] [Indexed: 05/27/2023]
Abstract
Circular RNA (circRNA) is a new class of non-coding RNA that has recently attracted researchers' interest. Studies have demonstrated that circRNA can function as microRNA sponges or competing endogenous RNAs. Although circRNA has been explored in some species and tissues, the genetic basis of testis development and spermatogenesis in cattle remains unknown. We performed ribo-depleted total RNA-Seq to detect circRNA expression profiles of neonatal (one week old) and adult (4 years old) Qinchuan cattle testes. We obtained 91 112 596 and 80 485 868 clean reads and detected 21 753 circRNAs. A total of 4248 circRNAs were significantly differentially expressed between neonatal and adult cattle testes. Among these circRNAs, 2225 were upregulated, and 2023 were downregulated in adult cattle testis. Genomic feature, length distribution and other characteristics of the circRNAs in cattle testis were studied. Moreover, Gene Ontology and KEGG pathway analyses were performed for source genes of circRNAs. These source genes were mainly involved in tight junction, adherens junction, TGFβ signalling pathway and reproduction, such as PIWIL1, DPY19L2, SLC26A8, IFT81, SMC1B, IQCG and TTLL5. CircRNA expression patterns were validated by RT-qPCR. Our discoveries provide a solid foundation for the identification and characterization of key circRNAs involved in testis development or spermatogenesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ruihua Dang
- Author for correspondence: Ruihua Dang e-mail:
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12
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Gao Y, Wu M, Fan Y, Li S, Lai Z, Huang Y, Lan X, Lei C, Chen H, Dang R. Identification and characterization of circular RNAs in Qinchuan cattle testis. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180413. [PMID: 30109096 PMCID: PMC6083711 DOI: 10.1098/rsos.180413] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/21/2018] [Indexed: 06/08/2023]
Abstract
Circular RNA (circRNA) is a new class of non-coding RNA that has recently attracted researchers' interest. Studies have demonstrated that circRNA can function as microRNA sponges or competing endogenous RNAs. Although circRNA has been explored in some species and tissues, the genetic basis of testis development and spermatogenesis in cattle remains unknown. We performed ribo-depleted total RNA-Seq to detect circRNA expression profiles of neonatal (one week old) and adult (4 years old) Qinchuan cattle testes. We obtained 91 112 596 and 80 485 868 clean reads and detected 21 753 circRNAs. A total of 4248 circRNAs were significantly differentially expressed between neonatal and adult cattle testes. Among these circRNAs, 2225 were upregulated, and 2023 were downregulated in adult cattle testis. Genomic feature, length distribution and other characteristics of the circRNAs in cattle testis were studied. Moreover, Gene Ontology and KEGG pathway analyses were performed for source genes of circRNAs. These source genes were mainly involved in tight junction, adherens junction, TGFβ signalling pathway and reproduction, such as PIWIL1, DPY19L2, SLC26A8, IFT81, SMC1B, IQCG and TTLL5. CircRNA expression patterns were validated by RT-qPCR. Our discoveries provide a solid foundation for the identification and characterization of key circRNAs involved in testis development or spermatogenesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ruihua Dang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
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13
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Wu S, Guo J, Zhu L, Yang J, Chen S, Yang X. Identification and characterisation of microRNAs and Piwi-interacting RNAs in cockerels' spermatozoa by Solexa sequencing. Br Poult Sci 2018; 59:371-380. [PMID: 29667432 DOI: 10.1080/00071668.2018.1464123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
1. There has been substantial research focused on the roles of microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs) derived from mammalian spermatozoa; however, comparatively little is known about the role of spermatozoa-derived miRNAs and piRNAs within breeding cockerels' spermatozoa. 2. A small RNA library of cockerels' spermatozoa was constructed using Illumina high-throughput sequencing technology. Unique sequences with lengths of 18-26 nucleotides were mapped to miRBase 21.0 and unique sequences with lengths of 25-37 nucleotides were mapped to a piRNA database. A total of 1311 miRNAs and 2448 potential piRNAs were identified. Based on stem-loop qRT-PCR, 8 miRNAs were validated. 3. Potential target genes of the abundant miRNAs were predicted, and further Kyoto Encyclopedia of Genes and Genomes database (KEGG) and Gene Ontology (GO) analyses were performed, which revealed that some candidate miRNAs were involved in the spermatogenesis process, spermatozoa epigenetic programming and further embryonic development. 5. GO and KEGG analyses based on mapping genes of expressed piRNAs were performed, which revealed that spermatozoal piRNAs could play important regulatory roles in embryonic development of offspring. 6. The search for endogenous spermatozoa miRNAs and piRNAs will contribute to a preliminary database for functional and molecular mechanistic studies in embryonic development and spermatozoa epigenetic programming.
