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Wang P, Paquet ÉR, Robert C. Comprehensive transcriptomic analysis of long non-coding RNAs in bovine ovarian follicles and early embryos. PLoS One 2023; 18:e0291761. [PMID: 37725621 PMCID: PMC10508637 DOI: 10.1371/journal.pone.0291761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been the subject of numerous studies over the past decade. First thought to come from aberrant transcriptional events, lncRNAs are now considered a crucial component of the genome with roles in multiple cellular functions. However, the functional annotation and characterization of bovine lncRNAs during early development remain limited. In this comprehensive analysis, we review lncRNAs expression in bovine ovarian follicles and early embryos, based on a unique database comprising 468 microarray hybridizations from a single platform designed to target 7,724 lncRNA transcripts, of which 5,272 are intergenic (lincRNA), 958 are intronic, and 1,524 are antisense (lncNAT). Compared to translated mRNA, lncRNAs have been shown to be more tissue-specific and expressed in low copy numbers. This analysis revealed that protein-coding genes and lncRNAs are both expressed more in oocytes. Differences between the oocyte and the 2-cell embryo are also more apparent in terms of lncRNAs than mRNAs. Co-expression network analysis using WGCNA generated 25 modules with differing proportions of lncRNAs. The modules exhibiting a higher proportion of lncRNAs were found to be associated with fewer annotated mRNAs and housekeeping functions. Functional annotation of co-expressed mRNAs allowed attribution of lncRNAs to a wide array of key cellular events such as meiosis, translation initiation, immune response, and mitochondrial related functions. We thus provide evidence that lncRNAs play diverse physiological roles that are tissue-specific and associated with key cellular functions alongside mRNAs in bovine ovarian follicles and early embryos. This contributes to add lncRNAs as active molecules in the complex regulatory networks driving folliculogenesis, oogenesis and early embryogenesis all of which are necessary for reproductive success.
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Affiliation(s)
- Pengmin Wang
- Département des sciences animales, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Québec City, Québec, Canada
| | - Éric R. Paquet
- Département des sciences animales, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Québec City, Québec, Canada
| | - Claude Robert
- Département des sciences animales, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Québec City, Québec, Canada
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2
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Zhang Z, Shi Q, Zhu X, Jin L, Lang L, Lyu S, Xin X, Huang Y, Yu X, Li Z, Chen S, Xu Z, Zhang W, Wang E. Identification and Functional Analysis of Transcriptome Profiles, Long Non-Coding RNAs, Single-Nucleotide Polymorphisms, and Alternative Splicing from the Oocyte to the Preimplantation Stage of Sheep by Single-Cell RNA Sequencing. Genes (Basel) 2023; 14:1145. [PMID: 37372325 DOI: 10.3390/genes14061145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
Numerous dynamic and complicated processes characterize development from the oocyte to the embryo. However, given the importance of functional transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms, and alternative splicing during embryonic development, the effect that these features have on the blastomeres of 2-, 4-, 8-, 16-cell, and morula stages of development has not been studied. Here, we carried out experiments to identify and functionally analyze the transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms (SNPs), and alternative splicing (AS) of cells from sheep from the oocyte to the blastocyst developmental stages. We found between the oocyte and zygote groups significantly down-regulated genes and the second-largest change in gene expression occurred between the 8- and 16-cell stages. We used various methods to construct a profile to characterize cellular and molecular features and systematically analyze the related GO and KEGG profile of cells of all stages from the oocyte to the blastocyst. This large-scale, single-cell atlas provides key cellular information and will likely assist clinical studies in improving preimplantation genetic diagnosis.
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Affiliation(s)
- Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Qiaoting Shi
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Xiaoting Zhu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Lei Jin
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Limin Lang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Shijie Lyu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Xiaoling Xin
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiang Yu
- Henan Animal Health Supervision Institute, Zhengzhou 450003, China
| | - Zhiming Li
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China
| | - Sujuan Chen
- Synthetic Biology Engineering Lab of Henan Province, School of Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, China
| | - Zhaoxue Xu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Wei Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
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3
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Xie J, Xu X, Liu S. Intercellular communication in the cumulus-oocyte complex during folliculogenesis: A review. Front Cell Dev Biol 2023; 11:1087612. [PMID: 36743407 PMCID: PMC9893509 DOI: 10.3389/fcell.2023.1087612] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
During folliculogenesis, the oocyte and surrounding cumulus cells form an ensemble called the cumulus-oocyte complex (COC). Due to their interdependence, research on the COC has been a hot issue in the past few decades. A growing body of literature has revealed that intercellular communication is critical in determining oocyte quality and ovulation. This review provides an update on the current knowledge of COC intercellular communication, morphology, and functions. Transzonal projections (TZPs) and gap junctions are the most described structures of the COC. They provide basic metabolic and nutrient support, and abundant molecules for signaling pathways and regulations. Oocyte-secreted factors (OSFs) such as growth differentiation factor 9 and bone morphogenetic protein 15 have been linked with follicular homeostasis, suggesting that the communications are bidirectional. Using advanced techniques, new evidence has highlighted the existence of other structures that participate in intercellular communication. Extracellular vesicles can carry transcripts and signaling molecules. Microvilli on the oocyte can induce the formation of TZPs and secrete OSFs. Cell membrane fusion between the oocyte and cumulus cells can lead to sharing of cytoplasm, in a way making the COC a true whole. These findings give us new insights into related reproductive diseases like polycystic ovary syndrome and primary ovarian insufficiency and how to improve the outcomes of assisted reproduction.
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Affiliation(s)
- Jun Xie
- Reproductive Medicine Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiao Xu
- Department of Obstetrics and Gynecology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Suying Liu
- Reproductive Medicine Center, Zhongshan Hospital, Fudan University, Shanghai, China,*Correspondence: Suying Liu,
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4
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Yao Y, Meng Z, Li W, Xu Y, Wang Y, Suolang S, Xi G, Cao L, Guo M. Profiling and Functional Analysis of long non-coding RNAs in yak healthy and atretic follicles. Anim Reprod 2022; 19:e20210131. [PMID: 36313598 PMCID: PMC9613354 DOI: 10.1590/1984-3143-ar2021-0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 09/13/2022] [Indexed: 11/26/2022] Open
Abstract
Yak is the livestock on which people live in plateau areas, but its fecundity is low. Follicular development plays a decisive role in yak reproductive performance. As an important regulatory factor, the expression of long non-coding RNA (lncRNAs) in yak follicular development and its regulatory mechanism remains unclear. To explore the differentially expressed lncRNAs between healthy and atretic follicular in yaks. We used RNA-seq to construct lncRNA, miRNA, and mRNA expression profiles in yak atretic and healthy follicles, and the RNA sequence results were identified by qPCR. In addition, the correlation of lncRNA and targeted mRNA was also analyzed by Starbase software. Moreover, lncRNA/miRNA/mRNA networks were constructed by Cytoscape software, and the network was verified by dual-luciferase analysis. A total of 682 novel lncRNAs, 259 bta-miRNAs, and 1704 mRNAs were identified as differentially expressed between healthy and atretic follicles. Among them, 135 mRNAs were positively correlated with lncRNA expression and 97 were negatively correlated, which may be involved in the yak follicular development. In addition, pathway enrichment analysis of differentially expressed lncRNA host genes by Kyoto Genome Encyclopedia (KEGG) showed that host genes were mainly involved in hormone secretion, granulosa cell apoptosis, and follicular development. In conclusion, we identified a series of novel lncRNAs, constructed the lncRNA ceRNA regulatory network, and provided comprehensive resources for exploring the role of lncRNAs in yak ovarian follicular development.
