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Yu S, Wang G, Shen X, Chen J, Liao J, Yang Y, Aikebai G. Comprehensive analysis of changes in expression of lncRNA, microRNA and mRNA in liver tissues of chickens with high or low abdominal fat deposition. Br Poult Sci 2024:1-9. [PMID: 38808584 DOI: 10.1080/00071668.2024.2319779] [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: 09/30/2023] [Accepted: 12/07/2023] [Indexed: 05/30/2024]
Abstract
1. The liver of chickens is a dominant lipid biosynthetic tissue and plays a vital role in fat deposition, particularly in the abdomen. To determine the molecular mechanisms involved in its lipid metabolism, the livers of chickens with high (H) or low (L) abdominal fat content were sampled and sequencing on long non-coding RNA (lncRNA), messenger RNA (mRNA) and small RNA (microRNA) was performed.2. In total, 351 expressed protein-coding genes for long non-coding RNA (DEL; 201 upregulated and 150 downregulated), 400 differentially expressed genes (DEG; 223 upregulated and 177 downregulated) and 10 differentially expressed miRNA (DEM; four upregulated and six downregulated) were identified between the two groups. Multiple potential signalling pathways related to lipogenesis and lipid metabolism were identified via pathway enrichment analysis. In addition, 173 lncRNA - miRNA - mRNA interaction regulatory networks were identified, including 30 lncRNA, 27 mRNA and seven miRNA.3. These networks may help regulate lipid metabolism and fat deposition. Five promising candidate genes and two lncRNA may play important roles in the regulation of adipogenesis and lipid metabolism in chickens.
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Affiliation(s)
- S Yu
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - G Wang
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - X Shen
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - J Chen
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - J Liao
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - Y Yang
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
| | - G Aikebai
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, China
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Zhang R, Zhou Z, Wang P, He X, Liu Y, Chu M. The SLC19A1-AS/miR-1343/WNT11 axis is a novel positive regulatory ceRNA network governing goat granulosa cell proliferation. Int J Biol Macromol 2024; 264:130658. [PMID: 38484817 DOI: 10.1016/j.ijbiomac.2024.130658] [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: 01/29/2024] [Revised: 02/18/2024] [Accepted: 03/04/2024] [Indexed: 03/18/2024]
Abstract
Long noncoding RNAs (lncRNAs), as competitive endogenous RNAs (ceRNAs), can directly or indirectly affect the proliferation and apoptosis of granulosa cells by regulating microRNA (miRNA) pathways. A ceRNA network of the SLC19A1-AS-miR-1343-WNT11 axis was constructed via comprehensive transcriptome sequencing of ovaries from goats with various fertility levels to further elucidate the function and regulatory mechanism of SLC19A1-AS in modulating miR-1343 and WNT11 during granulosa cell proliferation and apoptosis. Subsequent validation experiments were conducted in vitro using granulosa cells. In these experiments, we performed RNA immunoprecipitation (RIP) and identified SLC19A1-AS as a ceRNA in goat granulosa cells that promoted proliferation. Through bioinformatics prediction, luciferase reporter gene assays, and RNA pulldown assays, we confirmed that SLC19A1-AS acts as a sponge for miR-1343, preventing its binding to WNT11 mRNA and thereby increasing the expression of WNT11. This interaction also influenced the proliferation and apoptosis of granulosa cells. Our study systematically validated the biological function of the lncRNA-miRNA-mRNA ceRNA network in goat ovaries and revealed the potential regulatory mechanism by which SLC19A1-AS functions as a ceRNA in granulosa cells. These findings are expected to provide an important experimental foundation for further elucidating the physiological regulatory network of the ovary and contributing to reproductive health in goats.
