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Zhu L, Jiao H, Gao W, Gong P, Shi C, Zhang F, Zhao J, Lu X, Liu B, Luo J. MiR-103-5p deficiency suppresses lipid accumulation via upregulating PLSCR4 and its host gene PANK3 in goat mammary epithelial cells. Int J Biol Macromol 2024; 267:131240. [PMID: 38583827 DOI: 10.1016/j.ijbiomac.2024.131240] [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: 01/07/2024] [Revised: 03/09/2024] [Accepted: 03/27/2024] [Indexed: 04/09/2024]
Abstract
Lipids are intimately related to the unique flavor and nutritional values of goat milk. MicroRNAs (miRNA) participate in the regulation of various biological functions, including the synthesis and degradation of lipids. Several studies have shown that miR-103 is involved in the regulation of lipid metabolism, however, the molecular mechanism by which miR-103 regulates lipid metabolism in goat mammary gland is poorly understood. In this study, miR-103 was knocked out in goat mammary epithelial cells (GMECs) by CRISPR/Cas9, and the accumulation of lipid droplets, triglycerides, and cholesterol in the cells was suppressed subsequently. Overexpression or knockdown of miR-103-5p and miR-103-3p in GMECs revealed that it was miR-103-5p that promoted lipid accumulation but not miR-103-3p. In addition, Pantothenate Kinase 3 (PANK3), the host gene of miR-103, and Phospholipid Scramblase 4 (PLSCR4) were identified as the target genes of miR-103-5p by dual fluorescein and miRNA pulldown. Furthermore, we identified that cellular lipid levels were negatively regulated by PANK3 and PLSCR4. Lastly, in miR-103 knockout GMECs, the knockdown of PANK and PLSCR4 rescued the lipid accumulation. These findings suggest that miR-103-5p promotes lipid accumulation by targeting PLSCR4 and the host gene PANK3 in GMECs, providing new insights for the regulation of goat milk lipids via miRNAs.
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Affiliation(s)
- Lu Zhu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Hongyun Jiao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wenchang Gao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ping Gong
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, China
| | - Chenbo Shi
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Fuhong Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jianqing Zhao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xuefeng Lu
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, China
| | - Baolong Liu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jun Luo
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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Li Z, Mao K, Jin R, Cai T, Qin Y, Zhang Y, He S, Ma K, Wan H, Ren X, Li J. miRNA novel_268 targeting NlABCG3 is involved in nitenpyram and clothianidin resistance in Nilaparvata lugens. Int J Biol Macromol 2022; 217:615-623. [PMID: 35853504 DOI: 10.1016/j.ijbiomac.2022.07.096] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/07/2022] [Accepted: 07/12/2022] [Indexed: 12/19/2022]
Abstract
The brown planthopper (BPH), Nilaparvata lugens (Stål), is one of the most destructive pests that seriously threatens the high-quality and safe production of rice. However, due to the unscientific use of chemical insecticides, N. lugens has developed varying levels of resistance to insecticides, including nitenpyram and clothianidin. The ATP-binding cassette (ABC) transporter plays a nonnegligible role in phase III of the detoxification process, which may play an important role in insecticide resistance. In the present study, NlABCG3 was significantly overexpressed in both the NR and CR populations compared with susceptible populations. Silencing NlABCG3 significantly increased the susceptibility of BPH to nitenpyram and clothianidin. In addition, RNAi-mediated knockdown of three key genes in the miRNA biogenesis pathway altered the level of NlABCG3. Subsequently, the luciferase reporter assays demonstrated that novel_268 binds to the NlABCG3 coding region and downregulates its expression. Furthermore, injection of miRNA inhibitors or mimics of novel_268 significantly altered the susceptibility of N. lugens to nitenpyram and clothianidin. These results suggest that miRNA novel_268 targeting NlABCG3 is involved in nitenpyram and clothianidin resistance in N. lugens. These findings may help to enhance our knowledge of the transcriptional regulation of the ABC transporter that mediate insecticide resistance in N. lugens.
