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Wang Y, Miao DZ, Zhang C, Chen J, Yang HM, Wang ZY. CircRNAs involved in the red light of effect on follicle selection in pigeons. Poult Sci 2024; 103:104010. [PMID: 38991383 PMCID: PMC11283211 DOI: 10.1016/j.psj.2024.104010] [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: 04/21/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/13/2024] Open
Abstract
Red light (RL) can enhance egg production in poultry. CircRNAs play a crucial role by serving as transcriptional regulators. However, their role in influencing follicle development in White King pigeons remains unexplored. In this study, 54 paired White King pigeons were chosen and divided into RL and white light (WL) groups, each with 3 subgroups. The egg production of paired pigeons in each replicate was recorded for 45 d, and the characteristics of follicle development were monitored during the laying interval (LI). The granulosa cell layer from follicles of the second-largest follicle (F2) was collected, and high-throughput sequencing was performed to elucidate the molecular mechanism of follicle development in pigeons. The study confirmed that RL enhances egg production in pigeons. Additionally, under RL, the F2 follicle was selected, while under WL, small follicles were kept on the third day (LI3). A total of 5,510 circRNAs were identified across all samples, revealing differentially expressed circRNAs (DECs) in various comparisons: 627 in RF1 vs. WF1, 900 in RF2 vs. WF2, 606 in RF1 vs. RF2, and 937 in WF1 vs. WF2. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that host genes of DECs were enriched in pathways like steroid hormone biosynthesis, oocyte meiosis, GnRH signaling pathway, and apoptosis pathway. Moreover, circRNA_5497, circRNA_2016, and circRNA_3328 were common DECs across 4 groups, sharing miRNA binding sites with follicle selection-associated genes. In conclusion, our findings suggest that RL promotes egg production by stimulating follicle selection during LI, offering insights into the regulatory mechanisms of circRNAs in follicle selection under RL. This knowledge can help enhance the reproductive performance of pigeons.
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Affiliation(s)
- Y Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China.
| | - D Z Miao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China
| | - C Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China
| | - J Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China
| | - H M Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China
| | - Z Y Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China
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Zhao X, Fan C, Qie T, Fu X, Chen X, Wang Y, Wu Y, Fu X, Shi K, Yan W, Yu H. Diaph1 knockout inhibits mouse primordial germ cell proliferation and affects gonadal development. Reprod Biol Endocrinol 2024; 22:82. [PMID: 39010074 PMCID: PMC11247884 DOI: 10.1186/s12958-024-01257-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND Exploring the molecular mechanisms of primordial germ cell (PGC) migration and the involvement of gonadal somatic cells in gonad development is valuable for comprehending the origins and potential treatments of reproductive-related diseases. METHODS Diaphanous related formin 1 (Diaph1, also known as mDia1) was screened by analyzing publicly available datasets (ATAC-seq, DNase-seq, and RNA-seq). Subsequently, the CRISPR-Cas9 technology was used to construct Diaph1 knockout mice to investigate the role of Diaph1 in gonad development. RESULTS Based on data from public databases, a differentially expressed gene Diaph1, was identified in the migration of mouse PGC. Additionally, the number of PGCs was significantly reduced in Diaph1 knockout mice compared to wild type mice, and the expression levels of genes related to proliferation (Dicer1, Mcm9), adhesion (E-cadherin, Cdh1), and migration (Cxcr4, Hmgcr, Dazl) were significantly decreased. Diaph1 knockout also inhibited Leydig cell proliferation and induced apoptosis in the testis, as well as granulosa cell apoptosis in the ovary. Moreover, the sperm count in the epididymal region and the count of ovarian follicles were significantly reduced in Diaph1 knockout mice, resulting in decreased fertility, concomitant with lowered levels of serum testosterone and estradiol. Further research found that in Diaph1 knockout mice, the key enzymes involved in testosterone synthesis (CYP11A1, 3β-HSD) were decreased in Leydig cells, and the estradiol-associated factor (FSH receptor, AMH) in granulosa cells were also downregulated. CONCLUSIONS Overall, our findings indicate that the knockout of Diaph1 can disrupt the expression of factors that regulate sex hormone production, leading to impaired secretion of sex hormones, ultimately resulting in damage to reproductive function. These results provide a new perspective on the molecular mechanisms underlying PGC migration and gonadal development, and offer valuable insights for further research on the causes, diagnosis, and treatment of related diseases.
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Affiliation(s)
- Xin Zhao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Chunbiao Fan
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Tongtong Qie
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Xinrui Fu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Xiaoshuang Chen
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Yujia Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Yuan Wu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Xinyao Fu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Kesong Shi
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China
| | - Wenlong Yan
- School of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, Guangdong Province, China.
| | - Haiquan Yu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010020, Inner Mongolia, China.
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3
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Liu J, Guo C, Fu J, Liu D, Liu G, Sun B, Deng M, Guo Y, Li Y. Identification and Functional Analysis of circRNAs during Goat Follicular Development. Int J Mol Sci 2024; 25:7548. [PMID: 39062792 PMCID: PMC11277404 DOI: 10.3390/ijms25147548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/24/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Litter size is a crucial quantitative trait in animals, closely linked to follicular development. Circular RNA (circRNA), a type of single-stranded closed-loop endogenous RNA with stable expression, plays pivotal roles in various biological processes, yet its function in goat follicular development remains unclear. In this study, we collected large (follicle diameter > 3 mm) and small (1 mm < follicle diameter < 3 mm) follicles from black goats in the Chuanzhong region for circRNA sequencing, with the aim of elucidating the functional circRNAs that influence follicle development in goats. Differential analysis revealed that 17 circRNAs were upregulated in large follicles, and 28 circRNAs were upregulated in small follicles. Functional enrichment analysis revealed significant enrichment of pathways related to reproduction, including cellular response to follicle-stimulating hormone stimulus, the PI3K-Akt signaling pathway, the MAPK signaling pathway, and the Notch signaling pathway. Based on the ceRNA mechanism, 45 differentially expressed circRNAs were found to target and bind a total of 418 miRNAs, and an intercalation network including miR-324-3p (circRNA2497, circRNA5650), miR-202-5p (circRNA3333, circRNA5501), and miR-493-3p (circRNA4995, circRNA5508) was constructed. In addition, conservation analysis revealed that 2,239 circRNAs were conserved between goats and humans. Prediction of translation potential revealed that 154 circRNAs may potentially utilize both N6-methyladenosine (m6A) and internal ribosome entry site (IRES) translation mechanisms. Furthermore, the differential expression and circularization cleavage sites of five circRNAs were validated through RT-qPCR and DNA sequencing. Our study constructed a circRNA map in goat follicle development, offering a theoretical foundation for enhancing goat reproductive performance.
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Affiliation(s)
- Jie Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.L.); (C.G.); (B.S.); (M.D.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Conghui Guo
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.L.); (C.G.); (B.S.); (M.D.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Junjie Fu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.L.); (C.G.); (B.S.); (M.D.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.L.); (C.G.); (B.S.); (M.D.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Guangbin Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.L.); (C.G.); (B.S.); (M.D.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Baoli Sun
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.L.); (C.G.); (B.S.); (M.D.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Ming Deng
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.L.); (C.G.); (B.S.); (M.D.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Yongqing Guo
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.L.); (C.G.); (B.S.); (M.D.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.L.); (C.G.); (B.S.); (M.D.); (Y.G.)
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
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4
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Yuan J, Li Q, Sun Y, Wang Y, Li Y, You Z, Ni A, Zong Y, Ma H, Chen J. Multi-tissue transcriptome profiling linked the association between tissue-specific circRNAs and the heterosis for feed intake and efficiency in chicken. Poult Sci 2024; 103:103783. [PMID: 38713987 PMCID: PMC11091503 DOI: 10.1016/j.psj.2024.103783] [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: 01/09/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/09/2024] Open
Abstract
Heterosis has been widely utilized in chickens. The nonadditive inheritance of genes contributes to this biological phenomenon. However, the role of circRNAs played in the heterosis is poorly determined. In this study, we observed divergent heterosis for residual feed intake (RFI) between 2 crossbreds derived from a reciprocal cross between White Leghorns and Beijing You chickens. Then, circRNA landscape for 120 samples covering the hypothalamus, liver, duodenum mucosa and ovary were profiled to elucidate the regulatory mechanisms of heterosis. We detected that a small proportion of circRNAs (7.83-20.35%) were additively and non-additively expressed, in which non-additivity was a major inheritance of circRNAs in the crossbreds. Tissue-specific expression of circRNAs was prevalent across 4 tissues. Weighted gene co-expression network analysis revealed circRNA-mRNA co-expression modules associated with feed intake and RFI in the hypothalamus and liver, and the co-expressed genes were enriched in oxidative phosphorylation pathway. We further identified 8 nonadditive circRNAs highly correlated with 16 nonadditive genes regulating negative heterosis for RFI in the 2 tissues. Circ-ITSN2 was validated in the liver tissue for its significantly positive correlation with PGPEP1L. Moreover, the bioinformatic analysis indicated that candidate circRNAs might be functioned by binding the microRNAs and interacting with the RNA binding proteins. The integration of multi-tissue transcriptome firstly linked the association between tissue-specific circRNAs and the heterosis for feed intake and efficiency in chicken, which provide novel insights into the molecular mechanism underlying heterosis for feed efficiency. The validated circRNAs can act as potential biomarkers for predicting RFI and its heterosis.
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Affiliation(s)
- Jingwei Yuan
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qin Li
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yanyan Sun
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuanmei Wang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yunlei Li
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhangjing You
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Aixin Ni
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yunhe Zong
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hui Ma
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jilan Chen
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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5
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Fabová Z, Loncová B, Harrath AH, Sirotkin AV. Involvement of circular RNAs in the control of porcine ovarian cell functions: Upregulation by ciR-00596 and downregulation by ciR-00646. Reprod Biol 2024; 24:100860. [PMID: 38762967 DOI: 10.1016/j.repbio.2024.100860] [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: 09/06/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 05/21/2024]
Abstract
The current understanding of the role of circular RNAs (circRNAs) in regulating ovarian functions is inadequate. To assess the impact of ciR-00596 and ciR-00646 on the regulation of basic porcine ovarian granulosa cell functions, we conducted upregulation (utilizing overexpressing vectors) and downregulation (utilizing shRNA vectors) of these circRNAs. The relative expression of both circRNAs, cell viability and proliferation (accumulation of PCNA, cyclin B1, and XTT-positive cells), cytoplasmic (accumulation of bax and caspase-3) and nuclear (DNA fragmentation) apoptosis, and the release of progesterone, testosterone, estradiol, IGF-I, and oxytocin were evaluated. Transfection of cells with the ciR-00596 overexpression vector resulted in increases in cell viability and proliferation and the release of progesterone and IGF-I, while it decreased the cytoplasmic and nuclear apoptosis, testosterone, estradiol, and oxytocin output. CiR-00596 inhibition had the opposite effects. The overexpression of ciR-00646 decreased cell viability and proliferation, and the release of progesterone, IGF-I, and oxytocin, while increasing cytoplasmic and nuclear apoptosis and the output of testosterone and estradiol. Our findings are the first to show the stimulatory action of ciR-00596 and the inhibitory effect of ciR-00646 on ovarian cell functions, including the cell cycle, apoptosis, and secretory activity.
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Affiliation(s)
- Zuzana Fabová
- Faculty of Natural Sciences and Informatics, Constantine the Philosopher University in Nitra, Nitra, Slovakia.
| | - Barbora Loncová
- Faculty of Natural Sciences and Informatics, Constantine the Philosopher University in Nitra, Nitra, Slovakia
| | - Abdel Halim Harrath
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Alexander V Sirotkin
- Faculty of Natural Sciences and Informatics, Constantine the Philosopher University in Nitra, Nitra, Slovakia
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6
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Wei Y, Shen X, Zhao X, He H, Zhang Y, Zhu Q, Yin H. Circular RNA circRPS19 promotes chicken granulosa cell proliferation and steroid hormone synthesis by interrupting the miR-218-5p/INHBB axis. Theriogenology 2024; 219:103-115. [PMID: 38422566 DOI: 10.1016/j.theriogenology.2024.02.026] [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: 05/21/2023] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 03/02/2024]
Abstract
Ovarian follicle development is an important physiological activity for females and makes great significance in maintaining female health and reproduction performance. The development of ovarian follicle is mainly affected by the granulosa cells (GCs), whose growth is regulated by a variety of factors. Here, we identified a novel circular RNA (circRNA) derived from the Ribosomal protein S19 (RPS19) gene, named circRPS19, which is differentially expressed during chicken ovarian follicle development. Further explorations identified that circRPS19 promotes GCs proliferation and steroid hormone synthesis. Furthermore, circRPS19 was found to target and regulate miR-218-5p through a competitive manner with endogenous RNA (ceRNA). Functionals investigation revealed that miR-218-5p attenuates GCs proliferation and steroidogenesis, which is opposite to that of circRPS19. In addition, we also confirmed that circRPS19 upregulates the expression of Inhibin beta B subunit (INHBB) by binding with miR-218-5p to facilitate GCs proliferation and steroidogenesis. Overall, this study revealed that circRPS19 regulates GCs development by releasing the repression of miR-218-5p on INHBB, which suggests a novel mechanism in respect to circRNA and miRNA regulation in ovarian follicle development.