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Affiliation(s)
- Runan Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Zuyang Zhou
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Peng Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Xiaoyun He
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yufang Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
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3
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Cai S, Chen M, Xue B, Zhu Z, Wang X, Li J, Wang H, Zeng X, Qiao S, Zeng X. Retinoic acid enhances ovarian steroidogenesis by regulating granulosa cell proliferation and MESP2/STAR/CYP11A1 pathway. J Adv Res 2024; 58:163-173. [PMID: 37315842 PMCID: PMC10982869 DOI: 10.1016/j.jare.2023.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/28/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023] Open
Abstract
INTRODUCTION Ovarian steroidogenesis not only affects the embryonic development and pregnancy outcome, but also associates with many diseases in mammals and women. Exploring the nutrients and mechanisms influencing ovarian steroidogenesis is critical to maintaining the optimal reproductive performance, as well as guaranteeing body health. OBJECTIVES This research aimed to explore the effect of retinol metabolism on ovarian steroidogenesis and the underlying mechanisms. METHODS Comparative transcriptomic analysis of ovaries from normal and low reproductive performance sows were performed to identify the main causes leading to low fertility. The metabolites regulating steroid hormones synthesis were investigated in ovarian granulosa cells. Gene interference, overexpression, dual-luciferase reporter assays, chromatin immunoprecipitation and transcriptome analysis were further conducted to explore the underlying mechanisms of Aldh1a1 mediating ovarian steroidogenesis. RESULTS Transcriptome analysis of ovaries from normal and low reproductive performance sows showed the significant differences in both retinol metabolism and steroid hormones synthesis, indicating retinol metabolism probably influenced steroid hormones synthesis. The related metabolite retinoic acid was furtherly proven a highly active and potent substance strengthening estrogen and progesterone synthesis in ovarian granulosa cells. For the first time, we revealed that retinoic acid synthesis in porcine and human ovarian granulosa cells was dominated by Aldh1a1, and required the assistance of Aldh1a2. Importantly, we demonstrated that Aldh1a1 enhanced the proliferation of ovarian granulosa cells by activating PI3K-Akt-hedgehog signaling pathways. In addition, Aldh1a1 regulated the expression of transcription factor MESP2, which targeted the transcription of Star and Cyp11a1 through binding to corresponding promoter regions. CONCLUSION Our data identified Aldh1a1 modulates ovarian steroidogenesis through enhancing granulosa cell proliferation and MESP2/STAR/CYP11A1 pathway. These findings provide valuable clues for improving ovarian health in mammals.
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Affiliation(s)
- Shuang Cai
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, PR China; Beijing Biofeed Additive Key Laboratory, China Agricultural University, Beijing 100193, PR China
| | - Meixia Chen
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, PR China; Beijing Biofeed Additive Key Laboratory, China Agricultural University, Beijing 100193, PR China; Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, PR China
| | - Bangxin Xue
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, PR China; Beijing Biofeed Additive Key Laboratory, China Agricultural University, Beijing 100193, PR China
| | - Zhekun Zhu
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, PR China; Beijing Biofeed Additive Key Laboratory, China Agricultural University, Beijing 100193, PR China
| | - Xinyu Wang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, PR China; Beijing Biofeed Additive Key Laboratory, China Agricultural University, Beijing 100193, PR China
| | - Jie Li
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, PR China
| | - Huakai Wang
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, PR China; Beijing Biofeed Additive Key Laboratory, China Agricultural University, Beijing 100193, PR China
| | - Xiangzhou Zeng
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, PR China; Beijing Biofeed Additive Key Laboratory, China Agricultural University, Beijing 100193, PR China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, PR China; Beijing Biofeed Additive Key Laboratory, China Agricultural University, Beijing 100193, PR China
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, PR China; Beijing Biofeed Additive Key Laboratory, China Agricultural University, Beijing 100193, PR China.