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Affiliation(s)
- Zhao Li
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, 40 Nongkenan Road, Hefei 230031, PR China; Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Kaikai Mao
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ruoheng Jin
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Tingwei Cai
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yao Qin
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yunhua Zhang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shun He
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Kangsheng Ma
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Hu Wan
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xuexiang Ren
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, 40 Nongkenan Road, Hefei 230031, PR China.
| | - Jianhong Li
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China.
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3
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Zhu D, Xiao Z, Wang Z, Hu B, Duan C, Zhu Z, Gao N, Zhu Y, Wang H. MEG3/MIR-376B-3P/HMGA2 axis is involved in pituitary tumor invasiveness. J Neurosurg 2021; 134:499-511. [PMID: 31899875 DOI: 10.3171/2019.10.jns191959] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/22/2019] [Indexed: 11/06/2022]
Abstract
OBJECTIVE To date, long noncoding RNAs (lncRNAs) have proven to function as key regulators in tumorigenesis. Among these lncRNAs, MEG3 displays low levels in various neoplasms and tumor cell lines. However, the regulatory mechanism of MEG3 and MIR-376B-3P, one of the microRNAs from downstream gene clusters of the DLK1-MEG3 locus, remains insufficiently defined. METHODS The authors used quantitative real-time polymerase chain reaction analysis to analyze whether decreased MEG3 and MIR-376B-3P expression levels were associated with the invasiveness of clinical nonfunctioning pituitary adenomas (CNFPAs) in 30 patients. Furthermore, functional experiments unveiled the pathophysiological role of MEG3, MIR-376B-3P, and HMGA2 in pituitary-derived folliculostellate (PDFS) cell lines. Moreover, dual-luciferase reporter assay, Western blot analysis, and immunofluorescence were applied to reveal the correlations among MEG3, MIR-376B-3P, and HMGA2. RESULTS MEG3 and MIR-376B-3P were decreased in patients with CNFPA, and their transcriptional levels were highly associated with invasive CNFPAs. Moreover, excessive expression of MEG3 and MIR-376B-3P inhibited tumorigenesis and promoted apoptosis in PDFS cells. Importantly, the authors found that MEG3 acted as an enhancer of MIR-376B-3P expression. Furthermore, as a target gene of MIR-376B-3P, HMGA2 served as an oncogene in pituitary adenoma and could be negatively regulated by MEG3 via enriching MIR-376B-3P. CONCLUSIONS This study offers a novel mechanism of an MEG3/MIR-376B-3P/HMGA2 regulatory network in CNFPAs, which may become a breakthrough for anticancer treatments.
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Affiliation(s)
- Dimin Zhu
- 1Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital of Sun Yat-sen University; and
| | - Zheng Xiao
- 1Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital of Sun Yat-sen University; and
| | - Zongming Wang
- 1Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital of Sun Yat-sen University; and
| | - Bin Hu
- 1Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital of Sun Yat-sen University; and
| | - Chengbin Duan
- 1Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital of Sun Yat-sen University; and
| | - Ziyan Zhu
- 2Department of Histology and Embryology, Medical School of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Nailin Gao
- 1Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital of Sun Yat-sen University; and
| | - Yonghong Zhu
- 2Department of Histology and Embryology, Medical School of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Haijun Wang
- 1Department of Neurosurgery and Pituitary Tumor Center, The First Affiliated Hospital of Sun Yat-sen University; and
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Zeidler M, Hüttenhofer A, Kress M, Kummer KK. Intragenic MicroRNAs Autoregulate Their Host Genes in Both Direct and Indirect Ways-A Cross-Species Analysis. Cells 2020; 9:cells9010232. [PMID: 31963421 PMCID: PMC7016697 DOI: 10.3390/cells9010232] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) function as master switches for post-transcriptional gene expression. Their genes are either located in the extragenic space or within host genes, but these intragenic miRNA::host gene interactions are largely enigmatic. The aim of this study was to investigate the location and co-regulation of all to date available miRNA sequences and their host genes in an unbiased computational approach. The majority of miRNAs were located within intronic regions of protein-coding and non-coding genes. These intragenic miRNAs exhibited both increased target probability as well as higher target prediction scores as compared to a model of randomly permutated genes. This was associated with a higher number of miRNA recognition elements for the hosted miRNAs within their host genes. In addition, strong indirect autoregulation of host genes through modulation of functionally connected gene clusters by intragenic miRNAs was demonstrated. In addition to direct miRNA-to-host gene targeting, intragenic miRNAs also appeared to interact with functionally related genes, thus affecting their host gene function through an indirect autoregulatory mechanism. This strongly argues for the biological relevance of autoregulation not only for the host genes themselves but, more importantly, for the entire gene cluster interacting with the host gene.
