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Hanif Q, Farooq M, Amin I, Mansoor S, Zhang Y, Khan QM. In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle. PLoS One 2018; 13:e0206154. [PMID: 30365525 PMCID: PMC6203363 DOI: 10.1371/journal.pone.0206154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 10/08/2018] [Indexed: 12/28/2022] Open
Abstract
The modern cattle was domesticated from aurochs, sharing its physiological traits into two subspecies Bos taurus and Bos indicus. MicroRNAs (miRNAs) are a class of non-coding short RNAs of ~22nt which have a key role in the regulation of many cellular and physiological processes in the animal. The current study was aimed to predict and annotate the potential mutations in indicine miRNAs throughout the genome using de novo and homology-based in silico approaches. Genome-wide mapping was performed in available indicine assembly by the homology-based approach and 768 miRNAs were recovered out of 808 reported taurine miRNAs belonging to 521 unique mature miRNA families. While 42 precursors were dropped due to lack of secondary miRNA structure, increasing stringency or decreasing similarity between the two genomes' miRNA. Increasing tendency of miRNAs incidence was observed on chr5, chr7, chr8, chr12 and chr21 with 19 polycistronic miRNA within 1-kilobase distance throughout the indicine genome. Notably, 12 miRNAs showed copy number variation. Eighteen miRNAs showed a mutation in their mature sequences in which eight were found in their seed region. Whilst in de novo based approach, 12 novel potential miRNAs on Y chromosome in indicine cattle along with a new miRNA (bind-miR-1264) on chrX were found. The final data set is annotated and explains the impending target genes that are responsible for enhanced immunity, heat tolerance and disease tolerance regulation in indicine. The study conforms to better understanding and perceptive approach towards indicine genome.
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Affiliation(s)
- Quratulain Hanif
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, PK
| | - Muhammad Farooq
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
| | - Imran Amin
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
| | - Shahid Mansoor
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
| | - Yi Zhang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qaiser Mahmood Khan
- Environmental Toxicology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
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microRNA profiles and functions in mosquitoes. PLoS Negl Trop Dis 2018; 12:e0006463. [PMID: 29718912 PMCID: PMC5951587 DOI: 10.1371/journal.pntd.0006463] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 05/14/2018] [Accepted: 04/19/2018] [Indexed: 11/19/2022] Open
Abstract
Mosquitoes are incriminated as vectors for many crippling diseases, including malaria, West Nile fever, Dengue fever, and other neglected tropical diseases (NTDs). microRNAs (miRNAs) can interact with multiple target genes to elicit biological functions in the mosquitoes. However, characterization and function of individual miRNAs and their potential targets have not been fully determined to date. We conducted a systematic review of published literature following PRISMA guidelines. We summarize the information about miRNAs in mosquitoes to better understand their metabolism, development, and responses to microorganisms. Depending on the study, we found that miRNAs were dysregulated in a species-, sex-, stage-, and tissue/organ-specific manner. Aberrant miRNA expressions were observed in development, metabolism, host-pathogen interactions, and insecticide resistance. Of note, many miRNAs were down-regulated upon pathogen infection. The experimental studies have expanded the identification of miRNA target from the 3' untranslated regions (UTRs) of mRNAs of mosquitoes to the 5' UTRs of mRNAs of the virus. In addition, we discuss current trends in mosquito miRNA research and offer suggestions for future studies.