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Kirian RD, Steinman D, Jewell CM, Zierden HC. Extracellular vesicles as carriers of mRNA: Opportunities and challenges in diagnosis and treatment. Theranostics 2024; 14:2265-2289. [PMID: 38505610 PMCID: PMC10945352 DOI: 10.7150/thno.93115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/05/2024] [Indexed: 03/21/2024] Open
Abstract
Extracellular vesicles (EVs) are produced by all cells in the body. These biological nanoparticles facilitate cellular communication through the transport of diverse cargoes, including small molecules, proteins, and nucleic acids. mRNA cargoes have gained particular interest given their role in the translation of functional proteins. As a biomarker platform, EVs can be found in nearly all biofluids-blood, mucus, urine, cerebrospinal fluid, and saliva-providing real-time insight into parent cell and tissue function. mRNAs carried by EVs are protected from degradation, resulting in improved detection compared to free mRNA, and recent work demonstrates promising results in using these mRNA cargoes as biomarkers for cancer, neurological diseases, infectious diseases, and gynecologic and obstetric outcomes. Furthermore, given the innate cargo carrying, targeting, and barrier crossing abilities of EVs, these structures have been proposed as therapeutic carriers of mRNA. Recent advances demonstrate methods for loading mRNAs into EVs for a range of disease indications. Here, we review recent studies using EVs and their mRNA cargoes as diagnostics and therapeutics. We discuss challenges associated with EVs in diagnostic and therapeutic applications and highlight opportunities for future development.
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Affiliation(s)
- Robert D. Kirian
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742
| | - Darby Steinman
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742
| | - Christopher M. Jewell
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742
- Department of Veterans Affairs, VA Maryland Health Care System, Baltimore, MD, USA
- Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, MD, 20742
- Robert E. Fischell Institute for Biomedical Devices, College Park, MD 20742, USA
| | - Hannah C. Zierden
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742
- Department of Chemical & Biomolecular Engineering, University of Maryland, College Park, MD, 20742
- Robert E. Fischell Institute for Biomedical Devices, College Park, MD 20742, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201
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Liu B, Liu L, Sulaiman Z, Wang C, Wang L, Zhu J, Liu S, Cheng Z. Comprehensive analysis of lncRNA-miRNA-mRNA ceRNA network and key genes in granulosa cells of patients with biochemical primary ovarian insufficiency. J Assist Reprod Genet 2024; 41:15-29. [PMID: 37847421 PMCID: PMC10789704 DOI: 10.1007/s10815-023-02937-2] [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: 03/29/2023] [Accepted: 09/06/2023] [Indexed: 10/18/2023] Open
Abstract
Primary ovarian insufficiency (POI) is a common condition leading to the pathological decline of ovarian function in women of reproductive age, resulting in amenorrhea, hypogonadism, and infertility. Biochemical premature ovarian insufficiency (bPOI) is an intermediate stage in the pathogenesis of POI in which the fertility of patients has been reduced. Previous studies suggest that granulosa cells (GCs) play an essential role in the pathogenesis of POI, but their pathogenetic mechanisms remain unclear. To further explore the potential pathophysiological mechanisms of GCs in POI, we constructed a molecular long non-coding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA) network using GC expression data collected from biochemical premature ovarian failure (bPOI) patients in the GEO database. We discovered that the GCs of bPOI patients had differential expression of 131 mRNAs, 191 lncRNAs, and 28 miRNAs. By systematic network analysis, we identified six key genes, including SRSF1, PDIA5, NEURL1B, UNK, CELF2, and CFL2, and five hub miRNAs, namely hsa-miR-27a-3p, hsa-miR-24-3p, hsa-miR-22-3p, hsa-miR-129-5p, and hsa-miR-17-5p, and the results suggest that the expression of these key genes may be regulated by two hub miRNAs, hsa-miR-27a-3p and hsa-miR-17-5p. Additionally, a POI model in vitro was created to confirm the expression of a few important genes. In this study, we discovered a unique lncRNA-miRNA-mRNA network based on the ceRNA mechanism in bPOI for the first time, and we screened important associated molecules, providing a partial theoretical foundation to better understand the pathogenesis of POI.
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Affiliation(s)
- Biting Liu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Li Liu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
- Institute of Gynecological Minimally Invasive Medicine, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Zubaidan Sulaiman
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Chunyan Wang
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Lian Wang
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
- Institute of Gynecological Minimally Invasive Medicine, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Jihui Zhu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
- Institute of Gynecological Minimally Invasive Medicine, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Shupeng Liu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China.