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Affiliation(s)
- Maximilian Zeidler
- Institute of Physiology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Alexander Hüttenhofer
- Institute of Genomics and RNomics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Michaela Kress
- Institute of Physiology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Kai K. Kummer
- Institute of Physiology, Medical University of Innsbruck, 6020 Innsbruck, Austria
- Correspondence: ; Tel.: +43-650-970-0514; Fax: +43-512-9003-73800
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5
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Ferro E, Enrico Bena C, Grigolon S, Bosia C. From Endogenous to Synthetic microRNA-Mediated Regulatory Circuits: An Overview. Cells 2019; 8:E1540. [PMID: 31795372 PMCID: PMC6952906 DOI: 10.3390/cells8121540] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs are short non-coding RNAs that are evolutionarily conserved and are pivotal post-transcriptional mediators of gene regulation. Together with transcription factors and epigenetic regulators, they form a highly interconnected network whose building blocks can be classified depending on the number of molecular species involved and the type of interactions amongst them. Depending on their topology, these molecular circuits may carry out specific functions that years of studies have related to the processing of gene expression noise. In this review, we first present the different over-represented network motifs involving microRNAs and their specific role in implementing relevant biological functions, reviewing both theoretical and experimental studies. We then illustrate the recent advances in synthetic biology, such as the construction of artificially synthesised circuits, which provide a controlled tool to test experimentally the possible microRNA regulatory tasks and constitute a starting point for clinical applications.
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Affiliation(s)
- Elsi Ferro
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo (Torino), Italy
| | - Chiara Enrico Bena
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo (Torino), Italy
| | - Silvia Grigolon
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Carla Bosia
- IIGM—Italian Institute for Genomic Medicine, c/o IRCCS, 10060 Candiolo (Torino), Italy
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
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6
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Steiman-Shimony A, Shtrikman O, Margalit H. Assessing the functional association of intronic miRNAs with their host genes. RNA (NEW YORK, N.Y.) 2018; 24:991-1004. [PMID: 29752351 PMCID: PMC6049507 DOI: 10.1261/rna.064386.117] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 04/26/2018] [Indexed: 05/07/2023]
Abstract
In human, nearly half of the known microRNAs (miRNAs) are encoded within the introns of protein-coding genes. The embedment of these miRNA genes within the sequences of protein-coding genes alludes to a possible functional relationship between intronic miRNAs and their hosting genes. Several studies, using predicted targets, suggested that intronic miRNAs influence their hosts' function either antagonistically or synergistically. New experimental data of miRNA expression patterns and targets enable exploring this putative association by relying on actual data rather than on predictions. Here, our analysis based on currently available experimental data implies that the potential functional association between intronic miRNAs and their hosting genes is limited. For host-miRNA examples where functional associations were detected, it was manifested by either autoregulation, common targets of the miRNA and hosting gene, or through the targeting of transcripts participating in pathways in which the host gene is involved. This low prevalence of functional association is consistent with our observation that many intronic miRNAs have independent transcription start sites and are not coexpressed with the hosting gene. Yet, the intronic miRNAs that do show functional association with their hosts were found to be more evolutionarily conserved compared to other intronic miRNAs. This might suggest a selective pressure to maintain this architecture when it has a functional consequence.