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Affiliation(s)
- Yuanhang Wei
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoxu Shen
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiyu Zhao
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Haorong He
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yao Zhang
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qing Zhu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Huadong Yin
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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7
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He H, Wei Y, Chen Y, Zhao X, Shen X, Zhu Q, Yin H. High expression circRALGPS2 in atretic follicle induces chicken granulosa cell apoptosis and autophagy via encoding a new protein. J Anim Sci Biotechnol 2024; 15:42. [PMID: 38468340 PMCID: PMC10926623 DOI: 10.1186/s40104-024-01003-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/29/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND The reproductive performance of chickens mainly depends on the development of follicles. Abnormal follicle development can lead to decreased reproductive performance and even ovarian disease among chickens. Chicken is the only non-human animal with a high incidence of spontaneous ovarian cancer. In recent years, the involvement of circRNAs in follicle development and atresia regulation has been confirmed. RESULTS In the present study, we used healthy and atretic chicken follicles for circRNA RNC-seq. The results showed differential expression of circRALGPS2. It was then confirmed that circRALGPS2 can translate into a protein, named circRALGPS2-212aa, which has IRES activity. Next, we found that circRALGPS2-212aa promotes apoptosis and autophagy in chicken granulosa cells by forming a complex with PARP1 and HMGB1. CONCLUSIONS Our results revealed that circRALGPS2 can regulate chicken granulosa cell apoptosis and autophagy through the circRALGPS2-212aa/PARP1/HMGB1 axis.
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Affiliation(s)
- Haorong He
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yuanhang Wei
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yuqi Chen
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xiyu Zhao
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xiaoxu Shen
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Qing Zhu
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Huadong Yin
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
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8
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Kui H, Li P, Wang T, Luo Y, Ning C, Li M, Liu S, Zhu Q, Li J, Li D. Dynamic mRNA expression during chicken ovarian follicle development. G3 (BETHESDA, MD.) 2023; 14:jkad237. [PMID: 37832513 PMCID: PMC10755205 DOI: 10.1093/g3journal/jkad237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 07/24/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023]
Abstract
Ovarian follicle development is a complex and well-orchestrated biological process of great economic significance for poultry production. Specifically, understanding the molecular mechanisms underlying follicular development is essential for high-efficiency follicular development can benefit the entire industry. In addition, domestic egg-laying hens often spontaneously develop ovarian cancer, providing an opportunity to study the genetic, biochemical, and environmental risk factors associated with the development of this cancer. Here, we provide high-quality RNA sequencing data for chicken follicular granulosa cells across 10 developmental stages, which resulted in a total of 204.57 Gb of clean sequencing data (6.82 Gb on average per sample). We also performed gene expression, time-series, and functional enrichment analyses across the 10 developmental stages. Our study revealed that SWF (small while follicle), F1 (F1 hierarchical follicles), and POFs (postovulatory follicles) best represent the transcriptional changes associated with the prehierarchical, preovulatory, and postovulatory stages, respectively. We found that the preovulatory stage F1 showed the greatest divergence in gene expression from the POF stage. Our research lays a foundation for further elucidation of egg-laying performance of chicken and human ovarian disease.
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Affiliation(s)
- Hua Kui
- School of Pharmacy, Chengdu University, Chengdu 610106, People’s Republic of China
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Xi Nan Gynecological Hospital Co., Ltd., 66 Bisheng Road, Chengdu 610000, People’s Republic of China
| | - Penghao Li
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Xi Nan Gynecological Hospital Co., Ltd., 66 Bisheng Road, Chengdu 610000, People’s Republic of China
| | - Tao Wang
- School of Pharmacy, Chengdu University, Chengdu 610106, People’s Republic of China
| | - Yingyu Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, People’s Republic of China
| | - Chunyou Ning
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, People’s Republic of China
| | - Mengmeng Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, People’s Republic of China
| | - Siying Liu
- School of Pharmacy, Chengdu University, Chengdu 610106, People’s Republic of China
| | - Qing Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, People’s Republic of China
| | - Jing Li
- College of Agriculture, Kunming University, Kunming 650214, People’s Republic of China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu 610106, People’s Republic of China
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9
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Du X, Zhu Q, Pian H, Yang X, Zhao D, Wu X, He J, Yu D. Transcriptome Analysis of Granulosa Cells Reveals Regulatory Mechanisms Related to Chicken Follicle Development. Animals (Basel) 2023; 14:20. [PMID: 38200750 PMCID: PMC10777934 DOI: 10.3390/ani14010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
In this study, we aimed to better understand the difference between the functions of the two types of granulosa cells and sought to discover more key genes involved in follicle development and follicle selection. Herein, we separately collected pre-hierarchical follicle granulosa cells (PHGCs) and preovulatory follicle granulosa cells (POGCs) for RNA extraction; the transcriptomes of the two groups were compared via RNA-seq. A total of 5273 differentially expressed genes (DEGs) were identified between the PHGCs and POGCs; 2797 genes were up-regulated and 2476 were down-regulated in the PHGCs compared with the POGCs. A qPCR analysis confirmed that the expression patterns of 16 randomly selected DEGs were highly consistent with the RNA-seq results. In the POGCs, many of the genes with the most significant increase in expression were related to steroid hormone synthesis. In addition, the genes with the most significant decline in expression, including AMH and WT1, were related to the inhibition of steroid hormone synthesis. These results suggest that steroid hormones play a key role in follicle development. Furthermore, a Gene Ontology (GO) analysis revealed that these DEGs were mainly involved in the primary metabolic process, the carbohydrate metabolic process, the cellular process, ribosomes, the cytoplasm, and intracellular processes. A Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the DEGs were mainly enriched in steroid biosynthesis, the cell cycle, ribosomes, the TGF-beta signaling pathway, focal adhesion, and so on. We also observed the morphology of the follicles at different developmental stages, and the results showed that the thickness of the granular layer of the small yellow follicles (SYFs) decreased significantly with further development. In addition, we also found that the thickness of the granulosa layer of hens over 300 days old was significantly lower than that of 200-day-old hens. In short, these data indicate that the tissue morphology and function of granulosa cells change throughout follicle development.
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Affiliation(s)
- Xubin Du
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (X.D.); (Q.Z.); (H.P.); (X.W.); (J.H.)
- Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing 210095, China;
| | - Qizhao Zhu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (X.D.); (Q.Z.); (H.P.); (X.W.); (J.H.)
| | - Huifang Pian
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (X.D.); (Q.Z.); (H.P.); (X.W.); (J.H.)
| | - Xiaolong Yang
- College of Animal Science, Xizang Agricultural and Animal Husbandry University, Linzhi 860000, China;
| | - Dong Zhao
- Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing 210095, China;
| | - Xinyue Wu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (X.D.); (Q.Z.); (H.P.); (X.W.); (J.H.)
| | - Jiawen He
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (X.D.); (Q.Z.); (H.P.); (X.W.); (J.H.)
| | - Debing Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (X.D.); (Q.Z.); (H.P.); (X.W.); (J.H.)
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10
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Shen M, Wang M, Li D, Feng Y, Qu L, Wang J. microRNA transcriptome analysis of granulosa cells predicts that the Notch and insulin pathways affect follicular development in chickens. Theriogenology 2023; 212:140-147. [PMID: 37717517 DOI: 10.1016/j.theriogenology.2023.08.030] [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: 03/19/2023] [Revised: 07/13/2023] [Accepted: 08/31/2023] [Indexed: 09/19/2023]
Abstract
MicroRNAs (miRNAs) have been documented to play critical roles in chicken reproduction. Granulosa cell (GC) development of the follicle is closely related to hierarchical follicle ordering, making it an important factor in determining laying performance. Thus, it is meaningful to mine follicular development-related miRNAs. To identify regulatory miRNAs and the biological mechanisms by which they control follicular development, we conducted small RNA sequencing of GCs isolated from prehierarchical follicles named small yellow follicle (SYFG), the smallest hierarchical follicle (F6G), and the largest hierarchical follicle (F1G). A total of 99, 196, and 110 differentially expressed miRNAs (DEMs) were identified in SYFG.vs.F6G, SYFG.vs.F1G, and F6G.vs.F1G, respectively. Of these, 22 miRNAs, including miR-223, miR-103a, miR-449c-3p, and miR-203a, were ubiquitously identified as DEMs in three stages. Target gene prediction suggested that these miRNAs are associated with the MAPK, TGF-β, and Wnt signaling pathways, which are all associated with follicular development. The Notch and insulin signaling pathways were commonly enriched in all three comparisons. RT-qPCR analysis further indicated that the expression levels of PSEN2, which encodes an essential factor regulating Notch and insulin signaling, was significantly changed in SYFG, F6G, and F1G. The current study provides basic data and offers a new foundation for further exploration of the roles of miRNAs in follicular development in chickens.
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Affiliation(s)
- Manman Shen
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China; Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China; Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, China.
| | - Mingzhu Wang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China.
| | - Dehui Li
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China.
| | - Yuan Feng
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China.
| | - Liang Qu
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, China.
| | - Jinyu Wang
- Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
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11
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Li Q, Li J, Li C, Wu X, Si S, Yang P, Li W, Han R, Li G, Liu X, Kang X, Tian Y. Transcriptome identification and characterization of long non-coding RNAs in the ovary of hens at four stages. Anim Biotechnol 2023; 34:1342-1353. [PMID: 35209802 DOI: 10.1080/10495398.2021.2024217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Long non-coding RNAs (lncRNAs) play important roles in transcriptional and post-transcriptional regulation. LncRNAs, which are defined as non-coding RNAs more than 200 bp in length, are involved in key biological processes, such as cell proliferation and differentiation, epigenetic regulation, and gene transcriptional translation. Recent studies have shown that lncRNAs also play major regulatory roles in the reproduction of mammals. However, knowledge of the roles of lncRNAs in the chicken ovary lacking. In this study, we performed RNA-seq analyses of ovarian tissue from Hy-Line brown laying hens at four physiological stages [15, 20, 30, and 68 weeks of age (W)]. We identified 657 lncRNA transcripts that were differentially expressed during ovarian development, the number of down-regulated lncRNAs was higher than the number of up-regulated lncRNAs during development. We predicted the cis and trans target genes of the DE lncRNAs and constructed a lncRNA-mRNA interaction network, which indicated that the DE genes (DEGs) and the target genes of the DE lncRNAs are mainly involved in signaling pathways associated with ovarian development, including oocyte meiosis, calcium signaling pathways, ECM-receptor interactions, and ribosome and focal adhesion. Overall, we found that twelve lncRNAs were strongly involved in ovarian development: LNC_013443, LNC_001029, LNC_005713, LNC_016762, ENSGALT00000101857, LNC_003913, LNC_013692, LNC_012219, LNC_004140, ENSGALT00000096941, LNC_009356, and ENSGALT00000098716. In summary, our study utilized RNA-seq analysis of hen ovaries to explore key lncRNAs involved in ovarian development and function. Furthermore, the comprehensive analysis identified the target genes of these lncRNAs providing a better understanding of the mechanisms underlying ovarian development in hens and a theoretical basis for further research.
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Affiliation(s)
- Qi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Jing Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Chong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Xing Wu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Sujin Si
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Pengkun Yang
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, China
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12
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Fan L, Ren J, Wang Y, Chen Y, Chen Y, Chen L, Lin Q, Liao M, Ding C, Xiang B, Ren T. Circular RNAs are associated with the resistance to Newcastle disease virus infection in duck cells. Front Vet Sci 2023; 10:1181916. [PMID: 37841466 PMCID: PMC10570413 DOI: 10.3389/fvets.2023.1181916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/18/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction Newcastle disease virus (NDV) is prevalent worldwide with an extensive host range. Among birds infected with velogenic NDV strains, chickens experience high pathogenicity and mortality, whereas ducks mostly experience mild symptoms or are asymptomatic. Ducks have a unique, innate immune system hypothesized to induce antiviral responses. Circular RNAs (circRNAs) are among the most abundant and conserved eukaryotic transcripts. These participate in innate immunity and host antiviral response progression. Methods In this study, circRNA expression profile differences post-NDV infection in duck embryo fibroblast (DEF) cells were analyzed using circRNA transcriptome sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to reveal significant enrichment of differentially expressed (DE) circRNAs. The circRNA-miRNA-mRNA interaction networks were used to predict the related functions of circRNAs. Moreover, circ-FBXW7 was selected to determine its effect on NDV infection in DEFs. Results NDV infection altered circRNA expression profiles in DEF cells, and 57 significantly differentially expressed circRNAs were identified post-NDV infection. DEF responded to NDV by forming circRNAs to regulate apoptosis-, cell growth-, and protein degradation-related pathways via GO and KEGG enrichment analyses. circRNA-miRNA-mRNA interaction networks demonstrated that DEF cells combat NDV infection by regulating cellular pathways or apoptosis through circRNA-targeted mRNAs and miRNAs. circ-FBXW7 overexpression and knockdown inhibited and promoted viral replication, respectively. DEF cells mainly regulated cell cycle alterations or altered cellular sensing to combat NDV infection. Conclusion These results demonstrate that DEF cells exert antiviral responses by forming circRNAs, providing novel insights into waterfowl antiviral responses.