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Affiliation(s)
- Yilong Yao
- Animal Science Department, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhaoyi Meng
- Animal Science Department, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China.,Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease Research, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China
| | - Wangchang Li
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yefen Xu
- Animal Science Department, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China.,Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease Research, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China
| | - Yunlu Wang
- Animal Science Department, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China.,Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease Research, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China
| | - Sizhu Suolang
- Animal Science Department, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China
| | - Guangyin Xi
- College of Animal Sciences and Technology, China Agricultural University, Haidian, Beijing, China
| | - Lei Cao
- Animal Science Department, Tibet Agriculture & Animal Husbandry College, Nyingchi, Tibet, China
| | - Min Guo
- College of Animal Sciences and Technology, China Agricultural University, Haidian, Beijing, China
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5
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Hosseinzadeh S, Masoudi AA, Torshizi RV, Ehsani A. Identification of differentially expressed long noncoding RNAs in the ovarian tissue of ewes Shal and Sangsari using RNA-seq. Vet Med Sci 2022; 8:2138-2146. [PMID: 35667079 PMCID: PMC9514483 DOI: 10.1002/vms3.859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Background The ovary has an important role in reproductive function. Animal reproduction is dominated by numerous coding genes and noncoding elements. Although long noncoding RNAs (LncRNAs) are important in biological activity, little is known about their role in the ovary and fertility. Methods Three adult Shal ewes and three adult Sangsari ewes were used in this investigation. LncRNAs in ovarian tissue from two breeds were identified using bioinformatics analyses, and then target genes of LncRNAs were discovered. Target genes were annotated using the DAVID database, and their interactions were examined using the STRING database and Cytoscape software. The expression levels of seven LncRNAs with their target genes were assessed by real‐time PCR to confirm the RNA‐seq. Results Among all the identified LncRNAs, 124 LncRNAs were detected with different expression levels between the two breeds (FDR < 0.05). According to the DAVID database, target genes were discovered to be engaged in one biological process, one cellular component, and 21 KEGG pathways (FDR < 0.05). The PES1, RPS9, EF‐1, Plectin, SURF6, CYC1, PRKACA MAPK1, ITGB2 and BRD2 genes were some of the most crucial target genes (hub genes) in the ovary. Conclusion These results could pave the way for future efforts to address sheep prolificacy barriers.
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Affiliation(s)
- Shahram Hosseinzadeh
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Ali Akbar Masoudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Rasoul Vaez Torshizi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Alireza Ehsani
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
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6
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Zhao D, Wang C, Yan S, Chen R. Advances in the identification of long non-coding RNA binding proteins. Anal Biochem 2021; 639:114520. [PMID: 34896376 DOI: 10.1016/j.ab.2021.114520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/04/2021] [Accepted: 12/04/2021] [Indexed: 02/06/2023]
Abstract
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nt without evident protein coding function. They play important regulatory roles in many biological processes, e.g., gene regulation, chromatin remodeling, and cell fate determination during development. Dysregulation of lncRNAs has been observed in various diseases including cancer. Interacting with proteins is a crucial way for lncRNAs to play their biological roles. Therefore, the characterization of lncRNA binding proteins is important to understand their functions and to delineate the underlying molecular mechanism. Large-scale studies based on mass spectrometry have characterized over a thousand new RNA binding proteins without known RNA-binding domains, thus revealing the complexity and diversity of RNA-protein interactions. In addition, several methods have been developed to identify the binding proteins for particular RNAs of interest. Here we review the progress of the RNA-centric methods for the identification of RNA-protein interactions, focusing on the studies involving lncRNAs, and discuss their strengths and limitations.
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Affiliation(s)
- Dongqing Zhao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Chunqing Wang
- The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China
| | - Shuai Yan
- Peking University First Hospital, Peking University Health Science Center, Beijing, 100191, China
| | - Ruibing Chen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.
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7
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Lagarrigue S, Lorthiois M, Degalez F, Gilot D, Derrien T. LncRNAs in domesticated animals: from dog to livestock species. Mamm Genome 2021; 33:248-270. [PMID: 34773482 PMCID: PMC9114084 DOI: 10.1007/s00335-021-09928-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022]
Abstract
Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.
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Affiliation(s)
| | - Matthias Lorthiois
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France
| | - Fabien Degalez
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, 35590, Saint-Gilles, France
| | - David Gilot
- CLCC Eugène Marquis, INSERM, Université Rennes, UMR_S 1242, 35000, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France.
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8
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Cai X, Wu S, Mipam T, Luo H, Yi C, Xu C, Zhao W, Wang H, Zhong J. Testis transcriptome profiling identified lncRNAs involved in spermatogenic arrest of cattleyak. Funct Integr Genomics 2021; 21:665-678. [PMID: 34626308 DOI: 10.1007/s10142-021-00806-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/31/2021] [Accepted: 09/11/2021] [Indexed: 02/07/2023]
Abstract
Cattleyaks are the crossbred offspring between cattle and yaks, exhibiting the prominent adaptability to the harsh environment as yaks and much higher growth performances than yaks around Qinghai-Tibet plateau. Unfortunately, cattleyak cannot be effectively used in yak breeding due to its male infertility resulted from spermatogenic arrest. In this study, we performed RNA sequencing (RNA-seq) and bioinformatics analysis to determine the expression profiles of long noncoding RNA (lncRNA) from cattleyak and yak testis. A total of 604 differentially expressed (DE) lncRNAs (135 upregulated and 469 downregulated) were identified in cattleyak with respect to yak. Through gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, we identified several DE lncRNAs regulating the mitotic cell cycle processes by targeting the genes significantly associated with the mitotic cell cycle checkpoint and DNA damage checkpoint term and also significantly involved in p53 signaling pathway, mismatch repair and homologous recombination pathway (P < 0.05). The reverse transcription PCR (RT-PCR) and quantitative Real-Time PCR (qRT-PCR) analysis of the randomly selected fourteen DE lncRNAs and the seven target genes validated the RNA-seq data and their true expressions during spermatogenesis in vivo. Molecular cloning and sequencing indicated that the testis lncRNAs NONBTAT012170 and NONBTAT010258 presented higher similarity among different cattleyak and yak individuals. The downregulation of these target genes in cattleyak contributed to the abnormal DNA replication and spermatogenic arrest during the S phase of mitotic cell cycle. This study provided a novel insight into lncRNA expression profile changes associated with spermatogenic arrest of cattleyak.