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Affiliation(s)
- Avital Steiman-Shimony
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Orr Shtrikman
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
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7
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Tu R, Qian J, Rui M, Tao N, Sun M, Zhuang Y, Lv H, Han J, Li M, Xie W. Proteolytic cleavage is required for functional neuroligin 2 maturation and trafficking in Drosophila. J Mol Cell Biol 2018; 9:231-242. [PMID: 28498949 PMCID: PMC5907836 DOI: 10.1093/jmcb/mjx015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 05/03/2017] [Indexed: 01/15/2023] Open
Abstract
Neuroligins (Nlgs) are transmembrane cell adhesion molecules playing essential roles in synapse development and function. Genetic mutations in neuroligin genes have been linked with some neurodevelopmental disorders such as autism. These mutated Nlgs are mostly retained in the endoplasmic reticulum (ER). However, the mechanisms underlying normal Nlg maturation and trafficking have remained largely unknown. Here, we found that Drosophila neuroligin 2 (DNlg2) undergoes proteolytic cleavage in the ER in a variety of Drosophila tissues throughout developmental stages. A region encompassing Y642-T698 is required for this process. The immature non-cleavable DNlg2 is retained in the ER and non-functional. The C-terminal fragment of DNlg2 instead of the full-length or non-cleavable DNlg2 is able to rescue neuromuscular junction defects and GluRIIB reduction induced by dnlg2 deletion. Intriguingly, the autism-associated R598C mutation in DNlg2 leads to similar marked defects in DNlg2 proteolytic process and ER export, revealing a potential role of the improper Nlg cleavage in autism pathogenesis. Collectively, our findings uncover a specific mechanism that controls DNlg2 maturation and trafficking via proteolytic cleavage in the ER, suggesting that the perturbed proteolytic cleavage of Nlgs likely contributes to autism disorder.
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Affiliation(s)
- Renjun Tu
- Institute of Life Sciences, The Collaborative Innovation Center for Brain Science, Southeast University, 2 SiPaiLou Road, Nanjing 210096, China
| | - Jinjun Qian
- Institute of Life Sciences, The Collaborative Innovation Center for Brain Science, Southeast University, 2 SiPaiLou Road, Nanjing 210096, China
| | - Menglong Rui
- The Key Laboratory of Developmental Genes and Human Disease, Jiangsu Co-innovation Center of Neuroregeneration, Southeast University, 2 SiPaiLou Road, Nanjing 210096, China
| | - Nana Tao
- Institute of Life Sciences, The Collaborative Innovation Center for Brain Science, Southeast University, 2 SiPaiLou Road, Nanjing 210096, China
| | - Mingkuan Sun
- The Key Laboratory of Developmental Genes and Human Disease, Jiangsu Co-innovation Center of Neuroregeneration, Southeast University, 2 SiPaiLou Road, Nanjing 210096, China
| | - Yan Zhuang
- The Key Laboratory of Developmental Genes and Human Disease, Jiangsu Co-innovation Center of Neuroregeneration, Southeast University, 2 SiPaiLou Road, Nanjing 210096, China
| | - Huihui Lv
- Institute of Life Sciences, The Collaborative Innovation Center for Brain Science, Southeast University, 2 SiPaiLou Road, Nanjing 210096, China
| | - Junhai Han
- Institute of Life Sciences, The Collaborative Innovation Center for Brain Science, Southeast University, 2 SiPaiLou Road, Nanjing 210096, China.,The Key Laboratory of Developmental Genes and Human Disease, Jiangsu Co-innovation Center of Neuroregeneration, Southeast University, 2 SiPaiLou Road, Nanjing 210096, China
| | - Moyi Li
- Institute of Life Sciences, The Collaborative Innovation Center for Brain Science, Southeast University, 2 SiPaiLou Road, Nanjing 210096, China.,The Key Laboratory of Developmental Genes and Human Disease, Jiangsu Co-innovation Center of Neuroregeneration, Southeast University, 2 SiPaiLou Road, Nanjing 210096, China
| | - Wei Xie
- Institute of Life Sciences, The Collaborative Innovation Center for Brain Science, Southeast University, 2 SiPaiLou Road, Nanjing 210096, China.,The Key Laboratory of Developmental Genes and Human Disease, Jiangsu Co-innovation Center of Neuroregeneration, Southeast University, 2 SiPaiLou Road, Nanjing 210096, China