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Affiliation(s)
- Lei Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Jinlian Ren
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Yinchu Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Yiyi Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Yichun Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Libin Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Qiuyan Lin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Ming Liao
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chan Ding
- Shanghai Veterinary Research Institute (SHVRI), Chinese Academy of Agricultural Sciences (CAAS), Shanghai, China
| | - Bin Xiang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Tao Ren
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture, Guangzhou, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
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13
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Jing T, Wu Y, Wan A, Ge C, Chen ZJ, Du Y. Circular RNA as a Novel Regulator and Promising Biomarker in Polycystic Ovary Syndrome. Biomolecules 2023; 13:1101. [PMID: 37509138 PMCID: PMC10377156 DOI: 10.3390/biom13071101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/09/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is a prevalent metabolic and reproductive disorder that causes low fertility in females. Despite its detrimental effects on women's health, care for PCOS has been impeded by its undefined pathogenesis. Thus, there is an urgent need to explore novel biomarkers and therapeutic targets for the diagnosis and treatment of PCOS. Circular RNAs (circRNAs) are a class of noncoding RNAs with covalently closed cyclic structures, present in high abundance, and show development-stage specific expression patterns. Recent studies have demonstrated that circRNAs participate in PCOS progression by modulating various biological functions, including cell proliferation, apoptosis, and steroidogenesis. In addition, circRNAs are widely present in the follicular fluid of women with PCOS, indicating their potential as diagnostic biomarkers and therapeutic targets for PCOS. This review provides the current knowledge of circRNAs in PCOS, including their regulatory functions and molecular mechanisms, and explores their potential as diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
- Tianrui Jing
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, China
| | - Yifan Wu
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, China
| | - Anran Wan
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, China
| | - Chengmin Ge
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, China
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan 250012, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250012, China
- NMU-SD Suzhou Collaborative Innovation Center for Reproductive Medicine, Suzhou 215000, China
| | - Yanzhi Du
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai 200135, China
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14
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Shen M, Li T, Feng Y, Wu P, Serrano BR, Barcenas AR, Qu L, Zhao W. Effects of quercetin on granulosa cells from prehierarchical follicles by modulating MAPK signaling pathway in chicken. Poult Sci 2023; 102:102736. [PMID: 37209658 DOI: 10.1016/j.psj.2023.102736] [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: 12/12/2022] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 05/22/2023] Open
Abstract
Quercetin (Que), widely found in a huge variety of plants, plays important roles in ovarian function. However, to data, there have been no reports about Que regulating granulosa cells (GCs) in prehierarchical follicles in chicken. Herein, GCs from follicles diameter from 4 to 8 mm in chicken were treated by Que in vitro culture to investigate how Que exerts its effect on follicular development. GCs treated by Que in concentrations of 10, 100, and 1,000 ng/mL were tested for cell proliferation and progesterone secretion. Eight cDNA libraries were constructed from GCs (4 samples per group) to explore transcriptome expression changes. The role of the MAPK/ERK signaling pathway was validated in this process. Treatment with 100 and 1,000 ng/mL levels of Que significantly promoted cell proliferation and progesterone secretion (P < 0.05). RNA-seq analysis data showed that 402 and 263 differentially expressed genes (DEGs) were up- and down-regulated, respectively. Functional enrichment analysis that the pathways related to follicular development included biosynthesis of amino acids, MAPK signaling pathway, and calcium signaling pathway. Notably, the function exerted in GCs of the different levels of Que was associated with the suppression of the MAPK pathway. In conclusion, our results proved that low levels of Que could promote MAPK signaling pathway, but high levels of Que inhibit MAPK signaling pathway in GCs from the prehierarchical follicles, promote cell proliferation and progesterone secretion, and benefit follicle selection.
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Affiliation(s)
- Manman Shen
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 225108, China; Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Tao Li
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 225108, China
| | - Yuan Feng
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 225108, China
| | - Ping Wu
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 225108, China
| | | | | | - Liang Qu
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
| | - Weiguo Zhao
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 225108, China.
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15
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Transcriptome RNA Sequencing Reveals That Circular RNAs Are Abundantly Expressed in Embryonic Breast Muscle of Duck. Vet Sci 2023; 10:vetsci10020075. [PMID: 36851380 PMCID: PMC10004440 DOI: 10.3390/vetsci10020075] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/14/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
Circular RNAs are widespread in various species and have important roles in myogenesis. However, the circular RNAs involved in breast muscle development in ducks have not yet been studied. Here, to identify circular RNAs during duck skeletal muscle development, three pectorales from Shan Ma ducks at E13 and E19, which represent undifferentiated and differentiated myoblasts, respectively, were collected and subjected to RNA sequencing. A total of 16,622 circular RNAs were identified, of which approximately 80% were exonic circular RNAs and 260 were markedly differentially expressed between E19 and E13. The parental genes of the differentially expressed circular RNAs were significantly enriched in muscle-related biological processes. Moreover, we found that the overexpression of circGAS2-2 promoted cell cycle progression and increased the proliferation viability of duck primary myoblasts; conversely, knockdown of circGAS2-2 retarded the cell cycle and reduced the proliferation viability of myoblasts. Taken together, our results demonstrate that circular RNAs are widespread and variously expressed during the development of duck skeletal muscle and that circGAS2-2 is involved in the regulation of myogenesis.
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Zhao J, Pan H, Liu Y, He Y, Shi H, Ge C. Interacting Networks of the Hypothalamic-Pituitary-Ovarian Axis Regulate Layer Hens Performance. Genes (Basel) 2023; 14:141. [PMID: 36672882 PMCID: PMC9859134 DOI: 10.3390/genes14010141] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/19/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Egg production is a vital biological and economic trait for poultry breeding. The 'hypothalamic-pituitary-ovarian (HPO) axis' determines the egg production, which affects the layer hens industry income. At the organism level, the HPO axis is influenced by the factors related to metabolic and nutritional status, environment, and genetics, whereas at the cellular and molecular levels, the HPO axis is influenced by the factors related to endocrine and metabolic regulation, cytokines, key genes, signaling pathways, post-transcriptional processing, and epigenetic modifications. MiRNAs and lncRNAs play a critical role in follicle selection and development, atresia, and ovulation in layer hens; in particular, miRNA is known to affect the development and atresia of follicles by regulating apoptosis and autophagy of granulosa cells. The current review elaborates on the regulation of the HPO axis and its role in the laying performance of hens at the organism, cellular, and molecular levels. In addition, this review provides an overview of the interactive network regulation mechanism of the HPO axis in layer hens, as well as comprehensive knowledge for successfully utilizing their genetic resources.
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Affiliation(s)
- Jinbo Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University Kunming, Kunming 650201, China
- Branch of Animal Husbandry and Veterinary of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161005, China
| | - Hongbin Pan
- Faculty of Animal Science and Technology, Yunnan Agricultural University Kunming, Kunming 650201, China
| | - Yong Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University Kunming, Kunming 650201, China
| | - Yang He
- Faculty of Animal Science and Technology, Yunnan Agricultural University Kunming, Kunming 650201, China
| | - Hongmei Shi
- Faculty of Animal Science and Technology, Yunnan Agricultural University Kunming, Kunming 650201, China
| | - Changrong Ge
- Faculty of Animal Science and Technology, Yunnan Agricultural University Kunming, Kunming 650201, China
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17
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Chen X, Zhang Y, Zhang W, Nie R, Bao H, Zhang B, Zhang H. Regulatory effects of circular RNA on hypoxia adaptation in chicken embryos. J Anim Sci 2023; 101:skad344. [PMID: 37788641 PMCID: PMC10629444 DOI: 10.1093/jas/skad344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/03/2023] [Indexed: 10/05/2023] Open
Abstract
The Tibetan chicken, a native breed of the Tibetan plateau, is adapted to the high-altitude and hypoxic environment of the plateau. As endogenous molecules, circular RNAs (circRNAs) have been shown to play an important role in the adaptation to hypoxic environments and regulation of angiogenesis. In this study, highland Tibetan and lowland Chahua chicken eggs were incubated in a hypoxic environment and the chorionic allantoic membrane was collected for Ribo-Zero RNA sequencing. A total of 1,414 circRNAs, mostly derived from exons, were identified. Of these, 93 differentially expressed circRNAs were detected between Tibetan and Chahua chickens. Combined with the differentially expressed miRNAs and mRNAs identified in our previous study, we identified four circRNAs (circBRD1, circPRDM2, circPTPRS, and circDENND4C). These circRNAs may act as competing endogenous RNA (ceRNA) to upregulate APOA1 expression by absorbing novel_miR_589, thereby regulating angiogenesis and affecting hypoxia adaptation in chicken embryos. The regulatory circRNAs/novel_miR_589/APOA1 axis provides valuable evidence for a better understanding of the specific functions and molecular mechanisms of circRNAs in plateau hypoxia adaptation in Tibetan chickens.
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Affiliation(s)
- Xuejiao Chen
- State Key Laboratory of Farm Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ying Zhang
- General Department of Agricultural Museum, China Agricultural Museum, Beijing 100026, China
| | - Wenhui Zhang
- State Key Laboratory of Farm Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ruixue Nie
- State Key Laboratory of Farm Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Haigang Bao
- State Key Laboratory of Farm Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Bo Zhang
- State Key Laboratory of Farm Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hao Zhang
- State Key Laboratory of Farm Animal Biotech Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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18
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Zhang BB, Li MX, Wang HN, Liu C, Sun YY, Ma TH. An integrative analysis of lncRNAs and mRNAs highlights the potential roles of lncRNAs in the process of follicle selection in Taihang chickens. Theriogenology 2023; 195:122-130. [DOI: 10.1016/j.theriogenology.2022.10.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 11/07/2022]
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19
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Ye Y, Fan X, Cai Z, Wu Y, Zhang W, Zhao H, Guo S, Feng P, Li Q, Zou P, Chen M, Fan N, Chen D, Guo R. Unveiling the circRNA-Mediated Immune Responses of Western Honey Bee Larvae to Ascosphaera apis Invasion. Int J Mol Sci 2022; 24:613. [PMID: 36614055 PMCID: PMC9820429 DOI: 10.3390/ijms24010613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/14/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
Western honey bee (Apis mellifera), a eusocial insect with a superior economic and ecological value, is widely used in the beekeeping industry throughout the world. As a new class of non-coding RNAs (ncRNAs), circular RNAs (circRNAs) participate in the modulation of considerable biological processes, such as the immune response via diverse manners. Here, the identification, characteristic investigation, and molecular verification of circRNAs in the Apis mellifera ligustica larval guts were conducted, and the expression pattern of larval circRNAs during the Ascosphaera apis infection was analyzed, followed by the exploration of the potential regulatory part of differentially expressed circRNAs (DEcircRNAs) in host immune responses. A total of 2083 circRNAs in the larval guts of A. m. ligustcia were identified, with a length distribution ranging from 106 nt to 92,798 nt. Among these, exonic circRNAs were the most abundant type and LG1 was the most distributed chromosome. Additionally, 25, 14, and 30 up-regulated circRNAs as well as 26, 25, and 62 down-regulated ones were identified in the A. apis-inoculated 4-, 5-, and 6-day-old larval guts in comparison with the corresponding un-inoculated larval guts. These DEcircRNAs were predicted to target 35, 70, and 129 source genes, which were relative to 12, 23, and 20 GO terms as well as 11, 10, and 27 KEGG pathways, including 5 cellular and humoral immune pathways containing apoptosis, autophagy, endocytosis, MAPK, Toll, and Imd signaling pathways. Furthermore, complex competing endogenous RNA (ceRNA) regulatory networks were detected to be formed among DEcircRNAs, DEmiRNAs, and DEmRNAs. The Target DEmRNAs were engaged in 24, 20, and 25 functional terms as well as 62, 80, and 159 pathways, including several vital immune defense-associated pathways, namely the lysosome, endocytosis, phagosome, autophagy, apoptosis, MAPK, Jak-STAT, Toll, and Imd signaling pathways. Finally, back-splicing sites within 15 circRNAs and the difference in the 9 DEcircRNAs' expression between un-inoculated and A. apis-inoculated larval guts were confirmed utilizing molecular methods. These findings not only enrich our understanding of bee host-fungal pathogen interactions, but also lay a foundation for illuminating the mechanism underlying the DEcircRNA-mediated immune defense of A. m. ligustica larvae against A. apis invasion.
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Affiliation(s)
- Yaping Ye
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zongbing Cai
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ying Wu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wende Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haodong Zhao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sijia Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peilin Feng
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiming Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peiyuan Zou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengjun Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Nian Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
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MA TENGHE, LI MENGXIAO, ZHANG BEIBEI, LI XUENAN, WEI JIARONG, WANG HONGNA, WANG BIN, SHI YUXIANG. Expression spectrum of new circFBN1 in various tissues and follicles of Taihang chicken. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2022. [DOI: 10.56093/ijans.v92i11.127498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this study, the new circFBN1 derived from the FBN1 gene was identified. The expression spectrum of circFBN1 in various tissues and follicles of Taihang chickens was verified and analyzed. The effects on proliferation of GCs were checked. The results revealed that circFBN1 is indeed present and was differentially expressed in tissues and follicles and significantly promoted cell proliferation. In conclusion, our results suggested that circFBN1 could affect chicken follicular development by regulating the proliferation of GCs. These results will enable us recognize the molecular mechanisms in animal reproductive regulation.