- Institute of Gynecological Minimally Invasive Medicine, School of Medicine, Tongji University, Shanghai, 200072, China.
| | - Zhongping Cheng
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China.
- Institute of Gynecological Minimally Invasive Medicine, School of Medicine, Tongji University, Shanghai, 200072, China.
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Han X, Pan Y, Fan J, Wang M, Wang L, Wang J, Afedo SY, Zhao L, Wang Y, Zhao T, Zhang T, Zhang R, Cui Y, Yu S. LncRNA MEG3 regulates ASK1/JNK axis-mediated apoptosis and autophagy via sponging miR-23a in granulosa cells of yak tertiary follicles. Cell Signal 2023; 107:110680. [PMID: 37086956 DOI: 10.1016/j.cellsig.2023.110680] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 04/24/2023]
Abstract
Apoptosis and autophagy in granulosa cells (GCs) are highly related to follicular development and atresia. It has also been reported that they are related to LncRNA MEG3, miR-23a and apoptosis signal-regulating kinase 1 (ASK-1). However, their relationship to follicular development and the extent to which follicle stimulating hormone (FSH) or luteinizing hormone (LH) can regulate this process remain unknown. Here, we found that ASK1 and JNK were expressed in the GCs of gonadotropin-dependent follicles, and those levels were significantly higher (p < 0.05) in yak Tertiary follicles compared to that of Secondary follicles and Graafian follicles. Then, the effect of LncRNA MEG3 / miR-23a on apoptosis and autophagy via ASK1/JNK (c-Jun N-terminal kinase) in yak GCs was studied. Overexpressing LncRNA MEG3 reduced miR-23a levels and p-967 protein expression, but enhanced ASK1 and JNK mRNA levels as well as t-ASK1, p-845, t-JNK, and p-JNK proteins levels. And Up-regulation of LncRNA MEG3 promoted apoptosis while attenuating autophagy. The targeting relationship between miR-23a and the binding sites of LncRNA MEG3 and ASK1 was also confirmed with the dual luciferase reporter assay. And, the relationship between LncRNA MEG3 and miR-23a was observed as a negative feedback regulation, and changes in LncRNA MEG3 and miR-23a levels can alter the expression of ASK1/JNK axis in yaks GCs. In addition, FSH (10 μg/mL) or LH (100 μg/mL) ability to reverse the effects of LncRNA MEG3 on miR-23a levels and ASK1/JNK axis-mediated apoptosis and autophagy was verified in yak GCs. This is significantly beneficial for decreasing abnormal follicular atresia for yaks tertiary follicles.
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Affiliation(s)
- Xiaohong Han
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Yangyang Pan
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiangfeng Fan
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Meng Wang
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Libin Wang
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Jinglei Wang
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Seth Yaw Afedo
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Ling Zhao
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Yaying Wang
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Tian Zhao
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Tongxiang Zhang
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Rui Zhang
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Yan Cui
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China; Laboratory of Animal Anatomy & Tissue Embryology, Department of Basic Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Sijiu Yu
- Gansu Province Livestock Embryo Engineering Research Center, Department of Clinical Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China; Laboratory of Animal Anatomy & Tissue Embryology, Department of Basic Veterinary Medicine, Faculty of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China.