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8
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Ye RS, Li M, Chen T, Wei XC, Qi QE, Cheng X, Li CY, Jiang QY, Xi QY, Zhang YL. miRNAome, mRNAome and degradome analysis of Tibetan minipigs anterior pituitary. Gen Comp Endocrinol 2018; 259:104-114. [PMID: 29174487 DOI: 10.1016/j.ygcen.2017.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 12/11/2022]
Abstract
Tibetan minipig is an important animal model for human diseases. The anterior pituitary is the master gland responsible for growth, reproduction, and metabolism and is regulated by thousands of miRNAs/mRNAs molecules. However, little is known about miRNAs and their relationships with mRNAs in Tibetan minipig anterior pituitary. Using microarray and mRNA-Sequencing, we identified 203 miRNAs and 12,040 mRNA transcripts from the anterior pituitary of Tibetan minipigs. These miRNAs were corresponding to 194 hairpin precursors, 25 miRNA clusters and 24 miRNA families. In addition, 64 intragenic miRNAs were annotated. Using three bioinformatic algorithms (TargetScan, miRanda and RNAhybrid), 359,184 possible miRNA-mRNA interactions were predicted, and an integrated network of miRNAs and pituitary-specific mRNA transcripts was established. To validate the predicted results, the degradome sequencing was employed to confirm miRNA-mRNA interactions, totally, 30 miRNA-mRNA pairs were identified. The present study provided a general overview of miRNA and mRNA annotation in Tibetan minipig anterior pituitary and established a miRNA-mRNA interactions database at the whole genome scale, which helps shed light on the molecular mechanisms in the anterior pituitary of pigs even other mammals.
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Affiliation(s)
- Rui-Song Ye
- Chinese National Engineering Research Center for Breeding Swine Industry, SCAU-Alltech Research Joint Alliance, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Meng Li
- Chinese National Engineering Research Center for Breeding Swine Industry, SCAU-Alltech Research Joint Alliance, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Ting Chen
- Chinese National Engineering Research Center for Breeding Swine Industry, SCAU-Alltech Research Joint Alliance, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Chen Wei
- Chinese National Engineering Research Center for Breeding Swine Industry, SCAU-Alltech Research Joint Alliance, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Qi-En Qi
- Chinese National Engineering Research Center for Breeding Swine Industry, SCAU-Alltech Research Joint Alliance, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xiao Cheng
- Chinese National Engineering Research Center for Breeding Swine Industry, SCAU-Alltech Research Joint Alliance, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Chao-Yun Li
- Chinese National Engineering Research Center for Breeding Swine Industry, SCAU-Alltech Research Joint Alliance, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Qing-Yan Jiang
- Chinese National Engineering Research Center for Breeding Swine Industry, SCAU-Alltech Research Joint Alliance, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Qian-Yun Xi
- Chinese National Engineering Research Center for Breeding Swine Industry, SCAU-Alltech Research Joint Alliance, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Yong-Liang Zhang
- Chinese National Engineering Research Center for Breeding Swine Industry, SCAU-Alltech Research Joint Alliance, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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9
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Yang C, Zheng J, Xue Y, Yu H, Liu X, Ma J, Liu L, Wang P, Li Z, Cai H, Liu Y. The Effect of MCM3AP-AS1/miR-211/KLF5/AGGF1 Axis Regulating Glioblastoma Angiogenesis. Front Mol Neurosci 2018; 10:437. [PMID: 29375300 PMCID: PMC5767169 DOI: 10.3389/fnmol.2017.00437] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/18/2017] [Indexed: 01/23/2023] Open
Abstract