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Wu Y, Li H, Zhao X, Baki G, Ma C, Yao Y, Li J, Yao Y, Wang L. Differential expression of circRNAs of testes with high and low sperm motility in Yili geese. Front Genet 2022; 13:970097. [PMID: 36226183 PMCID: PMC9548634 DOI: 10.3389/fgene.2022.970097] [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: 06/15/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
The aim of this study was to explore the potential biological function of circular RNAs (circRNAs) in the sperm motility traits of Xinjiang Yili geese, and to provide a reference for analyzing the mechanism of regulation of Yili geese sperm motility. The 10 selected Xinjiang Yili Geese with high or low sperm motility (five for each group) were 3 years old, in good health, and were kept in the same feeding conditions. Yili geese were slaughtered for the collection of testicular tissue and high-throughput sequencing technology was used to screen differentially expressed circRNAs for bioinformatics analysis. Combined with the previously screened miRNAs related to the sperm motility of Yili geese, the circRNAs miRNAs regulatory network was constructed. The results showed that a total of 26,311 circRNAs were obtained from testicular tissues with high and low sperm motility, and 173 DECs were screened between the two groups (p < 0.05, |log2Foldchange|>0), of which 82 were up-regulated and 91 were down-regulated. Functional analysis of the source genes of these DECs showed that the source genes were mainly involved in biological processes. KEGG enrichment analysis showed that the source genes of DECs were mainly enriched in autophagy-animal, ubiquinone and other terpenoid-quinone biosynthesis, progesterone-mediated oocyte maturation, regulation of the actin cytoskeleton and other pathways. Furthermore, the visual regulatory network of differential circRNA-miRNA-mRNA was constructed, including 20 circRNAs, 18 miRNAs and 177 mRNAs, and nine core regulatory circRNAs were screened, including novell_circ_0045314, novel_circ_0019994 and novel_circ_0020422, etc., targeting ppy-mir-16, hsa-mir-221–3p, gga-mir-499–5p, etc. The results suggest that circRNAs may interact with miRNAs to further regulate mRNA to regulate sperm motility in Yili geese, so as to provide a reference for analyzing the molecular mechanism of sperm motility regulation.
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Li Y, Xia G, Tan Y, Shuai J. Expression profile of circular RNAs in continuous light-induced ovarian dysfunction. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 242:113861. [PMID: 35835072 DOI: 10.1016/j.ecoenv.2022.113861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/23/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
PURPOSE This study aims to elucidate the underlying relationship between the expression profiles of circular RNAs (circRNAs) and the ovarian dysfunction induced by continuous light. METHODS High-throughput sequencing was used to profile the transcriptome of differentially expressed circRNAs (DEcircRNAs) in rat ovary under continuous light exposure (12 h:12 h light/light cycle, L/L group) and a control cycle (12 h:12 h light/dark cycle, L/D group). Gene ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and circRNAs-microRNAs-messenger RNAs networks were performed to predict the role of DEcircRNAs in biological processes and pathways. A quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) assay was conducted to verify the high-throughput sequencing results and the expression level of circadian rhythm genes. RESULTS In total, 305 circRNAs were differentially expressed between the L/L and L/D groups. Among these, 211 circRNAs were up regulated, while 94 were down regulated. Eight candidate circRNAs from 305 DEcircRNAs were verified by qRT-PCR. Further bioinformatics analysis revealed that interactions between DEcircRNAs and a set of microRNAs involved in ovarian dysfunction-related pathways, such as regulation of androgen receptors, gonadotrophin releasing hormone signaling pathway, endocrine resistance, etc. Subsequently, we identified rno_circ:chr2:86868285-86964272 and rno_circ:chr1:62330221-62360073 may participate in the pathophysiology of ovarian dysfunction by constructing circRNAs-microRNAs-messenger RNAs networks. Meanwhile, constant light reduced the expression of circadian rhythm genes CLOCK, BAML1, PER1, and PER2 compared with that of controls. Caspase3 and Bax were up regulated in the L/L group compared with the L/D group, while Bcl-2 was down regulated. CONCLUSIONS In summary, the results reveal that the expression profiles and potential functions of DEcircRNAs in rat ovaries may play important roles in continuous light-induced ovarian dysfunction. These findings provide novel clues and molecular targets for studying the mechanisms and clinical therapy of ovarian dysfunction.
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Affiliation(s)
- Yuling Li
- Nanjing University of Chinese Medicine, Nanjing 210029, China; Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
| | - Guicheng Xia
- Nanjing University of Chinese Medicine, Nanjing 210029, China; Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
| | - Yong Tan
- Nanjing University of Chinese Medicine, Nanjing 210029, China; Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China.
| | - Jiaqi Shuai
- Bachelor of Medicine, University of Antwerp, Antwerp, Belgium
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He Z, Ma Z, Yang D, Chen Q, He Z, Hu J, Deng F, Zhang Q, He J, Ye L, Chen H, He L, Huang X, Luo W, Yang S, Gu X, Zhang M, Yan T. Circular RNA expression profiles and CircSnd1-miR-135b/c-foxl2 axis analysis in gonadal differentiation of protogynous hermaphroditic ricefield eel Monopterus albus. BMC Genomics 2022; 23:552. [PMID: 35922747 PMCID: PMC9347082 DOI: 10.1186/s12864-022-08783-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The expression and biological functions of circular RNAs (circRNAs) in reproductive organs have been extensively reported. However, it is still unclear whether circRNAs are involved in sex change. To this end, RNA sequencing (RNA-seq) was performed in gonads at 5 sexual stages (ovary, early intersexual stage gonad, middle intersexual stage gonad, late intersexual stage gonad, and testis) of ricefield eel, and the expression profiles and potential functions of circRNAs were studied. RESULTS Seven hundred twenty-one circRNAs were identified, and the expression levels of 10 circRNAs were verified by quantitative real-time PCR (qRT-PCR) and found to be in accordance with the RNA-seq data, suggesting that the RNA-seq data were reliable. Then, the sequence length, category, sequence composition and the relationship between the parent genes of the circRNAs were explored. A total of 147 circRNAs were differentially expressed in the sex change process, and GO and KEGG analyses revealed that some differentially expressed (such as novel_circ_0000659, novel_circ_0004005 and novel_circ_0005865) circRNAs were closely involved in sex change. Furthermore, expression pattern analysis demonstrated that both circSnd1 and foxl2 were downregulated in the process of sex change, which was contrary to mal-miR-135b. Finally, dual-luciferase reporter assay and RNA immunoprecipitation showed that circSnd1 and foxl2 can combine with mal-miR-135b and mal-miR-135c. These data revealed that circSnd1 regulates foxl2 expression in the sex change of ricefield eel by acting as a sponge of mal-miR-135b/c. CONCLUSION Our results are the first to demonstrate that circRNAs have potential effects on sex change in ricefield eel; and circSnd1 could regulate foxl2 expression in the sex change of ricefield eel by acting as a sponge of mal-miR-135b/c. These data will be useful for enhancing our understanding of sequential hermaphroditism and sex change in ricefield eel or other teleosts.
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Affiliation(s)
- Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhijun Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiqi Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhide He
- Luzhou City Department of Agricultural and Rural Affairs, Luzhou, 646000, Sichuan, China
| | - Jiaxiang Hu
- Sichuan Water Conservancy Vocational College, Chengdu, 611231, Sichuan, China
| | - Faqiang Deng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qian Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jiayang He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lijuan Ye
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hongjun Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Liang He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoli Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wei Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shiyong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaobin Gu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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24
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Regulation of Non-Coding RNA in the Growth and Development of Skeletal Muscle in Domestic Chickens. Genes (Basel) 2022; 13:genes13061033. [PMID: 35741795 PMCID: PMC9222894 DOI: 10.3390/genes13061033] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/28/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023] Open
Abstract
Chicken is the most widely consumed meat product worldwide and is a high-quality source of protein for humans. The skeletal muscle, which accounts for the majority of chicken products and contains the most valuable components, is tightly correlated to meat product yield and quality. In domestic chickens, skeletal muscle growth is regulated by a complex network of molecules that includes some non-coding RNAs (ncRNAs). As a regulator of muscle growth and development, ncRNAs play a significant function in the development of skeletal muscle in domestic chickens. Recent advances in sequencing technology have contributed to the identification and characterization of more ncRNAs (mainly microRNAs (miRNAs), long non-coding RNAs (LncRNAs), and circular RNAs (CircRNAs)) involved in the development of domestic chicken skeletal muscle, where they are widely involved in proliferation, differentiation, fusion, and apoptosis of myoblasts and satellite cells, and the specification of muscle fiber type. In this review, we summarize the ncRNAs involved in the skeletal muscle growth and development of domestic chickens and discuss the potential limitations and challenges. It will provide a theoretical foundation for future comprehensive studies on ncRNA participation in the regulation of skeletal muscle growth and development in domestic chickens.
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25
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Liu Y, Zhou Z, He X, Jiang Y, Ouyang Y, Hong Q, Chu M. Differentially Expressed Circular RNA Profile Signatures Identified in Prolificacy Trait of Yunshang Black Goat Ovary at Estrus Cycle. Front Physiol 2022; 13:820459. [PMID: 35492611 PMCID: PMC9049588 DOI: 10.3389/fphys.2022.820459] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/10/2022] [Indexed: 01/10/2023] Open
Abstract
CircRNAs acting as miRNA sponges play important roles in the growth process of animal individuals. The prolificacy trait of goats is involved in many pathways, however, the variation of circRNA expression profiles in the different phases of the estrus cycle at high and low fecundity groups is still unknown. Here, we analyzed the circRNA profiles of ovarian tissues among high and low fecundity groups in the follicular phase (HF vs LF), high and low fecundity groups in the luteal phase (HL vs LL), and high and low fecundity in the whole estrus cycle (HF vs HL and LF vs LL) using RNA-seq. A total of 283 (114 upregulated and 169 downregulated), 559 (299 upregulated and 260 downregulated), 449 (254 upregulated and 195 downregulated), and 314 (210 upregulated and 104 downregulated) differentially expressed (DE) circRNAs were screened in HF vs LF, HF vs HL, HL vs LL, and LF vs LL groups, respectively. Enrichment analysis suggested that the targeting of DE circRNAs was mainly enriched in oocyte meiosis, the GnRH signaling pathway, and estrogen signaling pathway. After integrating our previous study of miRNA-seq, there were 56 miRNAs that could target to 192 DE circRNAs, including the miR-133 family (including miR-133a-3p and miR-133b), miR-129-3p, and miR-21, which also had important influence on the prolificacy trait of goats. Then, 18 circRNAs with coding potential were obtained by four software predictions, and 9 circRNAs were validated by RT-qPCR. Together, circRNAs play a key role in the prolificacy trait and the transformation of the follicular phase to the luteal phase in the estrus cycle of goats.
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Affiliation(s)
- Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Zuyang Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanting Jiang
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Yina Ouyang
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Qionghua Hong
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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26
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Lu L, Zhang L, Zeng T, Du X, Tao Z, Li G, Zhong S, Wen J, Zhou C, Xu X. Transcriptome analyses of potential regulators of pre- and post-ovulatory follicles in the pigeon ( Columba livia). Reprod Fertil Dev 2022; 34:689-697. [PMID: 35366957 DOI: 10.1071/rd21239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/03/2022] [Indexed: 11/23/2022] Open
Abstract
To identify the dominant genes controlling follicular maturation, ovulation and regression for pigeon, we used RNA-seq to explore the gene expression profiles of pre- and post-ovulatory follicles of pigeon. We obtained total of 4.73million (96% of the raw data) high-quality clean reads, which could be aligned with 20282 genes. Gene expression profile analysis identified 1461 differentially expressed genes (DEGs) between the pre- (P4) and post-ovulatory follicles (P5). Of these, 843 genes were upregulated, and 618 genes were down-regulated. Furthermore, many DEGs were significantly enriched in some pathways closely related to follicle maturation, ovulation and regression, such as ECM-receptor interaction, vascular smooth muscle contraction, progesterone-mediated oocyte maturation, phagosome. Importantly, the DGEs in ECM-receptor interaction pathway included COL1A1 , COL1A2 , COL4A1 , COL4A2 , ITGA11 , ITGB3 and SDC3 , in the progesterone-mediated oocyte maturation pathway involved CDK1 , CDC25A , CCNB3 , CDC20 and Plk1 , and in the vascular smooth muscle contraction covered CALD1 , KCNMA1 , KCNMB1 , CACNA1 , ACTA2 , MYH10 , MYL3 , MYL6 , MYL9 , closely related to promoting follicular maturation and ovulation in pre-ovulatory follicles. Moreover, it seems that the lysosomal cathepsin family has a decisive role in the regression of early stage of post-ovulatory follicle. Taken together, these data enrich the research of molecular mechanisms of pigeon follicular activities at the transcriptional level and provide novel insight of breeding-related physiology for birds.