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7
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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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Differential expression and functional analysis of circRNA in the ovaries of Yili geese at different egg-laying stages. Genes Genomics 2022; 44:1171-1180. [PMID: 35951157 DOI: 10.1007/s13258-022-01290-5] [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: 04/08/2022] [Accepted: 07/16/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Ovarian development is regulated by genes that are expressed dynamically and stage-specifically. Circular RNA (circRNA) has been proven to play a significant role in the regulation of animal reproduction. OBJECTIVE Studying the expression characteristics of circRNAs in goose ovaries at various egg-laying stages can provide a reference for the molecular regulation mechanism of ovary development in geese that is mediated by circRNAs. METHODS In this study, the expression profiles of circRNAs were compared in ovary tissues from Yili geese in three different breeding periods, namely the prelaying period (KL), laying period (CL), and ceased period (XL), and differentially expressed circRNAs related to ovarian development in Yili geese were screened. The potential biological functions of differential circRNAs were predicted by bioinformatics, and the differential circRNA-miRNA regulatory network was constructed. RESULTS The results showed that a total of 4483 circRNAs were identified in 12 ovarian tissue samples from Yili geese at different laying stages. In the KL vs. CL, XL vs. CL, and XL vs. KL groups, 159, 455, and 383 differentially expressed circRNAs were identified, respectively. The host genes of the differential circRNAs were mostly enriched in the signal transduction, metabolism, and other related pathways, such as those for phototransduction, glycerophospholipid metabolism, aminoacyl-tRNA biosynthesis, and retinol metabolism. Finally, we constructed circRNA-miRNA regulation networks. Nine differential circRNAs were randomly selected for qRT-PCR verification, and the expression trends were consistent with the sequencing results. CONCLUSIONS Our results indicated that significant differences in the expression profiles of circRNAs in the ovaries of Yili geese at different egg-laying stages. Meanwhile, through analyzing the differential circRNA-miRNA interaction network, core regulators such as circRNA NW_013186107.1:36835|52,574 and gga-miR-34b-5p were screened. This study provides a reference for the further analysis of the molecular regulatory mechanism of the circRNAs regulating goose ovary development and enriches the theory of genetic regulation during goose ovary development.
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Mao H, Chen L, Bao R, Weng S, Wang M, Xu N, Qi L, Wang J. Mechanisms of Oogenesis-Related Long Non-coding RNAs in Porcine Ovaries Treated With Recombinant Pig Follicle-Stimulating Hormone. Front Vet Sci 2022; 8:838703. [PMID: 35281430 PMCID: PMC8908959 DOI: 10.3389/fvets.2021.838703] [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: 12/18/2021] [Accepted: 12/31/2021] [Indexed: 11/17/2022] Open
Abstract
Reproductive efficiency is of significant importance in pork production for it has a great impact on economic success. Ovulation rate is an early component of reproduction efficiency of pigs, and it contributes to the upper limit of litter size. In this study, we used the newly developed recombinant pig follicle stimulating hormone (rpFSH) instead of traditional PMSG to increase ovulation rate of pigs in order to achieve higher litter size, for it was better at stimulating ovulation, and showed more cheaper and greener. However, relatively little is known about the underlying genetic bases and molecular mechanisms. Consequently, an experiment was carried out in ovaries of replacement gilts to screen the key genes and lncRNAs that affect the fecundity of pigs by RNA-seq technology. Twenty gilts were divided into two groups, including 10 rpFSH treatment pigs and 10 control animals. After slaughtering and collecting the phenotypic data, ovaries of five pigs in each group were selected for RNA-seq. Total RNA was extracted to construct the library and then sequence on an Illumina Hiseq 4000 system. A comprehensive analysis of mRNAs and long non-coding RNAs (lncRNAs) from 10 samples was performed with bioinformatics. The phenotypic data showed that rpFSH treatment groups had the higher (P < 0.01) ovarian weight and more mature follicles. The RNA-seq results showed that a total of 43,499 mRNAs and 21,703 lncRNAs were identified, including 21,300 novel lncRNAs and 403 known lncRNAs, of which 585 mRNAs and 398 lncRNAs (P < 0.05) were significantly differentially expressed (DE) between the two groups of rpFSH treatment group and controlled group. GO and KEGG annotation analysis indicated that the target genes of DE lncRNAs and DE mRNAs were related to prolactin receptor activity, mitophagy by induced vacuole formation, and meiotic spindle. Moreover, we found that NR5A2 (nuclear receptor subfamily 5, group A, member 2), a target gene of lncRNA MSTRG.3902.1, was involved in regulating follicular development, ovulation, and estrogen production. Our study provided a catalog of lncRNAs and mRNAs associated with ovulation of rpFSH treatment, and they deserve further study to deepen the understanding of biological processes in the regulation of ovaries of rpFSH treatment pigs.