Glioblastoma (GBM) is the most aggressive and malignant primary tumor. Angiogenesis plays a critical role in the progression of GBM. Previous studies have indicated that long non-coding RNAs (lncRNAs) are abnormally expressed in various cancers and participate in the regulation of the malignant behaviors of tumors. The present study demonstrated that lncRNA antisense 1 to Micro-chromosome maintenance protein 3-associated protein (MCM3AP-AS1) was upregulated whereas miR-211 was downregulated in glioma-associated endothelial cells (GECs). Knockdown of MCM3AP-AS1 suppressed the cell viability, migration, and tube formation of GECs and played a role in inhibiting angiogenesis of GBM in vitro. Furthermore, knockdown of MCM3AP-AS1 increased the expression of miR-211. Luciferase reporter assay implicated that miR-211 targeted KLF5 3'-UTR and consequently inhibited KLF5 expression. Besides, in this study we found that MCM3AP-AS1 knockdown decreased KLF5 and AGGF1 expression by upregulating miR-211. In addition, KLF5 was associated with the promoter region of AGGF1. Knockdown of KLF5 decreased AGGF1 expression by transcriptional repression, and also inhibited the activation of PI3K/AKT and ERK1/2 signaling pathways. Overall, this study reveals that MCM3AP-AS1/miR-211/KLF5/AGGF1 axis plays a prominent role in the regulation of GBM angiogenesis and also serves as new therapeutic target for the anti-angiogenic therapy of glioma.
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Affiliation(s)
- Chunqing Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Jian Zheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Yixue Xue
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, Shenyang, China
| | - Hai Yu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Jun Ma
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, Shenyang, China
| | - Libo Liu
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, Shenyang, China
| | - Ping Wang
- Department of Neurobiology, College of Basic Medicine, China Medical University, Shenyang, China
- Key Laboratory of Cell Biology, Ministry of Public Health of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, Shenyang, China
| | - Zhen Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Heng Cai
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Liaoning Research Center for Clinical Medicine in Nervous System Disease, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
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10
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Tessema M, Yingling CM, Picchi MA, Wu G, Ryba T, Lin Y, Bungum AO, Edell ES, Spira A, Belinsky SA. ANK1 Methylation regulates expression of MicroRNA-486-5p and discriminates lung tumors by histology and smoking status. Cancer Lett 2017; 410:191-200. [PMID: 28965852 PMCID: PMC5675764 DOI: 10.1016/j.canlet.2017.09.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
Abstract
The intragenic tumor-suppressor microRNA miR-486-5p is often down-regulated in non-small cell lung cancer (NSCLC) but the mechanism is unclear. This study investigated epigenetic co-regulation of miR-486-5p and its host gene ANK1. MiR-486-5p expression in lung tumors and cell lines was significantly reduced compared to normal lung (p < 0.001) and is strongly correlated with ANK1 expression. In vitro, siRNA-mediated ANK1 knockdown in NSCLC cells also reduced miR-486-5p while the DNA methylation inhibitor 5-aza-2'-deoxycytidine induced expression of both. ANK1 promoter CpG island was unmethylated in normal lung but methylated in 45% (118/262) lung tumors and 55% (17/31) NSCLC cell lines. After adjustment for tumor histology and smoking, methylation was significantly more prevalent in adenocarcinoma (101/200, 51%) compared to squamous cell carcinoma (17/62, 27%), p < 0.001; HR = 3.513 (CI: 1.818-6.788); and in smokers (73/128, 57%) than never-smokers (28/72, 39%), p = 0.014; HR = 2.086 (CI: 1.157-3.759). These results were independently validated using quantitative methylation data for 809 NSCLC cases from The Cancer Genome Atlas project. Together, our data indicate that aberrant ANK1 methylation is highly prevalent in lung cancer, discriminate tumors by histology and patients' smoking history, and contributes to miR-486-5p repression.