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Affiliation(s)
- Lizhi Lu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, 310021 Hangzhou, Zhejiang, China
| | - Long Zhang
- Institute of Ecology, Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, 637009 Nanchong, Sichuan, China
| | - Tao Zeng
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, 310021 Hangzhou, Zhejiang, China
| | - Xue Du
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, 310021 Hangzhou, Zhejiang, China
| | - Zhengrong Tao
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, 310021 Hangzhou, Zhejiang, China
| | - Guoqin Li
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Science, 310021 Hangzhou, Zhejiang, China
| | - Shengliang Zhong
- PingYang XingLiang Pigeon Farming Co. Ltd., 325000 Wenzhou, Zhejiang, China
| | - Jihui Wen
- PingYang AoFeng Pigeon Farming Co. Ltd., 325000 Wenzhou, Zhejiang, China
| | - Caiquan Zhou
- Institute of Ecology, Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, 637009 Nanchong, Sichuan, China
| | - Xiaoqin Xu
- Institute of Ecology, Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, 637009 Nanchong, Sichuan, China
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27
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Wang Y, Guo Z, Zi C, Wu P, Lv X, Chen L, Chen F, Zhang G, Wang J. CircRNA expression in chicken granulosa cells illuminated with red light. Poult Sci 2022; 101:101734. [PMID: 35202895 PMCID: PMC8866055 DOI: 10.1016/j.psj.2022.101734] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 01/03/2022] [Accepted: 01/12/2022] [Indexed: 11/19/2022] Open
Abstract
Red light (RL) can improve egg production in Jinghai Yellow hens. Circular RNAs (circRNAs) are novel, non-coding RNAs, but the molecular mechanism underlying circRNA function during follicular development in hens under monochromatic light has not been established. Herein, we compared expression profiles of granulosa cells (GCs) from small yellow follicles (SYFs) from hens under RL and white light (WL). A total of 2,468 circRNAs were identified, of which 22 were differentially expressed (DE) in the RL and WL groups. DE circRNA host genes were enriched in ovarian steroidogenesis, and MAPK and PI3K-Akt signaling pathways. Furthermore, DE circRNA_0320 and circRNA_0185 interacted with miR-143-3p, which targets the follicle-stimulating hormone receptor and is essential for GC differentiation and follicle development. These findings will facilitate further analysis of the molecular mechanism leading to GC development in hens raised under monochromatic light, which could lead to increased egg production.
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Affiliation(s)
- Ying Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China
| | - Zhenyu Guo
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China
| | - Chen Zi
- Department of Pathology, Linyi People's Hospital, Linyi 276000, Shandong Province, China
| | - Pengfei Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China
| | - Xiaoyang Lv
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China
| | - Lan Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China
| | - Fuxiang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, P. R. China.
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28
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Liu Y, Wang P, Zhou Z, He X, Tao L, Jiang Y, Lan R, Hong Q, Chu M. Expression Profile Analysis to Identify Circular RNA Expression Signatures in the Prolificacy Trait of Yunshang Black Goat Pituitary in the Estrus Cycle. Front Genet 2022; 12:801357. [PMID: 35140742 PMCID: PMC8820483 DOI: 10.3389/fgene.2021.801357] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/03/2021] [Indexed: 12/20/2022] Open
Abstract
The pituitary gland is an important organ. It is a complex area of the brain involved in endocrine function and reproductive regulation. However, the function of the pituitary in goat reproduction is still unclear. Herein, RNA sequencing was used to explore the expression patterns of circle RNAs (circRNAs) in the pituitary of Yunshang black goats during the various estrus phases. Then the host genes of the circRNAs were predicted, and a competing endogenous RNA (ceRNA) network was constructed. The results showed a total of 6,705 circRNAs in the pituitary of Yunshang black goats, among which 388 differentially expressed (DE) circRNAs (214 were upregulated, while 174 were downregulated) were identified between high- and low-yield Yunshang black goats in the follicular phase (HF vs. LF); moreover, 361 DE circRNAs (136 were upregulated, while 225 were downregulated) were identified between high- and low-yield Yunshang black goats in the luteal phase (HL vs. LL). There were 65 DE circRNAs targeting 40 miRNAs in the HF vs. LF comparison and 46 DE circRNAs targeting 31 miRNAs in the HL vs. LL comparison. We identified chi_circ_0030920, chi_circ_0043017, chi_circ_0008353, chi_circ_0041580, and chi_circ_0016478 as the key circRNAs through functional enrichment analysis. The ceRNA network analysis showed that chi_circ_0031209 and chi_circ_0019448 might play an important role in reproduction by influencing the expression of prolactin receptor (PRLR) in high- and low-yielding goats during the luteal phase, whereas chi_circ_0014542 regulates the expression of WNT5A during the follicular phase. Our study provided the overall expression profiles of circRNAs in the goat pituitary during the estrus phase, which provides new insight into the mechanism of high-yield goats, which can be helpful to guide goat breeding.
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Affiliation(s)
- Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Peng Wang
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Zuyang Zhou
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin Tao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanting Jiang
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Rong Lan
- Yunnan Animal Science and Veterinary Institute, Kunming, China
| | - Qionghua Hong
- Yunnan Animal Science and Veterinary Institute, Kunming, China
- *Correspondence: Qionghua Hong, ; Mingxing Chu,
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Qionghua Hong, ; Mingxing Chu,
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Duan X, Yu L, Luo Q, Han R. Analysis of amino acid in albumen and circular RNAs in ovaries of laying hens by chromatographic analysis and RNA-seq. J LIQ CHROMATOGR R T 2022. [DOI: 10.1080/10826076.2021.2023022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Xiaoyan Duan
- Office of Academic Affairs, Hebei North University, Zhang Jiakou, China
| | - Liu Yu
- Department of Laboratory Animal Center, Hebei North University, Zhang Jiakou, China
| | - Qiang Luo
- Life Science Research Center, Hebei North University, Zhang Jiakou, China
| | - Rui Han
- Department of Laboratory Animal Center, Hebei North University, Zhang Jiakou, China
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Cao X, Xu X, Dong J, Xue Y, Sun L, Zhu Y, Liu T, Jin Q. Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages. BMC Genomics 2022; 23:21. [PMID: 34983376 PMCID: PMC8725419 DOI: 10.1186/s12864-021-08184-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 11/18/2021] [Indexed: 12/28/2022] Open
Abstract
Background Circular RNAs (circRNAs) are a group of noncoding RNAs that participate in gene expression regulation in various pathways. The essential roles of circRNAs have been revealed in many species. However, knowledge of circRNAs in fungi is still not comprehensive. Results Trichophyton rubrum (T. rubrum) is considered a model organism of human pathogenic filamentous fungi and dermatophytes. In this study, we performed a genome-wide investigation of circRNAs in T. rubrum based on high-throughput sequencing and ultimately identified 4254 circRNAs. Most of these circRNAs were specific to the conidial or mycelial stage, revealing a developmental stage-specific expression pattern. In addition, 940 circRNAs were significantly differentially expressed between the conidial and mycelial stages. PCR experiments conducted on seven randomly selected differentially expressed (DE-) circRNAs confirmed the circularized structures and relative expression levels of these circRNAs. Based on their genome locations, most circRNAs originated from intergenic regions, unlike those in plants and animals. Furthermore, we constructed circRNA-miRNA-mRNA regulatory networks that included 661 DE-circRNAs targeting 140 miRNAs and further regulating 2753 mRNAs. The relative expression levels of two randomly selected circRNA-miRNA-mRNA axes were investigated by qRT-PCR, and the competing endogenous RNA (ceRNA) network theory was validated. Functional enrichment analysis of the target genes suggested that they were significantly involved in posttranscriptional processes and protein synthesis as well as some small-molecule metabolism processes. CircRNAs are relatively more conserved in closely related dermatophytes but rarely conserved in distantly related species. Tru_circ07138_001 is a highly conserved circRNA that was conserved in all ten dermatophytes analyzed in our study and three distantly related species. Its host gene TERG_07138 was also highly conserved in two of these distantly related species Gallus gallus and Caenorhabditis elegans. The specific role of this circRNA deserves further exploration. Conclusions Our study is the first to provide a global profile of circRNAs in T. rubrum as well as dermatophytes. These results could serve as valuable resources for research on circRNA regulatory mechanisms in fungi and reveal new insights for further investigation of the physical characteristics of these significant human fungal pathogens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08184-y.
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Affiliation(s)
- Xingwei Cao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xingye Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Ying Xue
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Lilian Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yafang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Tao Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China.
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31
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Gao G, Hu S, Zhang K, Wang H, Xie Y, Zhang C, Wu R, Zhao X, Zhang H, Wang Q. Genome-Wide Gene Expression Profiles Reveal Distinct Molecular Characteristics of the Goose Granulosa Cells. Front Genet 2021; 12:786287. [PMID: 34992633 PMCID: PMC8725158 DOI: 10.3389/fgene.2021.786287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/30/2021] [Indexed: 11/24/2022] Open
Abstract
Granulosa cells (GCs) are decisive players in follicular development. In this study, the follicle tissues and GCs were isolated from the goose during the peak-laying period to perform hematoxylin-eosin staining and RNA-seq, respectively. Moreover, the dynamic mRNA and lncRNA expression profiles and mRNA-lncRNA network analysis were integrated to identify the important genes and lncRNAs. The morphological analysis showed that the size of the GCs did not significantly change, but the thickness of the granulosa layer cells differed significantly across the developmental stages. Subsequently, 14,286 mRNAs, 3,956 lncRNAs, and 1,329 TUCPs (transcripts with unknown coding potential) were detected in the GCs. We identified 37 common DEGs in the pre-hierarchical and hierarchical follicle stages, respectively, which might be critical for follicle development. Moreover, 3,089 significant time-course DEGs (Differentially expressed genes) and 13 core genes in 4 clusters were screened during goose GCs development. Finally, the network lncRNA G8399 with CADH5 and KLF2, and lncRNA G8399 with LARP6 and EOMES were found to be important for follicular development in GCs. Thus, the results would provide a rich resource for elucidating the reproductive biology of geese and accelerate the improvement of the egg-laying performance of geese.
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Affiliation(s)
- Guangliang Gao
- Chongqing Academy of Animal Sciences, Chongqing, China
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
- *Correspondence: Guangliang Gao, ; Hongmei Zhang, ; Qigui Wang,
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Keshan Zhang
- Chongqing Academy of Animal Sciences, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Haiwei Wang
- Chongqing Academy of Animal Sciences, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Youhui Xie
- Chongqing Academy of Animal Sciences, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Changlian Zhang
- Chongqing Academy of Animal Sciences, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Rui Wu
- Chongqing Academy of Animal Sciences, Chongqing, China
| | - Xianzhi Zhao
- Chongqing Academy of Animal Sciences, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
| | - Hongmei Zhang
- Department of Cardiovascular Ultrasound and Non-invasive Cardiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
- Ultrasound in Cardiac Electrophysiology and Biomechanics Key Laboratory of Sichuan Province, Chengdu, China
- *Correspondence: Guangliang Gao, ; Hongmei Zhang, ; Qigui Wang,
| | - Qigui Wang
- Chongqing Academy of Animal Sciences, Chongqing, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, China
- *Correspondence: Guangliang Gao, ; Hongmei Zhang, ; Qigui Wang,
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Zhang Y, Gong S, Su Y, Yao M, Liu X, Gong Z, Sui H, Luo M. Follicular development in livestock: Influencing factors and underlying mechanisms. Anim Sci J 2021; 92:e13657. [PMID: 34796578 DOI: 10.1111/asj.13657] [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: 05/14/2021] [Revised: 09/23/2021] [Accepted: 10/26/2021] [Indexed: 12/01/2022]
Abstract
Livestock farming development has become increasingly important in recent years. It not only provides us with meat nutrition and pet feeding but also increases the economic value by providing numerous employment opportunities, which improves our life quality. The livestock farming development depends on successful animal reproduction. As a vital process in animal reproduction, folliculogenesis and its influencing factors as well as their underlying mechanisms need to be understood thoroughly. This review is aimed at summarizing the factors such as cellular processes, gene regulation, noncoding RNAs and other endocrine or paracrine regulatory factors that affect follicular development, and their underlying mechanisms of action in livestock in order to provide novel insights for future studies. The above factors were found as significant determinants influencing the follicular development in livestock through various signaling pathways.