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Affiliation(s)
- Xin Cai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China.
| | - Shixin Wu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, Sichuan, China
| | - TserangDonko Mipam
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China
| | - Hui Luo
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, Sichuan, China
| | - Chuanping Yi
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, Sichuan, China
| | - Chuanfei Xu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, Sichuan, China
| | - Wangsheng Zhao
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, Sichuan, China
| | - Hongying Wang
- College of Chemistry&Environment, Southwest Minzu University, Chengdu, 610041, Sichuan, China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China.
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9
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Zhang D, Xia T, Li H, Li Z, Sun G, Li G, Tian Y, Liu X, Xu D, Kang X. Estrogen enhances the expression of a growth-associated long noncoding RNA in chicken liver via ERα. Br Poult Sci 2021; 62:336-345. [PMID: 33390024 DOI: 10.1080/00071668.2020.1868405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
1. The long noncoding RNA lncGLM is significantly differentially expressed in the livers of peak-laying hens compared with that in the livers of pre-laying hens, but its potential biological role and expression regulation are unclear.2. To explore the potential biological function of lncGLM, single nucleotide polymorphism (SNP) detection and association analysis were carried out in the Gushi×Anka F2 resource population.3. The tissues and spatiotemporal expression characteristics of lncGLM were analysed by real-time quantitative PCR. The effects of 17β-oestradiol on the expression of lncGLM expression were analysed through in vitro and in vivo experiments.4. The results showed that a g.19069338 T > C SNP was present in lncGLM. Association analysis revealed that lncGLM was significantly associated with body slanting length at 12 weeks, body weight at 12 weeks, shank length at four weeks, chest depth at eight weeks, pelvic width at 12 weeks, eviscerated weight, head weight, pancreas weight, pectoralis weight, leg muscle weight, muscular stomach weight rate, pancreas weight rate, carcase weight, aspartate aminotransferase, creatinine and pectoral muscle water loss rate.5. The expression of lncGLM in the liver was higher than that in other sampled tissues. In addition, the expression of lncGLM in the liver was significantly higher in the peak-laying period than at the pre-laying period. Both in vitro and in vivo experiments showed that lncGLM expression was regulated by 17β-oestradiol via oestrogen receptor alpha (ER-α). These results demonstrated that the chicken lncGLM gene is highly expressed in liver tissue and regulated by oestrogen through ER-α.
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Affiliation(s)
- D Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - T Xia
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - H Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - Z Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - G Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - G Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - Y Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - X Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
| | - D Xu
- Henan Liujiang Ecological Animal Husbandry Co., Ltd, Hebi, China
| | - X Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Henan Agricultural University, Zhengzhou, China
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10
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Liu A, Liu M, Li Y, Chen X, Zhang L, Tian S. Differential expression and prediction of function of lncRNAs in the ovaries of low and high fecundity Hanper sheep. Reprod Domest Anim 2021; 56:604-620. [PMID: 33475207 DOI: 10.1111/rda.13898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022]
Abstract
Litter size is an important trait that determines the production efficiency of sheep bred for meat. Its detailed investigation can reveal the molecular mechanisms that control the fecundity of sheep and possibly accelerate the breeding process of new varieties of sheep that have high prolificacy. Long non-coding RNAs (lncRNAs) have proven to be an important factor in the regulation of follicular development. However, the mechanisms by which lncRNAs regulate litter size in sheep remain unclear. In the present study, ovarian tissues from the follicular (F) or luteal phase (L) of Hanper sheep that were either monotocous (M) or polytocous (P; FM, FP, LM and LP groups) were collected and sequenced to identify differentially expressed lncRNAs and predict their function. The results indicate that the number of up- and down-regulated lncRNAs in the follicular phase (FM vs. FP) was 95 and 111 and 109 and 49, respectively, in the luteal phase (LM vs. LP). The functional enrichment of the different lncRNAs coexpressed with mRNA was analysed. The results demonstrated that the KISS1-GnRH-LH/FSH-E2 and EGF-EGFR-RAS-PI3K signalling pathways promoted the initiation of the primordial period, follicular development and ovulation in the follicular phase (FM vs. FP). During the luteal phase (LM vs. LP), the production and development of the corpus luteum in ewes was influenced by the KITLG-KIT/FGF-FGFR/HGF-MET-RAS-ERK signalling pathway. STEM clustering functional enrichment analysis of the differentially expressed lncRNAs indicated that profile11 was principally enriched in the Cytokine-Jak-STAT, PDGF-PDGFR-PI3K and KITLG-KIT-RAS-ERK signalling pathways. By analysis of the differential expression of the lncRNAs and their expression in each group, lncRNAs Xist (loc101112291) and Gtl2 (loc101123329) were found to be highly expressed, suggesting that regulation of follicular development was mediated through methylation processes.
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Affiliation(s)
- Aiju Liu
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Menghe Liu
- Discipline of Obstetrics and Gynaecology, School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Yuexin Li
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Xiaoyong Chen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Limeng Zhang
- Laboratory of Molecular Biology, Zhengzhou Normal University, Zhengzhou, China
| | - Shujun Tian
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, China.,The Research Center of Cattle and Sheep, Embryonic Technique of Hebei Province, Baoding, China
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11
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Movahed E, Shabani R, Hosseini S, Shahidi S, Salehi M. Interfering Effects of In Vitro Fertilization and Vitrification on Expression of Gtl2 and Dlk1 in Mouse Blastocysts. INTERNATIONAL JOURNAL OF FERTILITY & STERILITY 2020; 14:110-115. [PMID: 32681622 PMCID: PMC7382687 DOI: 10.22074/ijfs.2020.5984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 11/04/2019] [Indexed: 12/31/2022]
Abstract
Background Embryo vitrification is a key instrument in assisted reproductive technologies (ARTs). However, there is increasing concern that vitrification adversely affects embryo development. This study intends to assess the effect of vitrification on developmental competence, in addition to expressions of long non-coding RNA (lncRNA) gene trap locus 2 (Gtl2) and its reciprocal imprinted gene delta-like homolog 1 (Dlk1), in mouse blastocysts. Materials and Methods In this experimental study, we have designed three experimental groups: control (fresh blastocysts collected from superovulated mice), in vitro fertilization (IVF; blastocysts derived from IVF) and vitrification (IVF derived blastocysts subjected to vitrification/warming at the 2-cell stage). Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to assess the expression levels of Gtl2 and Dlk1 in the blastocysts. Results The results showed that vitrification group had significantly lower blastocyst and hatching rates compared to the IVF group (P<0.037) and (P<0.041), respectively. Gtl2 was down-regulated and Dlk1 was up-regulated following the IVF and vitrification (P<0.05). Conclusion These results suggested that IVF and vitrification disturbed genomic imprinting and lncRNA gene expressions, which might affect the health of IVF children.