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Affiliation(s)
- Haiguang Mao
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
| | - Lu Chen
- Ningbo Sansheng Biological Technology Co., Ltd., Ningbo, China
| | - Rupo Bao
- Ningbo Sansheng Biological Technology Co., Ltd., Ningbo, China
| | - Shiqiao Weng
- Ningbo Sansheng Biological Technology Co., Ltd., Ningbo, China
| | - Mengting Wang
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
| | - Ningying Xu
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Lili Qi
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
- *Correspondence: Lili Qi
| | - Jinbo Wang
- School of Biological and Chemical Engineering, NingboTech University, Ningbo, China
- Jinbo Wang
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Li Z, Cai X, Zou W, Zhang J. CDKN2B-AS1 promotes the proliferation, clone formation, and invasion of nasopharyngeal carcinoma cells by regulating miR-98-5p/E2F2 axis. Am J Transl Res 2021; 13:13406-13422. [PMID: 35035684 PMCID: PMC8748104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/19/2021] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To explore the effect of CDKN2B antisense RNA 1 (CDKN2B-AS1) on the proliferation, clone formation, and invasion of nasopharyngeal carcinoma (NPC) cells by regulating miR-98-5p/E2F transcription factor 2 (E2F2) axis. METHODS The expressions of CDKN2B-AS1, miR-98-5p, and E2F2 in NPC tissues and cell lines (SUNE-1, 5-8F, 6-10B, and HK-1) as well as in peritumoral normal tissues and cell line NP69 were determined by qRT-PCR. Subcellular localization of CDKN2B-AS1 was detected using the fluorescence in situ hybridization assay. The targeting relationships between CDKN2B-AS1 and miR-98-5p as well as between miR-98-5p and E2F2 were analyzed by the dual-luciferase reporter assay and RNA binding protein immunoprecipitation assay. The proliferation, clone formation and invasion of 5-8F cells were measured using the CCK-8 assay, Clone formation assay, and transwell assay, respectively. RESULTS CDKN2B-AS1 was highly expressed in NPC tissues and cells, whereas the expression of miR-98-5p decreased in the NPC tissues and cells. Silencing of CDKN2B-AS1 inhibited the proliferation, clone formation, and invasion of NPC cells (all P<0.05). CDKN2B-AS1 acted asceRNA of miR-98-5p, and miR-98-5p inhibitor could partially reverse the inhibitory effect of silencing CDKN2B-AS1 on NPC cells (all P<0.05). CDKN2B-AS1 upregulated E2F2 by inhibiting miR-98-5p, and the upregulation of E2F2 partially reversed the inhibitory effect of miR-98-5p overexpression on the NPC cells (all P<0.05). CONCLUSION CDKN2B-AS1, as a lncRNA, can regulate E2F2 by sponging miR-98-5p to promote the proliferation, clone formation, and invasion of NPC cells.