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Affiliation(s)
- S Wu
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - J Guo
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - L Zhu
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - J Yang
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - S Chen
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - X Yang
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
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14
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van Son M, Tremoen NH, Gaustad AH, Myromslien FD, Våge DI, Stenseth EB, Zeremichael TT, Grindflek E. RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars. BMC Vet Res 2017; 13:362. [PMID: 29183316 PMCID: PMC5706377 DOI: 10.1186/s12917-017-1279-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 11/16/2017] [Indexed: 11/17/2022] Open
Abstract
Background Sperm DNA is protected against fragmentation by a high degree of chromatin packaging. It has been demonstrated that proper chromatin packaging is important for boar fertility outcome. However, little is known about the molecular mechanisms underlying differences in sperm DNA fragmentation. Knowledge of sequence variation influencing this sperm parameter could be beneficial in selecting the best artificial insemination (AI) boars for commercial production. The aim of this study was to identify genes differentially expressed in testis tissue of Norwegian Landrace and Duroc boars, with high and low sperm DNA fragmentation index (DFI), using transcriptome sequencing. Results Altogether, 308 and 374 genes were found to display significant differences in expression level between high and low DFI in Landrace and Duroc boars, respectively. Of these genes, 71 were differentially expressed in both breeds. Gene ontology analysis revealed that significant terms in common for the two breeds included extracellular matrix, extracellular region and calcium ion binding. Moreover, different metabolic processes were enriched in Landrace and Duroc, whereas immune response terms were common in Landrace only. Variant detection identified putative polymorphisms in some of the differentially expressed genes. Validation showed that predicted high impact variants in RAMP2, GIMAP6 and three uncharacterized genes are particularly interesting for sperm DNA fragmentation in boars. Conclusions We identified differentially expressed genes between groups of boars with high and low sperm DFI, and functional annotation of these genes point towards important biochemical pathways. Moreover, variant detection identified putative polymorphisms in the differentially expressed genes. Our results provide valuable insights into the molecular network underlying DFI in pigs. Electronic supplementary material The online version of this article (10.1186/s12917-017-1279-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Nina Hårdnes Tremoen
- Department of Natural Sciences and Technology, Inland Norway University of Applied Sciences, 2318, Hamar, Norway.,Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Ann Helen Gaustad
- Topigs Norsvin, 2317, Hamar, Norway.,Department of Natural Sciences and Technology, Inland Norway University of Applied Sciences, 2318, Hamar, Norway
| | - Frøydis Deinboll Myromslien
- Department of Natural Sciences and Technology, Inland Norway University of Applied Sciences, 2318, Hamar, Norway
| | - Dag Inge Våge
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Else-Berit Stenseth
- Department of Natural Sciences and Technology, Inland Norway University of Applied Sciences, 2318, Hamar, Norway
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15
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Hu P, Guan K, Feng Y, Ma C, Song H, Li Y, Xia X, Li J, Li F. miR-638 Inhibits immature Sertoli cell growth by indirectly inactivating PI3K/AKT pathway via SPAG1 gene. Cell Cycle 2017; 16:2290-2300. [PMID: 29119857 DOI: 10.1080/15384101.2017.1380130] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Numerous studies have demonstrated that microRNAs (miRNAs) play important roles in cell growth, apoptosis and spermatogenesis. Our previous study showed that miR-638 was differentially expressed in sexually immature and mature testes of Large White boars. Here we reported that sperm-associated antigen 1 (SPAG1) was a direct target gene of miR-638. Moreover, miR-638 inhibited cell proliferation and cell cycle, and promoted apoptosis of porcine immature Sertoli cells. Key genes including phosphorylated phosphatidylinositide 3-kinases (p-PI3K) and phosphorylated serine/ threonine kinase (p-AKT) in PI3K/AKT pathway as well as cell cycle factors including c-MYC, cyclin-D1 (CCND1), cyclin-E1 (CCNE1) and cyclin-dependent kinase 4 (CDK4) were all significantly down-regulated after overexpression of miR-638 or RNAi of SPAG1. Notably, mRNA levels of SRY-related HMG-box 2 (SOX2) and POU domain, class 5, transcription factor 1 (POU5F1) essential for spermatogonia proliferation were significantly suppressed in SPAG1 siRNA- transfected ST cells. This study suggests that miR-638 regulates immature Sertoli cell growth and apoptosis by targeting SPAG1 gene which can indirectly inactivate PI3K/AKT pathway, and plays roles in pig spermatogenesis.