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Affiliation(s)
- Elham Movahed
- Department of Anatomical Sciences, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ronak Shabani
- Department of Anatomical Sciences, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran. Electronic Address:
| | - Sara Hosseini
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Solmaz Shahidi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Salehi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran. Electronic Address:
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12
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Yang CX, Wang PC, Liu S, Miao JK, Liu XM, Miao YL, Du ZQ. Long noncoding RNA 2193 regulates meiosis through global epigenetic modification and cytoskeleton organization in pig oocytes. J Cell Physiol 2020; 235:8304-8318. [PMID: 32239703 DOI: 10.1002/jcp.29675] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 03/10/2020] [Indexed: 12/13/2022]
Abstract
Long noncoding RNAs (lncRNAs) regulate a variety of physiological and pathological processes. However, the biological function of lncRNAs in mammalian germ cells remains largely unexplored. Here we identified one novel lncRNA (lncRNA2193) from single-cell RNA sequencing performed on porcine oocytes and investigated its function in oocyte meiosis. During in vitro maturation (IVM), from germinal vesicle (GV, 0 hr), GV breakdown (GVBD, 24 hr), to metaphase II stage (MII, 44 hr), the transcriptional abundance of lncRNA2193 remained stable and high. LncRNA2193 interference by small interfering RNA microinjection into porcine GV oocytes could significantly inhibit rates of GVBD and the first polar body extrusion, but enhance the rates of oocytes with a nuclear abnormality. Moreover, lncRNA2193 knockdown disturbed cytoskeletal organization (F-actin and spindle), and decreased DNA 5-methylcytosine (5mC) and histone trimethylation (H3K4me3, H3K9me3, H3K27me3, and H3K36me3) levels. The lncRNA2193 downregulation induced a decrease of 5mC level could be partially due to the reduction of DNA methyltransferase 3A and 3B, and the elevation of 5mC-hydroxylase ten-11 translocation 2 (TET2). After parthenogenetic activation of MII oocytes, parthenotes exhibited higher fragmentation but lower cleavage rates in the lncRNA2193 downregulated group. However, lncRNA2193 interference performed on mature MII oocytes and parthenotes at 1-cell stage did not affect the cleavage and blasctocyst rates of pathenotes. Taken together, lncRNA2193 plays an important role in porcine oocyte maturation, providing more insights for relevant investigations on mammalian germ cells.
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Affiliation(s)
- Cai-Xia Yang
- College of Animal Science, Yangtze University, Jingzhou, Hubei, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Pei-Chao Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Shuai Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Jia-Kun Miao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xiao-Man Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhi-Qiang Du
- College of Animal Science, Yangtze University, Jingzhou, Hubei, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
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13
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Zhang L, Yu M, Xu H, Wei X, Liu Y, Huang C, Chen H, Guo Z. RNA sequencing revealed the abnormal transcriptional profile in cloned bovine embryos. Int J Biol Macromol 2020; 150:492-500. [PMID: 32035150 DOI: 10.1016/j.ijbiomac.2020.02.026] [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] [Received: 07/31/2019] [Revised: 02/04/2020] [Accepted: 02/04/2020] [Indexed: 12/11/2022]
Abstract
Somatic cell nuclear transfer (SCNT) has potential applications in agriculture and biomedicine, but the efficiency of cloning is still low. In this study, the transcriptional profiles in cloned and fertilized embryos were measured and compared by RNA sequencing. The 2-cell embryos were detected to identify the earliest transcriptional differences between embryos derived through IVF and SCNT. As a result, 364 genes showed decreased expression in cloned 2-cell embryos and were enriched in "intracellular protein transport" and "ubiquitin mediated proteolysis". In blastocysts, 593 genes showed decreased expression in cloned blastocysts and were enriched in "RNA binding", "nucleotide binding", "embryo development", and "adherens junction". We identified 14 development related genes that were not activated in the cloned embryos. Then, 68 and 245 long non-coding RNAs were recognized abnormally expressed in cloned 2-cell embryos and cloned blastocysts, respectively. Furthermore, we found that incomplete RNA-editing occurred in cloned embryos and might be caused by decreased ADAR expression. In conclusion, our study revealed the abnormal transcripts and deficient RNA-editing sites in cloned embryos and provided new data for further mechanistic studies of somatic nuclear reprogramming.
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Affiliation(s)
- Lei Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
| | - Mengying Yu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
| | - Hongyu Xu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
| | - Xing Wei
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
| | - Yingxiang Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
| | - Chenyang Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
| | - Huanhuan Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
| | - Zekun Guo
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
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14
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Sabara PH, Jakhesara SJ, Panchal KJ, Joshi CG, Koringa PG. Transcriptomic analysis to affirm the regulatory role of long non-coding RNA in horn cancer of Indian zebu cattle breed Kankrej (Bos indicus). Funct Integr Genomics 2019; 20:75-87. [PMID: 31368028 DOI: 10.1007/s10142-019-00700-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/15/2019] [Accepted: 07/01/2019] [Indexed: 01/08/2023]
Abstract
Long non-coding RNA (lncRNA) was previously considered as a non-functional transcript, which now established as part of regulatory elements of biological events such as chromosome structure, remodeling, and regulation of gene expression. The study presented here showed the role of lncRNA through differential expression analysis on cancer-related coding genes in horn squamous cell carcinoma of Indian zebu cattle. A total of 10,360 candidate lncRNAs were identified and further analyzed for its coding potential ability using three tools (CPC, CPAT, and PLEK) that provide 8862 common lncRNAs. Pfam analysis of these common lncRNAs gave 8612 potential candidates for lncRNA differential expression analysis. Differential expression analysis showed a total of 59 significantly differentially expressed genes and 19 lncRNAs. Pearson's correlation analysis was used to identify co-expressed mRNA-lncRNAs to established relation of the regulatory role of lncRNAs in horn cancer. We established a positive relation of seven upregulated (XLOC_000016, XLOC_002198, XLOC_002851, XLOC_ 007383, XLOC_010701, XLOC_010272, and XLOC_011517) and one downregulated (XLOC_011302) lncRNAs with eleven genes that are related to keratin family protein, keratin-associated protein family, cornifelin, corneodesmosin, serpin family protein, and metallothionein that have well-established role in squamous cell carcinoma through cellular communication, cell growth, cell invasion, and cell migration. These biological events were found to be related to the MAPK pathway of cell cycle regulation indicating the role of lncRNAs in manipulating cell cycle regulation during horn squamous cell carcinomas that will be useful in identifying molecular portraits related to the development of horn cancer.