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MESH Headings
- Adenocarcinoma/etiology
- Adenocarcinoma/genetics
- Adenocarcinoma/metabolism
- Adenocarcinoma/pathology
- Adenocarcinoma of Lung
- Ankyrins/genetics
- Ankyrins/metabolism
- Carcinoma, Non-Small-Cell Lung/etiology
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Squamous Cell/etiology
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Line, Tumor
- CpG Islands
- DNA Methylation
- Databases, Genetic
- Down-Regulation
- Epigenesis, Genetic
- Gene Expression Regulation, Neoplastic
- Humans
- Introns
- Lung Neoplasms/etiology
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Promoter Regions, Genetic
- Risk Factors
- Smoking/adverse effects
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Affiliation(s)
- Mathewos Tessema
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA.
| | - Christin M Yingling
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Guodong Wu
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Tyrone Ryba
- Division of Natural Sciences, New College of Florida, Sarasota, FL, USA
| | - Yong Lin
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Aaron O Bungum
- Departments of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Eric S Edell
- Departments of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Avrum Spira
- Department of Medicine, Boston University, Boston, MA, USA
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
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11
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Jin P, Li S, Sun L, Lv C, Ma F. Transcriptome-wide analysis of microRNAs in Branchiostoma belcheri upon Vibrio parahemolyticus infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 74:243-252. [PMID: 28487235 DOI: 10.1016/j.dci.2017.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 05/03/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
MicroRNAs (miRNAs) are endogenous small non-coding RNAs that participate in diverse biological processes via regulating expressions of target genes at post-transcriptional level. Amphioxus, as modern survivor of an ancient chordate lineage, is a model organism for comparative genomics study. However, miRNAs involved in regulating immune responses in Branchiostoma belcheri are largely unclear. Here, we systematically investigated the microRNAs (miRNAs) involved in regulating immune responses in the cephalochordate amphioxus (Branchiostoma belcheri) through next-generation deep sequencing of amphioxus samples infected with Vibrio parahemolyticus. We identified 198 novel amphioxus miRNAs, consisting of 12 conserved miRNAs, 33 candidate star miRNAs and 153 potential amphioxus-specific-miRNAs. Using microarray profiling, 14 miRNAs were differentially expressed post infection, suggesting they are immune-related miRNAs. Eight miRNAs (bbe-miR-92a-3p, bbe-miR-92c-3p, bbe-miR-210-5p, bbe-miR-22-3p, bbe-miR-1∼bbe-miR-133 and bbe-miR-217∼bbe-miR-216 clusters) were significantly increased at 12 h post-infection, while bbe-miR-2072-5p was downregulated at 6 h and 12 h. Three miRNAs, bbe-miR-1-3p, bbe-miR-22-3p and bbe-miR-92a-3p, were confirmed to be involved in immune responses to infection by qRT-PCR. Our findings further clarify important regulatory roles of miRNAs in the innate immune response to bacterial infection in amphioxus.
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Affiliation(s)
- Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Shengjie Li
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Lianjie Sun
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Caiyun Lv
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
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12
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Li JG, Ding Y, Huang YM, Chen WL, Pan LL, Li Y, Chen XL, Chen Y, Wang SY, Wu XN. FAMLF is a target of miR-181b in Burkitt lymphoma. ACTA ACUST UNITED AC 2017; 50:e5661. [PMID: 28492808 PMCID: PMC5441277 DOI: 10.1590/1414-431x20175661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/02/2017] [Indexed: 12/12/2022]
Abstract
Burkitt lymphoma (BL) is a highly malignant non-Hodgkin's lymphoma that is closely
related to the abnormal expression of genes. Familial acute myelogenous leukemia
related factor (FAMLF; GenBank accession No. EF413001.1) is a novel
gene that was cloned by our research group, and miR-181b is located in the intron of
the FAMLF gene. To verify the role of miR-181b and
FAMLF in BL, RNAhybrid software was used to predict target site
of miR-181b on FAMLF and real-time quantitative PCR (RQ-PCR) was
used to detect expression of miR-181b and FAMLF in BL patients, Raji
cells and unaffected individuals. miR-181b was then transfected into Raji and CA46
cell lines and FAMLF expression was examined by RQ-PCR and western
blotting. Further, Raji cells viability and proliferation were detected by MTT and
clone formation, and Raji cell cycle and apoptosis were detected by flow cytometry.