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Affiliation(s)
- Yanjun Zhang
- College of Animal Science and Veterinary, Shandong Agricultural University, Tai'an, China.,Jiaxiang County Animal Husbandry and Veterinary Bureau, Jining, China
| | - Shuai Gong
- College of Animal Science and Veterinary, Shandong Agricultural University, Tai'an, China
| | - Yanping Su
- Department of Histology and Embryology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China
| | - Minhua Yao
- Department of Histology and Embryology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China
| | - Xiaocui Liu
- Department of Histology and Embryology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China
| | - Zhaoqing Gong
- Department of Histology and Embryology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China
| | - Hongshu Sui
- Department of Histology and Embryology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China
| | - Mingjiu Luo
- College of Animal Science and Veterinary, Shandong Agricultural University, Tai'an, China
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Li M, Liu Y, Xie S, Ma L, Zhao Z, Gong H, Sun Y, Huang T. Transcriptome analysis reveals that long noncoding RNAs contribute to developmental differences between medium-sized ovarian follicles of Meishan and Duroc sows. Sci Rep 2021; 11:22510. [PMID: 34795345 PMCID: PMC8602415 DOI: 10.1038/s41598-021-01817-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 11/01/2021] [Indexed: 01/04/2023] Open
Abstract
Ovulation rate is an extremely important factor affecting litter size in sows. It differs greatly among pig breeds with different genetic backgrounds. Long non-coding RNAs (lncRNAs) can regulate follicle development, granulosa cell growth, and hormone secretion, which in turn can affect sow litter size. In this study, we identified 3554 lncRNAs and 25,491 mRNAs in M2 follicles of Meishan and Duroc sows. The lncRNA sequence and open reading frame lengths were shorter than mRNAs, and lncRNAs had fewer exons, were less abundant, and more conserved than protein-coding RNAs. Furthermore, 201 lncRNAs were differentially expressed (DE) between breeds, and quantitative trait loci analysis of DE lncRNAs were performed. A total of 127 DE lncRNAs were identified in 119 reproduction trait-related loci. In addition, the potential target genes of lncRNAs in cis or trans configurations were predicted. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that some potential target genes were involved in follicular development and hormone secretion-related biological processes or pathways, such as progesterone biosynthetic process, estrogen metabolic process, ovarian steroidogenesis, and PI3K-Akt signaling pathway. Furthermore, we also screened 19 differentially expressed lncRNAs in the PI3K-Akt signaling pathway as candidates. This study provides new insights into the roles of lncRNAs in follicular growth and development in pigs.
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Affiliation(s)
- Mengxun Li
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
| | - Yi Liu
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Su Xie
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
| | - Lipeng Ma
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
| | - Zhichao Zhao
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
- Guangxi Yangxiang Animal Husbandry Co. Ltd., Guangxi, Guigang, 537100, China
| | - Hongbin Gong
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
| | - Yishan Sun
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
| | - Tao Huang
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China.
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Tian W, Zhang B, Zhong H, Nie R, Ling Y, Zhang H, Wu C. Dynamic Expression and Regulatory Network of Circular RNA for Abdominal Preadipocytes Differentiation in Chicken ( Gallus gallus). Front Cell Dev Biol 2021; 9:761638. [PMID: 34869349 PMCID: PMC8633312 DOI: 10.3389/fcell.2021.761638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/26/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNA (circRNA), as a novel endogenous biomolecule, has been emergingly demonstrated to play crucial roles in mammalian lipid metabolism and obesity. However, little is known about their genome-wide identification, expression profile, and function in chicken adipogenesis. In present study, the adipogenic differentiation of chicken abdominal preadipocyte was successfully induced, and the regulatory functional circRNAs in chicken adipogenesis were identified from abdominal adipocytes at different differentiation stages using Ribo-Zero RNA-seq. A total of 1,068 circRNA candidates were identified and mostly derived from exons. Of these, 111 differentially expressed circRNAs (DE-circRNAs) were detected, characterized by stage-specific expression, and enriched in several lipid-related pathways, such as Hippo signaling pathway, mTOR signaling pathway. Through weighted gene co-expression network analyses (WGCNA) and K-means clustering analyses, two DE-circRNAs, Z:35565770|35568133 and Z:54674624|54755962, were identified as candidate regulatory circRNAs in chicken adipogenic differentiation. Z:35565770|35568133 might compete splicing with its parental gene, ABHD17B, owing to its strictly negative co-expression. We also constructed competing endogenous RNA (ceRNA) network based on DE-circRNA, DE-miRNA, DE-mRNAs, revealing that Z:54674624|54755962 might function as a ceRNA to regulate chicken adipogenic differentiation through the gga-miR-1635-AHR2/IRF1/MGAT3/ABCA1/AADAC and/or the novel_miR_232-STAT5A axis. Translation activity analysis showed that Z:35565770|35568133 and Z:54674624|54755962 have no protein-coding potential. These findings provide valuable evidence for a better understanding of the specific functions and molecular mechanisms of circRNAs underlying avian adipogenesis.
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Affiliation(s)
- Weihua Tian
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haian Zhong
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ruixue Nie
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yao Ling
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Changxin Wu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
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35
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Sharma D, Sehgal P, Sivasubbu S, Scaria V. A genome-wide circular RNA transcriptome in rat. Biol Methods Protoc 2021; 6:bpab016. [PMID: 34527809 PMCID: PMC8435660 DOI: 10.1093/biomethods/bpab016] [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: 03/22/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/26/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel class of noncoding RNAs that back-splice from 5ʹ donor site and 3ʹ acceptor sites to form a circular structure. A number of circRNAs have been discovered in model organisms including human, mouse, Drosophila, among other organisms. There are a few candidate-based studies on circRNAs in rat, a well-studied model organism as well. A number of pipelines have been published to identify the back splice junctions for the discovery of circRNAs but studies comparing these tools have suggested that a combination of tools would be a better approach to identify high-confidence circRNAs. The availability of a recent dataset of transcriptomes encompassing 11 tissues, 4 developmental stages, and 2 genders motivated us to explore the landscape of circRNAs in the organism in this context. In order to understand the difference among different pipelines, we employed five different combinations of tools to identify circular RNAs from the dataset. We compared the results of the different combination of tools/pipelines with respect to alignment, total number of circRNAs identified and read-coverage. In addition, we identified tissue-specific, development-stage specific and gender-specific circRNAs and further independently validated 16 circRNA junctions out of 24 selected candidates in 5 tissue samples and estimated the quantitative expression of five circRNA candidates using real-time polymerase chain reaction and our analysis suggests three candidates as tissue-enriched. This study is one of the most comprehensive studies which provides a map of circRNAs transcriptome as well as to understand the difference among different computational pipelines in rat.
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Affiliation(s)
- Disha Sharma
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
| | - Paras Sehgal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road (CSIR-IGIB), Delhi 110025, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road (CSIR-IGIB), Delhi 110025, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110025, India.,Academy of Scientific & Innovative Research (AcSIR), CSIR-IGIB South Campus, Mathura Road, Delhi 110025, India
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Comprehensive CircRNA Profiling and Selection of Key CircRNAs Reveal the Potential Regulatory Roles of CircRNAs throughout Ovarian Development and Maturation in Cynoglossus semilaevis. BIOLOGY 2021; 10:biology10090830. [PMID: 34571707 PMCID: PMC8468179 DOI: 10.3390/biology10090830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 01/22/2023]
Abstract
Simple Summary CircRNAs: as molecules involved in gene regulation, have become a new research hotspot in the non-coding RNA field. CircRNAs show tissue- or developmental stage-specific patterns of expression and can influence the expression levels of their parental genes. Recent studies have documented the potential biological roles of circRNAs in the growth, development, reproduction and health of humans and animals. Tongue sole (Cynoglossus semilaevis) is a marine flatfish that is an economically important farmed species in China. The commercial aquaculture of tongue sole has developed in the last few years because wild resources have decreased. Reproduction is regulated by brain-pituitary-gonad-liver axis which limits the development of artificial tongue sole culture. However, the roles of circRNAs in the ovarian development and maturation of tongue sole has never been reported. The identification of the potential functions of circRNAs provides a foundation for understanding the genetic mechanisms that regulate oocyte growth and maturation, which will allow the efficiency of tongue sole reproduction to be improved. Moreover, our findings extend the knowledge about a new type of endogenous RNA involved in regulating the ovarian development and maturation of tongue sole. Abstract CircRNAs are novel endogenous non-coding small RNAs involved in the regulation of multiple biological processes. However, little is known regarding circRNAs in ovarian development and maturation of fish. Our study, for the first time, provides the genome-wide overview of the types and relative abundances of circRNAs in tongue sole tissues during three ovarian developmental stages. We detected 6790 circRNAs in the brain, 5712 in the pituitary gland, 4937 in the ovary and 4160 in the liver. Some circRNAs exhibit tissue-specific expression, and qRT-PCR largely confirmed 6 differentially expressed (DE) circRNAs. Gene Ontology and KEGG pathway analyses of DE mRNAs were performed. Some DE circRNA parental genes were closely associated with biological processes in key signalling pathways and may play essential roles in ovarian development and maturation. We found that the selected circRNAs were involved in 10 pathways. RNase R digestion experiment and Sanger sequencing verified that the circRNA had a ring structure and was RNase R resistant. qRT-PCR results largely confirmed differential circRNA expression patterns from the RNA-seq data. These findings indicate that circRNAs are widespread in terms of present in production-related tissues of tongue sole with potentially important regulatory roles in ovarian development and maturation.
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Yin J, Huang HY, Long Y, Ma Y, Kamalibaike M, Dawuti R, Li L. circ_C20orf11 enhances DDP resistance by inhibiting miR-527/YWHAZ through the promotion of extracellular vesicle-mediated macrophage M2 polarization in ovarian cancer. Cancer Biol Ther 2021; 22:440-454. [PMID: 34382916 DOI: 10.1080/15384047.2021.1959792] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Ovarian cancer is a fatal gynecologic tumor, and conventional treatment is mainly limited by chemoresistance. The mechanism contributing to chemoresistance in ovarian cancer has yet to be established. This study aimed to investigate the specific role of circ_C20orf11 in regulating chemoresistance to cisplatin (DDP)in ovarian cancer. We first established two DDP-resistant ovarian cancer cell lines. Then, we identified the effect of circ_C20orf11 on specific cellular characteristics (proliferation, apoptosis, DDP resistance) via a series of experiments. The binding sites between circ_C20orf11 and miR-527 and between miR-527 and YWHAZ were predicted using a bioinformatics tool and confirmed with a dual-luciferase reporter assay. Furthermore, extracellular vesicles (EVs) derived from DDP-resistant cell lines were identified, and the effect of EVs on macrophage polarization was examined. circ_C20orf11 was upregulated in ovarian cancer. Increased circ_C20orf11 expression enhanced DDP resistance and cell proliferation and reduced cell apoptosis in DDP-resistant cell lines after DDP treatment by sponging miR-527 and promoting YWHAZ expression. In addition, we found that DDP-resistant cell-derived EVs can induce macrophage M2 polarization, whereas silencing of circ_C20orf11 inhibited EV-induced macrophage M2 polarization. Consistent with these results, silencing of circ_C20orf11 enhanced sensitivity to DDP in vivo. Importantly, we proved that circ_C20orf11 expression was upregulated in EVs extracted from the serum of DDP-resistant patients. Our study demonstrated that silencing circ_C20orf11 sensitizes ovarian cancer to DDP by promoting miR-527/YWHAZ signaling and EV-mediated macrophage M2 polarization.
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Affiliation(s)
- Jun Yin
- Department of Pharmacy, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, P.R. China
| | - Hai-Yan Huang
- Department of Medical Image Center, The Frist Affiliated Hospital of Xinjiang Medical University, Urumqi, P.R. China
| | - Ying Long
- Translational Medicine Center, Hunan Cancer Hospital, Changsha, Hunan Province, P.R. China
| | - Yan Ma
- Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, P.R. China
| | - Maerkeya Kamalibaike
- Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, P.R. China
| | - Reyanguli Dawuti
- Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, P.R. China
| | - Li Li
- Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, P.R. China
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Ma X, Wang G, Wu L, Liu H, Jiang H, Wang L, Liu Q, Wu Q, Tian X, Li X. Dynamic expression and functional analysis of circular RNA in the gonads of Chinese soft-shelled turtles (Pelodiscus sinensis). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100863. [PMID: 34237608 DOI: 10.1016/j.cbd.2021.100863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 10/21/2022]
Abstract
Circular RNA (circRNA) is a noncoding RNA that can regulate a variety of biological processes. CircRNAs can regulate gene expression posttranscriptionally by acting as microRNA sponges. Many turtle species are remarkable organisms due to their reproductive processes. However, information on circRNA in the gonads of turtles is limited. In this study, 6, 121 circRNAs were identified in the testes and ovaries of Chinese soft-shelled turtles (Pelodiscus sinensis) using the Illumina platform, and 710 circRNAs were significantly differentially expressed (DE). The DE circRNAs included 541 upregulated and 169 downregulated circRNAs in the testes. GO and KEGG pathway analysis indicated that the DE circRNAs were enriched in several signaling pathways, including GnRH, Wnt, FoxO, Progesterone mediated oocyte maturation, and mTOR signaling pathways. Five DE circRNAs were randomly selected, and their relative expression levels in ovaries and testes were detected by quantitative real-time PCR. All of these circRNAs were differentially expressed. In addition, 9, 883 interactions between circRNAs and miRNAs were predicted in the turtles. Target genes of the miRNAs include a range of genes regulating gonadal development. Seven ceRNA networks (DE circRNAs-DE miRNAs-DE mRNAs), including 7 DE circRNAs, 11 DE miRNAs and 20 DE mRNAs, were constructed. The networks included Cdc6, the miR-1 family, the miR-203 family, and the miR-302 family. The expression profile of gonadal circRNAs might help to elucidate the roles of nonprotein coding RNAs in turtle gonadal development.