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Affiliation(s)
- Pritesh H Sabara
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Subhash J Jakhesara
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Ketankumar J Panchal
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India.
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15
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Gao Y, Li S, Lai Z, Zhou Z, Wu F, Huang Y, Lan X, Lei C, Chen H, Dang R. Analysis of Long Non-Coding RNA and mRNA Expression Profiling in Immature and Mature Bovine ( Bos taurus) Testes. Front Genet 2019; 10:646. [PMID: 31333723 PMCID: PMC6624472 DOI: 10.3389/fgene.2019.00646] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/18/2019] [Indexed: 01/08/2023] Open
Abstract
Testis development and spermatogenesis are strictly regulated by numbers of genes and non-coding genes. However, long non-coding RNAs (lncRNAs) as key regulators in multitudinous biological processes have not been systematically identified in bovine testes during sexual maturation. In this study, we comprehensively analyzed lncRNA and mRNA expression profiling of six bovine testes at 3 days after birth and 13 months by RNA sequencing. 23,735 lncRNAs and 22,118 mRNAs were identified, in which 540 lncRNAs (P-value < 0.05) and 3,525 mRNAs (P-adjust < 0.05) were significantly differentially expressed (DE) between two stages. Correspondingly, the results of RT-qPCR analysis showed well correlation with the transcriptome data. Moreover, GO and KEGG enrichment analyses showed that DE genes and target genes of DE lncRNAs were enriched in spermatogenesis. Furthermore, we constructed lncRNA–gene interaction networks; consequently, 15 DE lncRNAs and 12 cis-target genes were involved. The target genes (SPATA16, TCF21, ZPBP, PACRG, ATP8B3, COMP, ACE, and OSBP2) were found associated with bovine sexual maturation. In addition, the expression of lncRNAs and cis-target genes was detected in bovine Leydig cells, Sertoli cells, and spermatogonia. Our study identified and analyzed lncRNAs and mRNAs in testis tissues, suggesting that lncRNAs may regulate testis development and spermatogenesis. Our findings provided new insights for further investigation of biological function in bovine lncRNA.
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Affiliation(s)
- Yuan Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shipeng Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhenyu Lai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zihui Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Fei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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16
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Lu C, Xing Y, Cai H, Shi Y, Liu J, Huang Y. Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos). BMC Genomics 2019; 20:36. [PMID: 30634898 PMCID: PMC6330444 DOI: 10.1186/s12864-018-5422-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are important component of mammalian genomes, where their numbers are even larger than that of protein-coding genes. For example, human (Homo sapiens) (96,308 vs. 20,376) and mouse (Mus musculus) (87,774 vs. 22,630) have more lncRNA genes than protein-coding genes in the NONCODEv5 database. Recently, mammalian lncRNAs were reported to play critical roles in immune response to influenza A virus infections. Such observation inspired us to identify lncRNAs related to immune response to influenza A virus in duck, which is the most important natural host of influenza A viruses. RESULTS We explored features of 62,447 lncRNAs from human, mouse, chicken, zebrafish and elegans, and developed a pipeline to identify lncRNAs using the identified features with transcriptomic data. We then collected 151,970 assembled transcripts from RNA-Seq data of 21 individuals from three tissues and annotated 4094 duck lncRNAs. Comparing to duck protein-coding transcripts, we found that 4094 lncRNAs had smaller number of exons (2.4 vs. 10.2) and longer length of transcripts (1903.0 bp vs. 1686.9 bp) on average. Among them, 3586 (87.6%) lncRNAs located in intergenic regions and 619 lncRNAs showed differential expression in ducks infected by H5N1 virus when compared to control individuals. 58 lncRNAs were involved into two co-expressional modules related to anti-influenza A virus immune response. Moreover, we confirmed that eight lncRNAs showed remarkably differential expression both in vivo (duck individuals) and in vitro (duck embryo fibroblast cells, DEF cells) after infected with H5N1 viruses, implying they might play important roles in response to influenza A virus infection. CONCLUSIONS This study presented an example to annotate lncRNA in new species based on model species using transcriptome data. These data and analysis provide information for duck lncRNAs' function in immune response to influenza A virus.
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Affiliation(s)
- Chang Lu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Yanling Xing
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Han Cai
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Yirong Shi
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Jinhua Liu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yinhua Huang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China.
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17
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Li Q, Qiao J, Zhang Z, Shang X, Chu Z, Fu Y, Chu M. Identification and analysis of differentially expressed long non-coding RNAs of Chinese Holstein cattle responses to heat stress. Anim Biotechnol 2018; 31:9-16. [PMID: 30589366 DOI: 10.1080/10495398.2018.1521337] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The mechanisms that dairy cattle respond to environmental stresses are very complicated. Previous research into the molecular mechanisms of mammalian heat stress has largely focused on the role of protein-coding genes and small non-coding RNAs. Recently, it has become apparent that large numbers of long non-coding RNAs transcribed from mammalian genomes play extensive roles in transcriptional regulation. However, the expression of lncRNAs and their biological functions in heat stress in dairy cattle remain unknown. In this study, we employed a deep RNA sequencing to examine lncRNA expression profiles of heat stressed and non-heat stressed Chinese Holstein cattle. We found that 24,795 novel and 3763 known lncRNAs were expressed in the bovine mammary gland, of which 174 were differentially expressed in heat stress condition, among them, 156 lncRNAs were up-regulated and 18 were down-regulated. Through Cis role analysis, 16,474 lncRNAs were transcribed close to protein-coding neighbors. In addition, 11 and 2024 lncRNAs harbored precursors of known and predicted microRNAs, respectively, were annotated in the precursor analysis of miRNAs. Taken together, our findings represent the first systematic investigation of lncRNA expression in heat stressed Chinese Holstein and provide a resource for further research into the molecular mechanisms of lncRNAs function in dairy cattle.