The results showed that miR-181b can bind to bases 21–42 of the
FAMLF 5′ untranslated region (UTR), FAMLF was
highly expressed and miR-181b was lowly expressed in BL patients compared with
unaffected individuals. FAMLF expression was significantly and
inversely correlated to miR-181b expression, and miR-181b negatively regulated
FAMLF at posttranscriptional and translational levels. A
dual-luciferase reporter gene assay identified that the 5′ UTR of
FAMLF mRNA contained putative binding sites for miR-181b.
Down-regulation of FAMLF by miR-181b arrested cell cycle, inhibited
cell viability and proliferation in a BL cell line model. Our findings explain a new
mechanism of BL pathogenesis and may also have implications in the therapy of
FAMLF-overexpressing BL.
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Affiliation(s)
- J G Li
- Department of Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Y Ding
- Union Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Y M Huang
- Union Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - W L Chen
- Union Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - L L Pan
- Department of Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Y Li
- Department of Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - X L Chen
- Union Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Y Chen
- Union Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - S Y Wang
- Department of Hematology, Fujian Institute of Hematology, Fujian Medical University Union Hospital, Fuzhou, China
| | - X N Wu
- School of Public Health, Fujian Medical University, Fuzhou, China
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13
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Nozawa M, Fujimi M, Iwamoto C, Onizuka K, Fukuda N, Ikeo K, Gojobori T. Evolutionary Transitions of MicroRNA-Target Pairs. Genome Biol Evol 2016; 8:1621-33. [PMID: 27189995 PMCID: PMC4898806 DOI: 10.1093/gbe/evw092] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
How newly generated microRNA (miRNA) genes are integrated into gene regulatory networks during evolution is fundamental in understanding the molecular and evolutionary bases of robustness and plasticity in gene regulation. A recent model proposed that after the birth of a miRNA, the miRNA is generally integrated into the network by decreasing the number of target genes during evolution. However, this decreasing model remains to be carefully examined by considering in vivo conditions. In this study, we therefore compared the number of target genes among miRNAs with different ages, combining experiments with bioinformatics predictions. First, we focused on three Drosophila miRNAs with different ages. As a result, we found that an older miRNA has a greater number of target genes than a younger miRNA, suggesting the increasing number of targets for each miRNA during evolution (increasing model). To further confirm our results, we also predicted all target genes for all miRNAs in D. melanogaster, considering co-expression of miRNAs and mRNAs in vivo. The results obtained also do not support the decreasing model but are reasonably consistent with the increasing model of miRNA-target pairs. Furthermore, our large-scale analyses of currently available experimental data of miRNA-target pairs also showed a weak but the same trend in humans. These results indicate that the current decreasing model of miRNA-target pairs should be reconsidered and the increasing model may be more appropriate to explain the evolutionary transitions of miRNA-target pairs in many organisms.
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Affiliation(s)
- Masafumi Nozawa
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan Department of Genetics, SOKENDAI, Shizuoka, Japan
| | - Mai Fujimi
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Chie Iwamoto
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Kanako Onizuka
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Nana Fukuda
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Kazuho Ikeo
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan Department of Genetics, SOKENDAI, Shizuoka, Japan
| | - Takashi Gojobori
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan King Abdullah University of Science and Technology, Computational Bioscience Research Center, Biological and Environmental Science and Engineering, Thuwal, Kingdom of Saudi Arabia
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