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Affiliation(s)
- Zhengwen Li
- Department of Otorhinolaryngology, Shanghai Tenth Peoples' Hospital, Tongji University Shanghai 200072, China
| | - Xiaojing Cai
- Department of Otorhinolaryngology, Shanghai Tenth Peoples' Hospital, Tongji University Shanghai 200072, China
| | - Wentao Zou
- Department of Otorhinolaryngology, Shanghai Tenth Peoples' Hospital, Tongji University Shanghai 200072, China
| | - Jiaxiong Zhang
- Department of Otorhinolaryngology, Shanghai Tenth Peoples' Hospital, Tongji University Shanghai 200072, China
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Whole Transcriptome Analysis: Implication to Estrous Cycle Regulation. BIOLOGY 2021; 10:biology10060464. [PMID: 34070240 PMCID: PMC8225199 DOI: 10.3390/biology10060464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023]
Abstract
Simple Summary The databases of mRNA and non-coding-RNAs (miRNA, circRNA, lncRNA) in the ovary of Xinong Sannen goat were reported in this study. The differential expression of mRNA and non-coding RNAs were analyzed, and the comprehensive analysis of the four databases provided RNA networks that regulate estrous cycle, which is essential to improve reproduction. Abstract Estrous cycle is one of the placental mammal characteristics after sexual maturity, including estrus stage (ES) and diestrus stage (DS). Estrous cycle is important in female physiology and its disorder may lead to diseases, such as polycystic ovary syndrome, ovarian carcinoma, anxiety, and epilepsy. In the latest years, effects of non-coding RNAs and messenger RNA (mRNA) on estrous cycle have started to arouse much concern, however, a whole transcriptome analysis among non-coding RNAs and mRNA has not been reported. Here, we report a whole transcriptome analysis of goat ovary in estrus and diestrus periods. Estrus synchronization was conducted to induce the estrus phase and on day 32, the goats shifted into the diestrus stage. The ovary RNA of estrus and diestrus stages was respectively collected to perform RNA-sequencing. Then, the circular RNA (circRNA), microRNA (miRNA), long non-coding RNA (lncRNA), and mRNA databases of goat ovary were acquired, and the differential expressions between estrus and diestrus stages were screened to construct circRNA-miRNA-mRNA/lncRNA and lncRNA-miRNA/mRNA networks, thus providing potential pathways that are involved in the regulation of estrous cycle. Differentially expressed mRNAs, such as MMP9, TIMP1, 3BHSD, and PTGIS, and differentially expressed miRNAs that play key roles in the regulation of estrous cycle, such as miR-21-3p, miR-202-3p, and miR-223-3p, were extracted from the network. Our data provided the miRNA, circRNA, lncRNA, and mRNA databases of goat ovary and each differentially expressed profile between ES and DS. Networks among differentially expressed miRNAs, circRNAs, lncRNAs, and mRNAs were constructed to provide valuable resources for the study of estrous cycle and related diseases.
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Hu H, Fu Y, Zhou B, Li Z, Liu Z, Jia Q. Long non-coding RNA TCONS_00814106 regulates porcine granulosa cell proliferation and apoptosis by sponging miR-1343. Mol Cell Endocrinol 2021; 520:111064. [PMID: 33091558 DOI: 10.1016/j.mce.2020.111064] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/14/2020] [Accepted: 10/18/2020] [Indexed: 12/14/2022]
Abstract
Recent evidence shows that long non-coding RNAs (lncRNAs), a class of non-coding RNAs, are involved in the regulation of reproductive processes. In this study, we identified a lncRNA, TCONS_00814106, that was upregulated in high-fecundity sow ovarian tissues and influenced by reproductive hormones. Bioinformatics analyses and luciferase reporter assays showed that TCONS_00814106 is a miR-1343 target. Cell counting kit (CCK)-8 and apoptosis assays showed that TCONS_00814106 promotes proliferation and inhibits apoptosis in porcine granulosa cells (GCs), and that this could be reversed by miR-1343. Also, we observed that transforming growth factor-β receptor type I (TGFBR1) is a functional target of miR-1343 in GCs. TCONS_00814106 serves as a competing endogenous RNA to regulate TGFBR1 expression by sponging miR-1343, thereby exerting regulatory functions in GCs. Overall, these results provide new insights into the biological function of the lncRNA TCONS_00814106.
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Affiliation(s)
- Huiyan Hu
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, 071000, China
| | - Yanfang Fu
- Hebei Provincial Animal Husbandry Station, Shijiazhuang, 050000, China
| | - Bo Zhou
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, 071000, China
| | - Zhiqiang Li
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, 071000, China
| | - Zhongwu Liu
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, 071000, China
| | - Qing Jia
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, 071000, China; Hebei Technology Innovation Center for Agriculture in Mountainous Areas, Baoding, 071000, China.
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