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Affiliation(s)
- Qiuling Li
- College of Life Sciences, Edible and Medicinal Fungi Research and Development Center, Langfang Normal University, Langfang, P. R. China
| | - Jie Qiao
- College of Life Sciences, Edible and Medicinal Fungi Research and Development Center, Langfang Normal University, Langfang, P. R. China
| | - Zhengfeng Zhang
- Agriculture, Forestry and Water Affairs Department, Langfang Administrative Examination and Approval Bureau, Langfang, P. R. China
| | - Xiaolan Shang
- College of Life Sciences, Edible and Medicinal Fungi Research and Development Center, Langfang Normal University, Langfang, P. R. China
| | - Zhuodong Chu
- College of Life Sciences, Edible and Medicinal Fungi Research and Development Center, Langfang Normal University, Langfang, P. R. China
| | - Yajuan Fu
- College of Life Sciences, Edible and Medicinal Fungi Research and Development Center, Langfang Normal University, Langfang, P. R. China
| | - Mingxing Chu
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
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18
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Ibeagha-Awemu EM, Li R, Dudemaine PL, Do DN, Bissonnette N. Transcriptome Analysis of Long Non-Coding RNA in the Bovine Mammary Gland Following Dietary Supplementation with Linseed Oil and Safflower Oil. Int J Mol Sci 2018; 19:E3610. [PMID: 30445766 PMCID: PMC6274745 DOI: 10.3390/ijms19113610] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 02/08/2023] Open
Abstract
This study aimed to characterize the long non-coding RNA (lncRNA) expression in the bovine mammary gland and to infer their functions in dietary response to 5% linseed oil (LSO) or 5% safflower oil (SFO). Twelve cows (six per treatment) in mid lactation were fed a control diet for 28 days followed by a treatment period (control diet supplemented with 5% LSO or 5% SFO) of 28 days. Mammary gland biopsies were collected from each animal on day-14 (D-14, control period), D+7 (early treatment period) and D+28 (late treatment period) and were subjected to RNA-Sequencing and subsequent bioinformatics analyses. Functional enrichment of lncRNA was performed via potential cis regulated target genes located within 50 kb flanking regions of lncRNAs and having expression correlation of >0.7 with mRNAs. A total of 4955 lncRNAs (325 known and 4630 novel) were identified which potentially cis targeted 59 and 494 genes in LSO and SFO treatments, respectively. Enrichments of cis target genes of lncRNAs indicated potential roles of lncRNAs in immune function, nucleic acid metabolism and cell membrane organization processes as well as involvement in Notch, cAMP and TGF-β signaling pathways. Thirty-two and 21 lncRNAs were differentially expressed (DE) in LSO and SFO treatments, respectively. Six genes (KCNF1, STARD13, BCL6, NXPE2, HHIPL2 and MMD) were identified as potential cis target genes of six DE lncRNAs. In conclusion, this study has identified lncRNAs with potential roles in mammary gland functions and potential candidate genes and pathways via which lncRNAs might function in response to LSO and SFA.
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Affiliation(s)
- Eveline M Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
| | - Ran Li
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Pier-Luc Dudemaine
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
| | - Duy N Do
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
- Department of Animal Science, McGill University, Ste-Anne-De-Bellevue, QC H9X 3V9, Canada.
| | - Nathalie Bissonnette
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
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19
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Gonzalez-Munoz E, Cibelli JB. Somatic Cell Reprogramming Informed by the Oocyte. Stem Cells Dev 2018; 27:871-887. [DOI: 10.1089/scd.2018.0066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Elena Gonzalez-Munoz
- LARCEL, Andalusian Laboratory of Cell Reprogramming (LARCel), Andalusian Center for Nanomedicine and Biotechnology-BIONAND, Málaga, Spain
- Department of Cell Biology, Genetics and Physiology, University of Málaga, Málaga, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine, (CIBER-BBN), Málaga, Spain
| | - Jose B. Cibelli
- LARCEL, Andalusian Laboratory of Cell Reprogramming (LARCel), Andalusian Center for Nanomedicine and Biotechnology-BIONAND, Málaga, Spain
- Department of Animal Science, Michigan State University, East Lansing, MI
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI
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20
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Zhong L, Mu H, Wen B, Zhang W, Wei Q, Gao G, Han J, Cao S. Long non-coding RNAs involved in the regulatory network during porcine pre-implantation embryonic development and iPSC induction. Sci Rep 2018; 8:6649. [PMID: 29703926 PMCID: PMC5923264 DOI: 10.1038/s41598-018-24863-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 04/05/2018] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNAs (lncRNA) play a key role in the orchestration of transcriptional regulation during development and many other cellular processes. The importance of the regulatory co-expression network was highlighted in the identification of the mechanism of these processes in humans and mice. However, elucidation of the properties of porcine lncRNAs involved in the regulatory network during pre-implantation embryonic development and fibroblast reprogramming to induced pluripotent stem cell (iPSC) has been limited to date. Using a weighted gene co-expression network analysis, we constructed the regulatory network and determined that the novel lncRNAs were functionally involved in key events of embryonic development during the pre-implantation period; moreover, reprogramming could be delineated by a small number of potentially functional modules of co-expressed genes. These findings indicate that lncRNAs may be involved in the transcriptional regulation of zygotic genome activation, first lineage segregation and somatic reprogramming to pluripotency. Furthermore, we performed a conservation and synteny analysis with the significant lncRNAs involved in these vital events and validated the results via experimental assays. In summary, the current findings provide a valuable resource to dissect the protein coding gene and lncRNA regulatory networks that underlie the progressive development of embryos and somatic reprogramming.
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Affiliation(s)
- Liang Zhong
- The Animal Science and Technology College, Beijing University of Agriculture, Beijing, China.,State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Haiyuan Mu
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Bingqiang Wen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wei Zhang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qingqing Wei
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, China
| | - Jianyong Han
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China.
| | - Suying Cao
- The Animal Science and Technology College, Beijing University of Agriculture, Beijing, China. .,Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Beijing University of Agriculture, Beijing, China.
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21
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Identification and functional analysis of long non-coding RNAs in human and mouse early embryos based on single-cell transcriptome data. Oncotarget 2018; 7:61215-61228. [PMID: 27542205 PMCID: PMC5308646 DOI: 10.18632/oncotarget.11304] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 08/08/2016] [Indexed: 11/25/2022] Open
Abstract
Epigenetics regulations have an important role in fertilization and proper embryonic development, and several human diseases are associated with epigenetic modification disorders, such as Rett syndrome, Beckwith-Wiedemann syndrome and Angelman syndrome. However, the dynamics and functions of long non-coding RNAs (lncRNAs), one type of epigenetic regulators, in human pre-implantation development have not yet been demonstrated. In this study, a comprehensive analysis of human and mouse early-stage embryonic lncRNAs was performed based on public single-cell RNA sequencing data. Expression profile analysis revealed that lncRNAs are expressed in a developmental stage-specific manner during human early-stage embryonic development, whereas a more temporal-specific expression pattern was identified in mouse embryos. Weighted gene co-expression network analysis suggested that lncRNAs involved in human early-stage embryonic development are associated with several important functions and processes, such as oocyte maturation, zygotic genome activation and mitochondrial functions. We also found that the network of lncRNAs involved in zygotic genome activation was highly preservative between human and mouse embryos, whereas in other stages no strong correlation between human and mouse embryo was observed. This study provides insight into the molecular mechanism underlying lncRNA involvement in human pre-implantation embryonic development.