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Affiliation(s)
- Pandi Hu
- a Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education , Huazhong Agricultural University , Wuhan , PR China
| | - Kaifeng Guan
- a Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education , Huazhong Agricultural University , Wuhan , PR China
| | - Yue Feng
- a Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education , Huazhong Agricultural University , Wuhan , PR China
| | - Changping Ma
- a Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education , Huazhong Agricultural University , Wuhan , PR China
| | - Huibin Song
- a Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education , Huazhong Agricultural University , Wuhan , PR China
| | - Yang Li
- a Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education , Huazhong Agricultural University , Wuhan , PR China
| | - Xuanyan Xia
- b College of Informatics, Huazhong Agricultural University , Wuhan , PR China
| | - Jialian Li
- a Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education , Huazhong Agricultural University , Wuhan , PR China
| | - Fenge Li
- a Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education , Huazhong Agricultural University , Wuhan , PR China.,c The Cooperative Innovation Center for Sustainable Pig Production , Wuhan , PR China
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16
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Wu SR, Guo W, Li YL, Ren XC, Lei XY, Li XY, Yao JH, Yang XJ. miRNA and piRNA expression profiles of breeder cock testes detected by next-generation sequencing. Reprod Domest Anim 2016; 52:203-213. [PMID: 27862381 DOI: 10.1111/rda.12880] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/25/2016] [Indexed: 11/29/2022]
Abstract
miRNAs are small non-coding regulatory RNAs that play key roles in diverse biological processes. In this study, we used the Solexa sequencing technique to profile miRNAs in breeder cock testes to illustrate their functions. A total of 663 co-expressed miRNAs and 3,180 co-expressed piRNAs were detected in three libraries. Based on Mir-X™ miRNA qRT-PCR, three miRNAs representing low, medium and high expression levels according to the sequencing results were selected randomly to validate the miRNAs' expression profiles. Results suggested that the miRNA expression profiles data could represent actual miRNA expression levels. Moreover, target genes prediction of the co-expressed miRNAs and further Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed, which revealed that some candidate miRNAs were involved in the regulation of the spermatogenesis process, spermatozoa function and testicular metabolism. In conclusion, we provided a useful resource for further elucidation of the miRNAs' regulatory role in spermatogenesis, contributing to a preliminary database for functional and molecular mechanistic studies in testicular metabolism, spermatogenesis and other testes functions.
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Affiliation(s)
- S R Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - W Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Y L Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - X C Ren
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - X Y Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - X Y Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - J H Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - X J Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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17
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Li Y, Li J, Fang C, Shi L, Tan J, Xiong Y, Bin Fan, Li C. Genome-wide differential expression of genes and small RNAs in testis of two different porcine breeds and at two different ages. Sci Rep 2016; 6:26852. [PMID: 27229484 PMCID: PMC4882596 DOI: 10.1038/srep26852] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/10/2016] [Indexed: 02/06/2023] Open
Abstract
Some documented evidences proved small RNAs (sRNA) and targeted genes are involved in mammalian testicular development and spermatogenesis. However, the detailed molecular regulation mechanisms of them remain largely unknown so far. In this study, we obtained a total of 10,716 mRNAs, 67 miRNAs and 16,953 piRNAs which were differentially expressed between LC and LW pig breeds or between the two sexual maturity stages. Of which, we identified 16 miRNAs and 28 targeted genes possibly related to spermatogenesis; 14 miRNA and 18 targeted genes probably associated with cell adhesion related testis development. We also annotated 579 piRNAs which could potentially regulate cell death, nucleosome organization and other basic biology process, which implied that those piRNAs might be involved in sexual maturation difference. The integrated network analysis results suggested that some differentially expressed genes were involved in spermatogenesis through the ECM-receptor interaction, focal adhesion, Wnt and PI3K-Akt signaling pathways, some particular miRNAs have the negative regulation roles and some special piRNAs have the positive and negative regulation roles in testicular development. Our data provide novel insights into the molecular expression and regulation similarities and diversities of spermatogenesis and testicular development in different pig breeds at different stages of sexual maturity.
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Affiliation(s)
- Yao Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jialian Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Guangxi Yangxiang Pig Gene Technology limited Company, Guigang, 537120, People's Republic of China
| | - Chengchi Fang
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Liang Shi
- Guangxi Yangxiang Incorporated Company, Guigang, 537100, People's Republic of China
| | - Jiajian Tan
- Guangxi Yangxiang Incorporated Company, Guigang, 537100, People's Republic of China
| | - Yuanzhu Xiong
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Bin Fan
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Guangxi Yangxiang Pig Gene Technology limited Company, Guigang, 537120, People's Republic of China
| | - Changchun Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
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