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Feng X, Wu J, Zhou S, Wang J, Hu W. Characterization and potential role of microRNA in the Chinese dominant malaria mosquito Anopheles sinensis (Diptera: Culicidae) throughout four different life stages. Cell Biosci 2018; 8:29. [PMID: 29682276 PMCID: PMC5898052 DOI: 10.1186/s13578-018-0227-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/04/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND microRNAs (miRNAs) are one kind of small non-coding RNAs widely distributed in insects. Many studies have shown that miRNAs play critical roles in development, differentiation, apoptosis, and innate immunity. However, there are a few reports describing miRNAs in Anopheles sinensis, the most common, and one of the dominant malaria mosquito in China. Here, we investigated the global miRNA expression profile across four different developmental stages including embryo, larval, pupal, and adult stages using Illumina Hiseq 2500 sequencing. RESULTS In total, 164 miRNAs were obtained out of 107.46 million raw sequencing reads. 99 of them identified as known miRNAs, and the remaining 65 miRNAs were considered as novel. By analyzing the read counts of miRNAs in all developmental stages, 95 miRNAs showed stage-specific expression (q < 0.01 and |log2 (fold change)| > 1) in consecutive stages, indicating that these miRNAs may be involved in critical physiological activity during development. Sixteen miRNAs were identified to be commonly dysregulated throughout four developmental stages. Many miRNAs showed stage-specific expression, such as asi-miR-2943 was exclusively expressed in the embryo stage, and asi-miR-1891 could not be detected in larval stage. The expression of six selected differentially expressed miRNAs identified by qRT-PCR were consistent with our sequencing results. Furthermore, 5296 and 1902 target genes were identified for the dysregulated 68 known and 27 novel miRNAs respectively by combining miRanda and RNAhybrid prediction. GO annotation and KEGG pathway analysis for the predicted genes of dysregulated miRNAs revealed that they might be involved in a broad range of biological processes related with the development, such as membrane, organic substance transport and several key pathways including protein processing in endoplasmic reticulum, propanoate metabolism and folate biosynthesis. Thirty-two key miRNAs were identified by microRNA-gene network analysis. CONCLUSION The present study represents the first global characterization of An. sinensis miRNAs in its four developmental stages. The presence and differential expression of An. sinensis miRNAs imply that such miRNAs may play critical roles in An. sinensis life cycle. A better understanding of the functions of these miRNAs will have great implication for the effective control of vector population and therefore interrupting malaria transmission.
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Affiliation(s)
- Xinyu Feng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, WHO Collaborating Center for Tropical Diseases, National Center for International Research On Tropical Diseases, Shanghai, 200025 People’s Republic of China
- Joint Research Laboratory of Genetics and Ecology on Parasites-hosts Interaction, National Institute of Parasitic Diseases-Fudan University, Shanghai, 200025 People’s Republic of China
| | - Jiatong Wu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, WHO Collaborating Center for Tropical Diseases, National Center for International Research On Tropical Diseases, Shanghai, 200025 People’s Republic of China
| | - Shuisen Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, WHO Collaborating Center for Tropical Diseases, National Center for International Research On Tropical Diseases, Shanghai, 200025 People’s Republic of China
| | - Jingwen Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438 People’s Republic of China
- Department of Microbiology and Microbial Engineering, School of Life Science, Fudan University, Shanghai, 200433 China
| | - Wei Hu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, WHO Collaborating Center for Tropical Diseases, National Center for International Research On Tropical Diseases, Shanghai, 200025 People’s Republic of China
- Joint Research Laboratory of Genetics and Ecology on Parasites-hosts Interaction, National Institute of Parasitic Diseases-Fudan University, Shanghai, 200025 People’s Republic of China
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438 People’s Republic of China
- Department of Microbiology and Microbial Engineering, School of Life Science, Fudan University, Shanghai, 200433 China
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Feng X, Zhou X, Zhou S, Wang J, Hu W. Analysis of microRNA profile of Anopheles sinensis by deep sequencing and bioinformatic approaches. Parasit Vectors 2018. [PMID: 29530087 PMCID: PMC5848538 DOI: 10.1186/s13071-018-2734-7] [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] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND microRNAs (miRNAs) are small non-coding RNAs widely identified in many mosquitoes. They are reported to play important roles in development, differentiation and innate immunity. However, miRNAs in Anopheles sinensis, one of the Chinese malaria mosquitoes, remain largely unknown. METHODS We investigated the global miRNA expression profile of An. sinensis using Illumina Hiseq 2000 sequencing. Meanwhile, we applied a bioinformatic approach to identify potential miRNAs in An. sinensis. The identified miRNA profiles were compared and analyzed by two approaches. The selected miRNAs from the sequencing result and the bioinformatic approach were confirmed with qRT-PCR. Moreover, target prediction, GO annotation and pathway analysis were carried out to understand the role of miRNAs in An. sinensis. RESULTS We identified 49 conserved miRNAs and 12 novel miRNAs by next-generation high-throughput sequencing technology. In contrast, 43 miRNAs were predicted by the bioinformatic approach, of which two were assigned as novel. Comparative analysis of miRNA profiles by two approaches showed that 21 miRNAs were shared between them. Twelve novel miRNAs did not match any known miRNAs of any organism, indicating that they are possibly species-specific. Forty miRNAs were found in many mosquito species, indicating that these miRNAs are evolutionally conserved and may have critical roles in the process of life. Both the selected known and novel miRNAs (asi-miR-281, asi-miR-184, asi-miR-14, asi-miR-nov5, asi-miR-nov4, asi-miR-9383, and asi-miR-2a) could be detected by quantitative real-time PCR (qRT-PCR) in the sequenced sample, and the expression patterns of these miRNAs measured by qRT-PCR were in concordance with the original miRNA sequencing data. The predicted targets for the known and the novel miRNAs covered many important biological roles and pathways indicating the diversity of miRNA functions. We also found 21 conserved miRNAs and eight counterparts of target immune pathway genes in An. sinensis based on the analysis of An. gambiae. CONCLUSIONS Our results provide the first lead to the elucidation of the miRNA profile in An. sinensis. Unveiling the roles of mosquito miRNAs will undoubtedly lead to a better understanding of mosquito biology and mosquito-pathogen interactions. This work lays the foundation for the further functional study of An. sinensis miRNAs and will facilitate their application in vector control.