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Integration of lncRNA and mRNA Transcriptome Analyses Reveals Genes and Pathways Potentially Involved in Calf Intestinal Growth and Development during the Early Weeks of Life. Genes (Basel) 2018; 9:genes9030142. [PMID: 29510583 PMCID: PMC5867863 DOI: 10.3390/genes9030142] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 02/15/2018] [Accepted: 02/21/2018] [Indexed: 12/17/2022] Open
Abstract
A better understanding of the factors that regulate growth and immune response of the gastrointestinal tract (GIT) of calves will promote informed management practices in calf rearing. This study aimed to explore genomics (messenger RNA (mRNA)) and epigenomics (long non-coding RNA (lncRNA)) mechanisms regulating the development of the rumen and ileum in calves. Thirty-two calves (≈5-days-old) were reared for 96 days following standard procedures. Sixteen calves were humanely euthanized on experiment day 33 (D33) (pre-weaning) and another 16 on D96 (post-weaning) for collection of ileum and rumen tissues. RNA from tissues was subjected to next generation sequencing and 3310 and 4217 mRNAs were differentially expressed (DE) between D33 and D96 in ileum and rumen tissues, respectively. Gene ontology and pathways enrichment of DE genes confirmed their roles in developmental processes, immunity and lipid metabolism. A total of 1568 (63 known and 1505 novel) and 4243 (88 known and 4155 novel) lncRNAs were detected in ileum and rumen tissues, respectively. Cis target gene analysis identified BMPR1A, an important gene for a GIT disease (juvenile polyposis syndrome) in humans, as a candidate cis target gene for lncRNAs in both tissues. LncRNA cis target gene enrichment suggested that lncRNAs might regulate growth and development in both tissues as well as posttranscriptional gene silencing by RNA or microRNA processing in rumen, or disease resistance mechanisms in ileum. This study provides a catalog of bovine lncRNAs and set a baseline for exploring their functions in calf GIT development.
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Identification of long non-coding RNAs in the immature and mature rat anterior pituitary. Sci Rep 2017; 7:17780. [PMID: 29259254 PMCID: PMC5736705 DOI: 10.1038/s41598-017-17996-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/04/2017] [Indexed: 12/21/2022] Open
Abstract
Many long non-coding RNAs (lncRNAs) have been identified in several types of human pituitary adenomas and normal anterior pituitary, some of which are involved in the pathogenesis of pituitary adenomas. However, a systematic analysis of lncRNAs expressed at different developmental stages of normal pituitary, particularly in rats, has not been performed. Therefore, we contrasted two cDNA libraries of immature (D15) and mature (D120) anterior pituitary in rat that were sequenced on an Illumina HiSeq Xten platform, and a total of 29,568,806,352 clean reads were identified. Notably, 7039 lncRNA transcripts corresponded to 4442 lncRNA genes, and 1181 lncRNA transcripts were significantly differentially expressed in D15 and D120. In addition, 6839 protein-coding genes (<100 kb upstream and downstream) were the nearest neighbors of 4074 lncRNA genes. An interaction network of lncRNAs and the follicle-stimulating hormone beta-subunit (FSHb) gene was constructed using the lncRNATargets platform, and three novel lncRNAs were obtained. Furthermore, we detected the expression of the novel lncRNAs and ten highly expressed lncRNAs that were randomly selected through quantitative PCR (qPCR). The rat anterior pituitary lncRNA content identified in this study provides a more in-depth understanding of the roles of these lncRNAs in hormone and reproduction development and regulation in mammals.
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Ling Y, Xu L, Zhu L, Sui M, Zheng Q, Li W, Liu Y, Fang F, Zhang X. Identification and analysis of differentially expressed long non-coding RNAs between multiparous and uniparous goat (Capra hircus) ovaries. PLoS One 2017; 12:e0183163. [PMID: 28934224 PMCID: PMC5608193 DOI: 10.1371/journal.pone.0183163] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 07/31/2017] [Indexed: 12/02/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play important roles in almost all biological processes. However, there is little information on the effects of lncRNAs on ovulation and lambing rates. In the present study, we used high-throughput RNA sequencing to identify differentially expressed lncRNAs between the ovaries of multiparous (Mul) and uniparous (Uni) Anhui White goats. Among the 107,255,422 clean reads, 183,754 lncRNAs were significantly differentially expressed between the Uni and Mul. Among them, 455 lncRNAs were co-expressed between the two samples, whereas, 157,523 lncRNAs were uniquely expressed in the Uni, and 25,776 uniquely lncRNAs were expressed in the Mul. Through Cis role analysis, 24 lncRNAs were predicted to overlap with cis-regulatory elements, which involved in Progesterone-mediated oocyte maturation, Steroid biosynthesis, Oocyte meiosis, and gonadotropin-releasing hormone (GnRH) signaling pathway. These 4 pathways were related to ovulation, and the KEGG pathway analysis on target genes of the differentially expressed lncRNAs confirmed this results. In addition, 10 lncRNAs harbored precursors of 40 miRNAs, such as TCONS_00320849 related to a mature miRNA sequence, miR-365a, which was reported to be related to proliferation, were annotated in the precursor analysis of miRNAs. The present expand the understanding of lncRNA biology and contribute to the annotation of the goat genome. The study will provide a resource for lncRNA studies of ovulation and lambing.
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Affiliation(s)
- Yinghui Ling
- College of Animal Science and Technology, Anhui Agricultural University, Anhui Hefei, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Anhui Hefei, China
| | - Lina Xu
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Long Zhu
- College of Animal Science and Technology, Anhui Agricultural University, Anhui Hefei, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Anhui Hefei, China
| | - Menghua Sui
- College of Animal Science and Technology, Anhui Agricultural University, Anhui Hefei, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Anhui Hefei, China
| | - Qi Zheng
- College of Animal Science and Technology, Anhui Agricultural University, Anhui Hefei, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Anhui Hefei, China
| | - Wenyong Li
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, Anhui, China
| | - Yong Liu
- Key Laboratory of Embryo Development and Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, Anhui, China
| | - Fugui Fang
- College of Animal Science and Technology, Anhui Agricultural University, Anhui Hefei, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Anhui Hefei, China
- * E-mail: (ZXR); (FFG)
| | - Xiaorong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Anhui Hefei, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Anhui Hefei, China
- * E-mail: (ZXR); (FFG)
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Abstract
Fully grown oocytes arrest meiosis at prophase I and deposit maternal RNAs. A subset of maternal transcripts is stored in a dormant state in the oocyte, and the timely driven translation of specific mRNAs guides meiotic progression, the oocyte-embryo transition, and early embryo development. In the absence of transcription, the regulation of gene expression in oocytes is controlled almost exclusively at the level of transcriptome and proteome stabilization and at the level of protein synthesis.This chapter focuses on the recent findings on RNA distribution related to the temporal and spatial translational control of the meiotic cycle progression in mammalian oocytes. We discuss the most relevant mechanisms involved in the organization of the oocyte's maternal transcriptome storage and localization, and the regulation of translation, in correlation with the regulation of oocyte meiotic progression.