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Affiliation(s)
- Xiao Ma
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Guiyu Wang
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Limin Wu
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Huifen Liu
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Hongxia Jiang
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Luming Wang
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Qian Liu
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Qisheng Wu
- Fisheries Research Institute of Fujian, Xiamen 361000, People's Republic of China.
| | - Xue Tian
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
| | - Xuejun Li
- College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China.
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Dynamic Expression Profiles of Circular RNAs during Brown to White Adipose Tissue Transformation in Goats ( Capra hircus). Animals (Basel) 2021; 11:ani11051351. [PMID: 34068539 PMCID: PMC8150810 DOI: 10.3390/ani11051351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 12/26/2022] Open
Abstract
Simple Summary In our study, we launched RNA-seq in order to investigate the potential functions of circRNA during brown adipose tissue (BAT) to white adipose tissue (WAT) transformation. As a result, 6610 circRNAs and 61 differentially expressed circRNAs (DEcircRNAs) were identified. Moreover, 65 miRNAs were detected that could potentially interact with DEcircRNAs. The present study provides a detailed circRNA expression landscape and evidence for circRNA functions in the transformation from BAT to WAT. Abstract Adipose tissues are mainly divided into brown adipose tissue (BAT) and white adipose tissue (WAT). WAT mainly functions to buffer excess calories, whereas BAT plays a role in the non-shivering thermogenesis to maintain body temperature and energy balance. Moreover, circRNAs play important roles in various biological processes. However, knowledge of the expression profile and function of circRNAs from BAT to WAT remains largely unknown. In this study, a total of 6610 unique circRNAs were identified in the perirenal adipose tissues of 1-day, 30-days, and 1-year goats. Functional annotation revealed that host genes of circRNAs were involved in some BAT-related pathways, such as the thyroid hormone signaling pathway, MAPK signaling pathway, and VEGF signaling pathway. Furthermore, a total of 61 DEcircRNAs were detected across three stages. Additionally, five selected circRNAs were validated by RNase R assay, qPCR, and Sanger sequencing. Finally, the circRNA–miRNA network was constructed between the DEcircRNAs and their miRNA binding sites.
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40
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Gao Q, Wang T, Pan L, Qian C, Wang J, Xin Q, Liu Y, Zhang Z, Xu Y, He X, Cao Y. Circular RNAs: Novel potential regulators in embryogenesis, female infertility, and pregnancy-related diseases. J Cell Physiol 2021; 236:7223-7241. [PMID: 33876837 DOI: 10.1002/jcp.30376] [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: 10/28/2020] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/19/2022]
Abstract
Circular RNAs (circRNAs) are endogenous noncoding RNAs with unique cyclic structures. Although they were previously considered as nonfunctional transcription byproducts, numerous studies have demonstrated that circRNAs regulate gene transcription and expression via different mechanisms. Reproductive health influences the quality of life and affects offspring propagation in women. CircRNAs have been found to modify pregnancy-related diseases, gynecologic cancers, polycystic ovary syndrome, aging, gamete, and embryo development. It's promising for circRNAs to be the novel diagnostic and therapeutic targets for multiple reproductive diseases. With the widespread application of assisted reproduction technology (ART), it has been revealed that circRNA identification contributes to estimating the quality of gametes and embryos, reflecting the success rate of ART. CRISPR-Cas9 gene editing technology has enabled the discovery of new roles of circRNAs. So far, the roles of circRNAs in the reproductive system remain poorly defined. In this review, we describe the classification and functions of circRNAs in embryogenesis and the female reproductive system diseases, revealing potential roles of circRNAs physiologically and pathologically. In so-doing, we provide ideas for developing circRNA-based therapeutic treatment and clinical application of various female reproductive system diseases.
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Affiliation(s)
- Qinyu Gao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Population Health Across Life Cycle, Ministry of Education of the People's Republic of China, Anhui Medical University, Hefei, Anhui, China
| | - Tianjuan Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Population Health Across Life Cycle, Ministry of Education of the People's Republic of China, Anhui Medical University, Hefei, Anhui, China
| | - Linxin Pan
- College of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Cheng Qian
- Center for Scientific Research, Anhui Medical University, Hefei, Anhui, China
| | - Juan Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, Anhui, China.,Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, Hefei, Anhui, China
| | - Qiong Xin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, Anhui, China.,Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, Hefei, Anhui, China
| | - Yajing Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, Anhui, China.,Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, Hefei, Anhui, China
| | - Zhiguo Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, Anhui, China.,Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, Hefei, Anhui, China
| | - Yuping Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, Anhui, China.,Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, Hefei, Anhui, China
| | - Xiaojin He
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, Anhui, China.,Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, Hefei, Anhui, China
| | - Yunxia Cao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Population Health Across Life Cycle, Ministry of Education of the People's Republic of China, Anhui Medical University, Hefei, Anhui, China
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Jin W, Zhao Y, Zhai B, Li Y, Fan S, Yuan P, Sun G, Jiang R, Wang Y, Liu X, Tian Y, Kang X, Li G. Characteristics and expression profiles of circRNAs during abdominal adipose tissue development in Chinese Gushi chickens. PLoS One 2021; 16:e0249288. [PMID: 33857153 PMCID: PMC8049301 DOI: 10.1371/journal.pone.0249288] [Citation(s) in RCA: 9] [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: 10/24/2020] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) play important roles in adipogenesis. However, studies on circRNA expression profiles associated with the development of abdominal adipose tissue are lacking in chickens. In this study, 12 cDNA libraries were constructed from the abdominal adipose tissue of Chinese domestic Gushi chickens at 6, 14, 22, and 30 weeks. A total of 1,766 circRNAs were identified by Illumina HiSeq 2500 sequencing. These circRNAs were primarily distributed on chr1 through chr10 and sex chromosomes, and 84.95% of the circRNAs were from gene exons. Bioinformatic analysis showed that each circRNA has 35 miRNA binding sites on average, and 62.71% have internal ribosome entry site (IRES) elements. Meanwhile, these circRNAs were primarily concentrated in TPM < 0.1 and TPM > 60, and their numbers accounted for 18.90% and 80.51%, respectively, exhibiting specific expression patterns in chicken abdominal adipose tissue. In addition, 275 differentially expressed (DE) circRNAs were identified by comparison analysis. Functional enrichment analysis showed that the parental genes of DE circRNAs were primarily involved in biological processes and pathways related to lipid metabolism, such as regulation of fat cell differentiation, fatty acid homeostasis, and triglyceride homeostasis, as well as fatty acid biosynthesis, fatty acid metabolism, and glycerolipid metabolism. Furthermore, ceRNA regulatory networks related to abdominal adipose development were constructed. The results of this study indicated that circRNAs can regulate lipid metabolism, adipocyte proliferation and differentiation, and cell junctions during abdominal adipose tissue development in chickens through complex ceRNA networks between circRNAs, miRNAs, genes, and pathways. The results of this study may help to expand the number of known circRNAs in abdominal adipose tissue and provide a valuable resource for further research on the function of circRNAs in chicken abdominal adipose tissue.
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Affiliation(s)
- Wenjiao Jin
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, P.R. China
| | - Yinli Zhao
- College of Biological Engineering, Henan University of Technology, Zhengzhou, Henan Province, P.R. China
| | - Bin Zhai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, P.R. China
| | - Yuanfang Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, P.R. China
| | - Shengxin Fan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, P.R. China
| | - Pengtao Yuan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, P.R. China
| | - Guirong Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, P.R. China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, P.R. China
| | - Yanbin Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, P.R. China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, P.R. China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, P.R. China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, P.R. China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, P.R. China
- * E-mail:
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42
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Wu Y, Xiao H, Pi J, Zhang H, Pan A, Pu Y, Liang Z, Shen J, Du J, Huang T. LncRNA lnc_13814 promotes the cells apoptosis in granulosa cells of duck by acting as apla-miR-145-4 sponge. Cell Cycle 2021; 20:927-942. [PMID: 33843432 DOI: 10.1080/15384101.2021.1911102] [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] [Indexed: 10/21/2022] Open
Abstract
Follicle development is a vital factor which determines the reproductive performance of poultry. Long noncoding RNAs (lncRNAs) have been reported to maintain animal reproductive function and play key roles in ovarian development and hormone secretion. But the regulatory mechanism of lncRNAs in duck follicle development has seldom been reported. In this study, to better explore the molecular mechanism of follicle development in ducks, the follicular lncRNA was sequenced and analyzed. A total of 9,551 lncRNAs were predicted in the duck follicles. Four hundred and forty-five lncRNAs were differentially expressed between the white follicles and yellow follicles. The results of our studies showed that lnc_13814 promoted cell apoptosis in duck GCs. Furthermore, the bioinformatics analysis results demonstrated that lnc_13814 was involved in a lncRNA-miRNA-mRNA coexpression network and it was observed to sponge two follicle-related miRNAs by a luciferase activity assay. Moreover, we found that overexpression of lnc_13814 significantly increased DNA damage inducible transcript 3 (DDIT3) expression and downregulated GCs apoptosis. Finally, we found that lnc_13814 directly binds to and inhibits apla-mir-145-4; then, lnc_13814 increases the expression of DDIT3 and up-regulates GCs apoptosis. Taken together, our findings demonstrate that lncRNAs have potential effects on duck ovarian follicles and lncRNAs may represent a new approach to understand follicular development.
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Affiliation(s)
- Yan Wu
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan, China.,Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Hubei Academy of Agricultural Science, Wuhan, China
| | - Hongwei Xiao
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan, China
| | - Jinsong Pi
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan, China
| | - Hao Zhang
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan, China
| | - Ailuan Pan
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan, China
| | - Yuejin Pu
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan, China
| | - Zhenhua Liang
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan, China
| | - Jie Shen
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan, China
| | - Jinping Du
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan, China
| | - Tao Huang
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan, China
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43
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Zhang Y, Zhong Y, Guo S, Zhu Y, Guo J, Fu Y, Li M. CircRNA profiling reveals circ880 functions as miR-375-3p sponge in medaka gonads. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100797. [PMID: 33714082 DOI: 10.1016/j.cbd.2021.100797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/25/2020] [Accepted: 01/23/2021] [Indexed: 01/22/2023]
Abstract
Circular RNAs (circRNAs) have been regarded as regulators in the biological processes of various species. However, there is no report about circRNAs in the gonads of model fish medaka (Oryzias latipes). In this study, 1157 and 1570 circRNAs were obtained in the ovary and testis by RNA-sequencing. The characteristics of circRNAs were explored in sequence length, exon composition, and chromosome position. 24 circRNAs were significantly up or down-regulated in the testis compared to the ovary, 9 of which were verified by qRT-PCR. Interestingly, circ452 was highly expressed in the testis while circ880 expression exhibited sexual dimorphism. In situ hybridization (ISH) revealed that circ452 and circ880 were expressed in meiotic germ cells, and circ880 was also abundant in spermatogonia. In addition, dual-luciferase reporter assay manifested that circ880 and Oldnd can combine with miR-375-3p. Overall, these results provide emerging circRNA libraries and open new avenues for future investigation of circRNAs in medaka.
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Affiliation(s)
- Yu Zhang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Ying Zhong
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Shaoyu Guo
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yefei Zhu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Jing Guo
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yuanshuai Fu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
| | - Mingyou Li
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China.
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Lin Z, Xu H, Su X, Ke Y, Wang W, Li Y, Zhuang M, Chen H, Liu Y, Wang K, Chen G, Ji T. Investigation of circular RNAs in an ectoparasitic mite Varroa destructor (Acarina: Varroidae) of the honey bee. Parasitol Res 2021; 120:715-723. [PMID: 33452589 DOI: 10.1007/s00436-020-07018-2] [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: 07/13/2020] [Accepted: 12/09/2020] [Indexed: 01/19/2023]
Abstract
Circular RNAs (circRNAs) are a large class of non-protein-coding transcripts that are involved in a diverse spectrum of regulatory mechanisms across a broad range of biological processes. To date, however, few studies on circRNAs have investigated their role in the biology of invertebrate parasites. The ectoparasitic mite Varroa destructor is perceived as the principal biotic threat towards global honey bee health. This parasite cannot be sustainably controlled partially due to the lack of knowledge about its basic molecular biology. In this paper, we unveil the circRNA profile of V. destructor for the first time and report the sources, distribution, and features of the identified circRNAs. Exonic, intronic, exon-intron, and intergenic circRNAs were discovered and exon-intron circRNAs were the most abundant within the largest spliced length. Three hundred and eighty-six (8.3%) circRNAs were predicted to possess translational potential. Eleven circRNAs, derived from six parental genes, exhibited strong bonds with miRNAs as sponges, suggesting an efficient post-transcriptional regulation. GO term and KEGG pathway enrichment analyses of the parental genes of the identified circRNAs showed that these non-coding RNAs were mainly engaged in protein processing, signal transduction, and various metabolism processes. To our knowledge, this is the first catalog of a circRNA profile of parasitiformes species, which reveals the prevalence of circRNAs in the parasite and provides biological insights for future genetic studies on this ubiquitous parasitic mite.