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Affiliation(s)
- Xinyu Feng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, People's Republic of China.,Joint Research Laboratory of Genetics and Ecology on Parasites-hosts Interaction, National Institute of Parasitic Diseases - Fudan University, Shanghai, 200025, China
| | - Xiaojian Zhou
- Institute of Software Engineering, Zhejiang University, Hangzhou, 310011, China
| | - Shuisen Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, People's Republic of China.
| | - Jingwen Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Wei Hu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology, National Health and Family Planning Commission, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, People's Republic of China. .,State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China.
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Huang X, Gao Y, Qin J, Lu S. The mechanism of long non-coding RNA MEG3 for hepatic ischemia-reperfusion: Mediated by miR-34a/Nrf2 signaling pathway. J Cell Biochem 2017; 119:1163-1172. [PMID: 28708282 DOI: 10.1002/jcb.26286] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/13/2017] [Indexed: 12/19/2022]
Abstract
To investigate the function of MEG3 in hepatic ischemia-reperfusion (HIR) progress, involving its association with the level of miR-34a during hypoxia-induced hypoxia re-oxygenation (H/R) in vitro. HIR mice model in vivo was established. MEG3, miR-34a expression, along with Nrf2 mRNA and protein level were detected in tissues and cells. Serum biochemical parameters (ALT and AST) were assessed in vivo. A potential binding region between MEG3 and miR34a was confirmed by luciferase assays. Hepatic cells HL7702 were subjected to hypoxia treatment in vitro for functional studies, including TUNEL-positive cells detection and ROS analysis. MEG3, Nrf2 expression was significantly down-regulated in infarction lesion from HIR mice, as opposed to increased miR-34a production, while similar results were also observed in H/R HL7702 cells, while the above effects were reversed by MEG3 over-expression. By using bioinformatics study and RNA pull down combined with luciferase assays, we demonstrated that MEG3 functioned as a competing endogenous RNA (ceRNA) for miR-34a, and there was reciprocal repression between MEG3 and miR-34a in an Argonaute 2-dependent manner. Functional studies demonstrated that MEG3 showed positive regulation on TUNEL-positive cells and ROS level. Further in vivo study confirmed that MEG3 over-expression could improve hepatic function of HIR mice, and markedly decreased the expression of serum ALT and AST. MEG3 protected hepatocytes from HIR injury through down-regulating miR-34a expression, which could add our understanding of the molecular mechanisms in HIR injury.
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Affiliation(s)
- Xinli Huang
- Center of Liver Transplantation, The First Affiliated Hospital of Nanjing Medical University, The Key Laboratory of Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, Jiangsu, China
| | - Yun Gao
- Center of Liver Transplantation, The First Affiliated Hospital of Nanjing Medical University, The Key Laboratory of Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, Jiangsu, China
| | - Jianjie Qin
- Center of Liver Transplantation, The First Affiliated Hospital of Nanjing Medical University, The Key Laboratory of Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, Jiangsu, China
| | - Sen Lu
- Center of Liver Transplantation, The First Affiliated Hospital of Nanjing Medical University, The Key Laboratory of Living Donor Liver Transplantation, National Health and Family Planning Commission, Nanjing, Jiangsu, China
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