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Bouckenheimer J, Assou S, Riquier S, Hou C, Philippe N, Sansac C, Lavabre-Bertrand T, Commes T, Lemaître JM, Boureux A, De Vos J. Long non-coding RNAs in human early embryonic development and their potential in ART. Hum Reprod Update 2016; 23:19-40. [PMID: 27655590 DOI: 10.1093/humupd/dmw035] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 07/20/2016] [Accepted: 08/23/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human long non-coding RNAs (lncRNAs) are an emerging category of transcripts with increasingly documented functional roles during development. LncRNAs and roles during human early embryo development have recently begun to be unravelled. OBJECTIVE AND RATIONALE This review summarizes the most recent knowledge on lncRNAs and focuses on their expression patterns and role during early human embryo development and in pluripotent stem cells (PSCs). Public mRNA sequencing (mRNA-seq) data were used to illustrate these expression signatures. SEARCH METHODS The PubMed and EMBASE databases were first interrogated using specific terms, such as 'lncRNAs', to get an extensive overview on lncRNAs up to February 2016, and then using 'human lncRNAs' and 'embryo', 'development', or 'PSCs' to focus on lncRNAs involved in human embryo development or in PSC.Recently published RNA-seq data from human oocytes and pre-implantation embryos (including single-cell data), PSC and a panel of normal and malignant adult tissues were used to describe the specific expression patterns of some lncRNAs in early human embryos. OUTCOMES The existence and the crucial role of lncRNAs in many important biological phenomena in each branch of the life tree are now well documented. The number of identified lncRNAs is rapidly increasing and has already outnumbered that of protein-coding genes. Unlike small non-coding RNAs, a variety of mechanisms of action have been proposed for lncRNAs. The functional role of lncRNAs has been demonstrated in many biological and developmental processes, including cell pluripotency induction, X-inactivation or gene imprinting. Analysis of RNA-seq data highlights that lncRNA abundance changes significantly during human early embryonic development. This suggests that lncRNAs could represent candidate biomarkers for developing non-invasive tests for oocyte or embryo quality. Finally, some of these lncRNAs are also expressed in human cancer tissues, suggesting that reactivation of an embryonic lncRNA program may contribute to human malignancies. WIDER IMPLICATIONS LncRNAs are emerging potential key players in gene expression regulation. Analysis of RNA-seq data from human pre-implantation embryos identified lncRNA signatures that are specific to this critical step. We anticipate that further studies will show that these new transcripts are major regulators of embryo development. These findings might also be used to develop new tests/treatments for improving the pregnancy success rate in IVF procedures or for regenerative medicine applications involving PSC.
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Affiliation(s)
- Julien Bouckenheimer
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | - Said Assou
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | - Sébastien Riquier
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | - Cyrielle Hou
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | - Nicolas Philippe
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France.,Coretec, Montpellier, France
| | - Caroline Sansac
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | | | - Thérèse Commes
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France.,Institut de Biologie Computationnelle, Montpellier F 34000, France
| | - Jean-Marc Lemaître
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France .,INSERM, U1183, Montpellier F 34000, France.,Stem Cell Core Facility SAFE-iPSC, INGESTEM, Saint-Eloi Hospital, Montpellier F 34000, France
| | - Anthony Boureux
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France.,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France
| | - John De Vos
- Institute for Regenerative Medicine and Biotherapy, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France .,INSERM, U1183, Montpellier F 34000, France.,Université de Montpellier, Montpellier F 34000, France.,Institut de Biologie Computationnelle, Montpellier F 34000, France.,Stem Cell Core Facility SAFE-iPSC, INGESTEM, Saint-Eloi Hospital, Montpellier F 34000, France.,Department of Cell and Tissue Engineering, CHU Montpellier, Saint-Eloi Hospital, Montpellier F 34000, France
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Weikard R, Demasius W, Kuehn C. Mining long noncoding RNA in livestock. Anim Genet 2016; 48:3-18. [DOI: 10.1111/age.12493] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2016] [Indexed: 02/01/2023]
Affiliation(s)
- R. Weikard
- Institute Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); 18196 Dummerstorf Germany
| | - W. Demasius
- Institute Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); 18196 Dummerstorf Germany
| | - C. Kuehn
- Institute Genome Biology; Leibniz Institute for Farm Animal Biology (FBN); 18196 Dummerstorf Germany
- Faculty of Agricultural and Environmental Sciences; University Rostock; 18059 Rostock Germany
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28
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Bidirectional communication between cumulus cells and the oocyte: Old hands and new players? Theriogenology 2016; 86:62-8. [DOI: 10.1016/j.theriogenology.2016.04.019] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/29/2016] [Accepted: 03/14/2016] [Indexed: 12/11/2022]
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Taylor DH, Chu ETJ, Spektor R, Soloway PD. Long non-coding RNA regulation of reproduction and development. Mol Reprod Dev 2015; 82:932-56. [PMID: 26517592 PMCID: PMC4762656 DOI: 10.1002/mrd.22581] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022]
Abstract
Noncoding RNAs (ncRNAs) have long been known to play vital roles in eukaryotic gene regulation. Studies conducted over a decade ago revealed that maturation of spliced, polyadenylated coding mRNA occurs by reactions involving small nuclear RNAs and small nucleolar RNAs; mRNA translation depends on activities mediated by transfer RNAs and ribosomal RNAs, subject to negative regulation by micro RNAs; transcriptional competence of sex chromosomes and some imprinted genes is regulated in cis by ncRNAs that vary by species; and both small-interfering RNAs and piwi-interacting RNAs bound to Argonaute-family proteins regulate post-translational modifications on chromatin and local gene expression states. More recently, gene-regulating noncoding RNAs have been identified, such as long intergenic and long noncoding RNAs (collectively referred to as lncRNAs)--a class totaling more than 100,000 transcripts in humans, which include some of the previously mentioned RNAs that regulate dosage compensation and imprinted gene expression. Here, we provide an overview of lncRNA activities, and then review the role of lncRNAs in processes vital to reproduction, such as germ cell specification, sex determination and gonadogenesis, sex hormone responses, meiosis, gametogenesis, placentation, non-genetic inheritance, and pathologies affecting reproductive tissues. Results from many species are presented to illustrate the evolutionarily conserved processes lncRNAs are involved in.
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Affiliation(s)
- David H. Taylor
- Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York
| | - Erin Tsi-Jia Chu
- Field of Comparative Biomedical Sciences, Cornell University, Ithaca, New York
| | - Roman Spektor
- Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York
| | - Paul D. Soloway
- Field of Genetics, Genomics and Development, Cornell University, Ithaca, New York
- Field of Comparative Biomedical Sciences, Cornell University, Ithaca, New York
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
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