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Affiliation(s)
- Zheguang Lin
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Hao Xu
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Xiaoling Su
- Jinhua Academy of Agricultural Sciences, Jinhua, 321017, China
| | - Yalu Ke
- Wuzhong Animal Health Supervision Institute, Suzhou, 215100, China
| | - Wei Wang
- Wuzhong Animal Health Supervision Institute, Suzhou, 215100, China
| | - Yujiao Li
- Shandong Apiculture Breeding of Improved Varieties and Extension Center, Taian, 271000, China
| | - Mingliang Zhuang
- Apicultural Science Institute of Jilin Province, Jilin, 132108, China
| | - Heng Chen
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Yibing Liu
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Kang Wang
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Guohong Chen
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Ting Ji
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
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Wang Y, Yang HM, Zi C, Gu J, Wang Z. The mediation of pigeon egg production by regulating the steroid hormone biosynthesis of pigeon ovarian granulosa cells. Poult Sci 2020; 99:6075-6083. [PMID: 33142527 PMCID: PMC7647703 DOI: 10.1016/j.psj.2020.06.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 11/17/2022] Open
Abstract
The aim of this study was to determine the molecular mechanism of miR-205b targeting 11β-hydroxysteroid dehydrogenase type 1 (HSD11B1) on the apoptosis and proliferation of granulosa cells (GC) of pigeons. Our previous studies suggested that HSD11B1 was the target gene of miR-205b and played a key role in steroid hormone biosynthesis and GC development. The adenovirus-miR-205b recombinant virus and adenovirus-cli-miR-205b-sh recombinant virus were generated, verified, and their characteristics determined. The recombinant viruses were used to infect the GC of pigeons, with real time quantitative PCR used to examine the expressions of HSD11B1 and related genes. The HSD11B1 antibody was obtained and verified, and Western blotting was used to detect the protein level of HSD11B1. The Cell Counting Kit-8 assay kit was used to detect cell viability, and the Annexin V-FITC/PI kit was used for the apoptosis assays. The expression of HSD11B1 was significantly lower in the overexpression (OE) than in OE negative control (OE-NC) treatments and significantly higher in short hairpin (SH) than in SH negative control (SH-NC) treatments. The expression levels of cytochrome P4503A5 was significantly higher in SH and lower in OE treatments, and the rhythms of cytochrome P450 aromatase mRNA levels were similar. The mRNA level of cytochrome P450scc in OE was lower than in OE-NC treatments and higher in SH than in SH-NC treatments. The protein expressions of HSD11B1 were decreased in the GC of OE, whereas increased in the SH group. The Cell Counting Kit-8 assay revealed that overexpression of miR-205b significantly suppressed proliferation of the GC of pigeons, whereas interference of miR-205b significantly induced the proliferation of the GC. The overexpression and the interference of miR-205b did not have a significant effect on cell cycle. The overexpression of miR-205b significantly increased the number of apoptotic cells, whereas the interference of miR-205b decreased the number of apoptotic cells. These findings indicated that miR-205b mediated pigeon egg production by regulating the steroid hormone biosynthesis of the pigeon ovarian GC by targeting HSD11B1, which may be useful in increasing pigeon egg production.
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Affiliation(s)
- Ying Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Hai-Ming Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China.
| | - Chen Zi
- Department of Pathology, Linyi People's Hospital, Linyi 276000, Shandong Province, China
| | - Jing Gu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
| | - Zhiyue Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province 225009, P. R. China
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Sun X, Yan X, Liu K, Wu M, Li Z, Wang Y, Zhong X, Qin L, Huang C, Wei X. lncRNA H19 acts as a ceRNA to regulate the expression of CTGF by targeting miR-19b in polycystic ovary syndrome. ACTA ACUST UNITED AC 2020; 53:e9266. [PMID: 33053114 PMCID: PMC7552896 DOI: 10.1590/1414-431x20209266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 06/25/2020] [Indexed: 02/03/2023]
Abstract
The etiology of polycystic ovary syndrome (PCOS) is complex and the pathogenesis is not fully understood. Some studies have shown that dysregulation of ovarian granulosa cells may be related to abnormal follicles and excessive androgen in women with PCOS. Our team has also confirmed the high expression status of H19 in PCOS patients in the early stage. However, the relationship between H19 and miR-19b in the development of PCOS is still unknown. Therefore, we used bioinformatics to predict the binding sites of human H19 and miR-19b, and of miR-19b and CTGF genes. After the silencing and overexpression of H19, real-time polymerase chain reaction (PCR) was used to detect the expressions of H19, miR-19b, and CTGF. Western blotting was used to detect CTGF protein. Proliferation of KGN cells after H19 silencing was detected by CCK8. Flow cytometry was used to detect the apoptosis of KGN cells after H19 silencing. After the overexpression of H19, it was found that the expression of miR-19b gene decreased and the expression of CTGF increased, whereas silencing of H19 did the opposite. In addition, H19 could promote cell proliferation and decrease cell apoptosis. Finally, luciferase reporter assays showed that the 3′-end sequences of lncRNA H19 and CTGF contained the binding site of miR-19b. In conclusion, our study indicated that lncRNA H19 acted as a ceRNA to bind to miR-19b via a “sponge” to regulate the effect of CTGF on KGN cells, which may play a vital role in PCOS.
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Affiliation(s)
- Xiuhong Sun
- School of Medicine, Jinan University, Guangzhou, Guangdong Province, China.,Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, China
| | - Xiumin Yan
- Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, China
| | - Kailiang Liu
- School of Medicine, Jinan University, Guangzhou, Guangdong Province, China.,Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, China
| | - Min Wu
- School of Medicine, Jinan University, Guangzhou, Guangdong Province, China.,Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, China
| | - Zhongyi Li
- School of Medicine, Jinan University, Guangzhou, Guangdong Province, China
| | - Yao Wang
- School of Medicine, Jinan University, Guangzhou, Guangdong Province, China
| | - Xingming Zhong
- Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, China
| | - Li Qin
- School of Medicine, Jinan University, Guangzhou, Guangdong Province, China.,Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, China
| | - Chuican Huang
- School of Medicine, Jinan University, Guangzhou, Guangdong Province, China.,Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, China
| | - Xiangcai Wei
- Guangdong Women and Children Hospital, Guangzhou, Guangdong Province, China
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Huang Y, Wang Y, Zhang C, Sun X. Biological functions of circRNAs and their progress in livestock and poultry. Reprod Domest Anim 2020; 55:1667-1677. [DOI: 10.1111/rda.13816] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/02/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Yong Huang
- College of Animal Science and Technology Henan University of Science and Technology Luoyang China
| | - Yanli Wang
- Development Planning Office Henan University of Science and Technology Luoyang China
| | - Cai Zhang
- College of Animal Science and Technology Henan University of Science and Technology Luoyang China
| | - Xihong Sun
- Development Planning Office Henan University of Science and Technology Luoyang China
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48
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Zhang M, Han Y, Zhai Y, Ma X, An X, Zhang S, Li Z. Integrative analysis of circRNAs, miRNAs, and mRNAs profiles to reveal ceRNAs networks in chicken intramuscular and abdominal adipogenesis. BMC Genomics 2020; 21:594. [PMID: 32847498 PMCID: PMC7450580 DOI: 10.1186/s12864-020-07000-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/17/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Tissue-specific fat deposition is regulated by a series of complex regulatory mechanisms. Reports indicate that epigenetic regulators, such as circular RNAs (circRNAs), are crucial in diseases progression, animal development, metabolism, and adipogenesis. In this study, to assess the functional roles of circRNAs in adipogenesis and tissue-specific fat deposition, we comprehensively analyzed the Ribo-Zero RNA-Seq and miRNAs data during chicken intramuscular and abdominal adipogenic differentiation. RESULTS circRNAs and miRNAs profiles during chicken adipogenic differentiation were found in adipocytes derived from various adipose tissues. It was also discovered that high levels of downregulated miRNAs potentially promote adipogenesis by activating their target genes which are associated with fatty acid metabolism and adipogenic differentiation. Through analysis of the correlation between the expression levels of circRNAs and adipogenic genes, as well as the dynamic expression patterns of circRNAs during adipogenic differentiation, several candidate circRNAs were identified. Moreover, competing endogenous RNA (ceRNAs) networks were constructed during chicken intramuscular and abdominal adipogenesis by combining miRNAs with mRNAs data. Several candidate circRNAs potentially influence adipogenesis by regulating miRNAs via PPAR and fatty acid metabolism-related pathways were identified, such as circLCLAT1, circFNDC3AL, circCLEC19A and circARMH1. CONCLUSION In conclusion, our findings reveal that circRNAs and the circRNA-miRNAs-mRNAs-ceRNAs network may play important roles in chicken adipocytes differentiation and tissue-specific fat deposition.
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Affiliation(s)
- Meng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021, Jilin, China
| | - Yu Han
- College of Veterinary Medicine, Jilin University, Changchun, 130021, Jilin, China
| | - Yanhui Zhai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021, Jilin, China
| | - Xiangfei Ma
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Xinglan An
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021, Jilin, China
| | - Sheng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021, Jilin, China.
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021, Jilin, China.
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49
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Zou K, Asiamah CA, Lu LL, Liu Y, Pan Y, Chen T, Zhao Z, Su Y. Ovarian transcriptomic analysis and follicular development of Leizhou black duck. Poult Sci 2020; 99:6173-6187. [PMID: 33142535 PMCID: PMC7647846 DOI: 10.1016/j.psj.2020.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 08/10/2020] [Accepted: 08/15/2020] [Indexed: 12/19/2022] Open
Abstract
This study investigated the factors that caused the differences in egg production during the development of ovarian follicles in Leizhou black ducks. Leizhou black ducks population was divided into 2 groups as high-yield group (HG) and low-yield group (LG). The number of eggs (NE), age at first egg (AFE), weight at first egg, and egg weight (EW) of both groups were recorded, and differences were analyzed using the t test. The logistic model was used to simulate the egg production curves to analyze the production rules. The ovarian follicles of both duck groups were collected to count the number of different grades sized follicles, weigh the ovaries, and observe follicular sections to analyze the developmental differences. Ovarian transcriptomic sequencing was performed to investigate differentially expressed genes and signal pathways in both duck groups. The results revealed a significant difference (P < 0.01) in the NE laid, AFE, and EW between both groups. Comparatively, HG had significantly more (P < 0.01) large yellow follicles (LYF) than LG. The density of medullary layer cells of the follicle section was greater in HG than LG ducks. Transcriptome sequencing revealed a total of 1,027 differentially expressed genes between the HG and LG ducks of which 495 genes were upregulated, and 532 genes were downregulated. Fifty genes were related to reproduction and reproductive processes. Kyoto Encyclopedia of Genes and Genomes–enriched signaling pathways revealed 274 signal pathways enriched in these differentially expressed genes of which the steroid biosynthesis pathway was significantly enriched. Analysis (Q < 0.05) showed that HSD3β → gonadotropin-releasing hormone (GnRH) and estrogen receptor (ESR) → LHβ/ERK1/2 were enriched in the steroid biosynthesis signal pathway. Follicle-stimulating hormone signal pathway mediated by HSD3β → GnRH and ESR → LHβ/ERK1/2 may be involved in ovarian follicle development to regulate LYF reserve process and affect its ovulation cycle, which in turn influence the egg production of Leizhou black ducks.
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Affiliation(s)
- Kun Zou
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524025, PR China
| | | | - Li-Li Lu
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524025, PR China
| | - Yuanbo Liu
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524025, PR China
| | - Yiting Pan
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524025, PR China
| | - Tongxin Chen
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524025, PR China
| | - Zhihui Zhao
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524025, PR China.
| | - Ying Su
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524025, PR China.
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50
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Transcriptome Analysis of circRNA and mRNA in Theca Cells during Follicular Development in Chickens. Genes (Basel) 2020; 11:genes11050489. [PMID: 32365656 PMCID: PMC7290432 DOI: 10.3390/genes11050489] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/19/2020] [Accepted: 04/27/2020] [Indexed: 12/11/2022] Open
Abstract
Development of ovarian follicles requires interactions between granulosa cells, theca cells, and oocytes. Multiple transcription levels are involved but information about the role of noncoding RNAs, especially circular RNAs (circRNAs), is lacking. Here, we used RNA sequencing to profile circRNAs and mRNAs in theca cells from three types of follicle: small yellow follicles (SYF), the smallest hierarchical follicles (F6), and the largest hierarchical follicles (F1). Using bioinformatics analysis, we identified a total of 14,502 circRNAs in all theca cells, with 5622 widely distributed in all stages of development. Differential expression analysis suggested that some genes display differential isoforms during follicular development. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed enrichment of both differentially expressed circRNAs and mRNAs in pathways associated with reproduction, including the TGF-β signaling pathway, oocyte meiosis, and vascular smooth muscle contraction. Our study provides the first visual information about circRNAs and mRNAs in theca cells during follicle development in chickens and adds to the growing body of knowledge about theca cells.
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