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Shi D, Huang H, Zhang Y, Qian Z, Du J, Huang L, Yan X, Lin S. The roles of non-coding RNAs in male reproductive development and abiotic stress responses during this unique process in flowering plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:111995. [PMID: 38266717 DOI: 10.1016/j.plantsci.2024.111995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Successful male reproductive development is the guarantee for sexual reproduction of flowering plants. Male reproductive development is a complicated and multi-stage process that integrates physiological processes and adaptation and tolerance to a myriad of environmental stresses. This well-coordinated process is governed by genetic and epigenetic machineries. Non-coding RNAs (ncRNAs) play pleiotropic roles in the plant growth and development. The identification, characterization and functional analysis of ncRNAs and their target genes have opened a new avenue for comprehensively revealing the regulatory network of male reproductive development and its response to environmental stresses in plants. This review briefly addresses the types, origin, biogenesis and mechanisms of ncRNAs in plants, highlights important updates on the roles of ncRNAs in regulating male reproductive development and emphasizes the contribution of ncRNAs, especially miRNAs and lncRNAs, in responses to abiotic stresses during this unique process in flowering plants.
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Affiliation(s)
- Dexi Shi
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Huiting Huang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Yuting Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Zhihao Qian
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Jiao Du
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xiufeng Yan
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China.
| | - Sue Lin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China.
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2
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You C, Yu Y, Wang Y. Small RNA in plant meiosis and gametogenesis. REPRODUCTION AND BREEDING 2022. [DOI: 10.1016/j.repbre.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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3
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Bednarek PT, Pachota KA, Dynkowska WM, Machczyńska J, Orłowska R. Understanding In Vitro Tissue Culture-Induced Variation Phenomenon in Microspore System. Int J Mol Sci 2021; 22:7546. [PMID: 34299165 PMCID: PMC8304781 DOI: 10.3390/ijms22147546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/24/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
In vitro tissue culture plant regeneration is a complicated process that requires stressful conditions affecting the cell functioning at multiple levels, including signaling pathways, transcriptome functioning, the interaction between cellular organelles (retro-, anterograde), compounds methylation, biochemical cycles, and DNA mutations. Unfortunately, the network linking all these aspects is not well understood, and the available knowledge is not systemized. Moreover, some aspects of the phenomenon are poorly studied. The present review attempts to present a broad range of aspects involved in the tissue culture-induced variation and hopefully would stimulate further investigations allowing a better understanding of the phenomenon and the cell functioning.
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Affiliation(s)
- Piotr Tomasz Bednarek
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzików, 05-870 Błonie, Poland; (K.A.P.); (W.M.D.); (J.M.); (R.O.)
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4
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Su A, Guo Y, Tian H, Zhou Y, Li W, Tian Y, Li K, Sun G, Jiang R, Yan F, Kang X. Analysis of miRNA and mRNA reveals core interaction networks and pathways of dexamethasone-induced immunosuppression in chicken bursa of Fabricius. Mol Immunol 2021; 134:34-47. [PMID: 33711668 DOI: 10.1016/j.molimm.2021.02.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 12/12/2022]
Abstract
Stress-induced immunosuppression is a serious problem affecting the production value of poultry, but its specific molecular mechanism has not yet been elucidated. We selected 7-day-old Gushi cocks as test animals and successfully established a stress-induced immunosuppression model by injecting 2.0 mg/kg (body weight) dexamethasone (Dex). We then constructed six cDNA libraries and two small RNA libraries of Bursa of Fabricius from the control group and the Dex group. RNA-seq results revealed 21,028 transcripts including 3920 novel transcripts; 500 miRNAs including 68 novel miRNAs were identified. Correlation analysis of miRNA, target genes and mRNA results indicated that the gga-miR-15 family, gga-miR-103-3p, gga-miR-456-3p, and gga-miR-27b-3p, as core differentially expressed miRNAs, may potentially regulate multiple genes which are involved in immune-related pathways; and that the core genes Suppressor of IKBKE 1 (SIKE1) and high mobility group AT-hook 2 (HMGA2) are associated with the miR-17 family (gga-miR-20a-5p, gga-miR-20b-5p, gga-miR-106-5p, and gga-miR-17-5p) and gga-let -7 family (gga-let-7b, gga-let-7i, gga-let-7c-5p, and gga-let-7f-5p). The interaction networks of mRNAs of significantly enrichment pathways and PPI (protein-protein interaction) networks showed that IL6, IL1B, IL8L1, CCL5, SOCS3, SOCS1, ITGB5, GSTA3, SQLE, FDFT1, FN1, IL18, IL10, MAPK11 and MAPK12 are network core nodes and that most of them are strongly associated with immune response. One of the candidate miRNAs, gga-miR-20b-5p, may play an important role in stress-induced immunosuppression. Luciferase assay and over-expression experiments suggested that gga-miR-20b-5p negatively regulated the expression of target gene SIKE1. These results provide better understanding of the mechanism of stress-induced immunosuppression in Gushi chicken bursa, and provide novel targets for subsequent research to improve poultry anti-stress capability.
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Affiliation(s)
- Aru Su
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China.
| | - Yujie Guo
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China.
| | - Huihui Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China.
| | - Yanting Zhou
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China.
| | - Wenting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China.
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China.
| | - Kui Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China.
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China.
| | - Ruirui Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China.
| | - Fengbin Yan
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China.
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China.
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5
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Zhang Z, Qiu M, Du H, Li Q, Yu C, Gan W, Peng H, Xia B, Xiong X, Song X, Yang L, Hu C, Chen J, Yang C, Jiang X. Small RNA sequencing reveals miRNAs important for hypoxic adaptation in the Tibetan chicken. Br Poult Sci 2020; 61:632-639. [PMID: 32631087 DOI: 10.1080/00071668.2020.1792835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
1. The Tibetan chicken, which is an indigenous breed living on the Tibetan Plateau, exhibits hypoxic adaptations to its high-altitude environment. However, the molecular mechanism behind this hypoxic adaptation is still unclear. This study aimed to investigate differentially expressed miRNAs involved in hypoxic adaptation through high-throughput RNA sequencing. 2. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to verify the differentially expressed miRNAs and their target genes in chicken embryonic heart tissues and fibroblasts. Luciferase reporter assays were performed to confirm the relationship between miRNAs and target genes. 3. The study identified 37 differentially expressed miRNAs in Tibetan chicken embryonic heart tissues, including 20 up- and 17 down-regulated miRNAs, compared to those found in lowland chickens. Differentially expressed miRNAs were mainly involved in biological processes, such as cell cycle arrest, toll-like receptor signalling pathways, and I-kappa B kinase/NF-kappa B signalling. The data showed that gga-miR-34 c-5p was significantly upregulated in Tibetan chicken tissues and hypoxic fibroblasts, while EHHADH, a target gene of gga-miR-34 c-5p, was downregulated. Moreover, gga-miR-34 c-5p dramatically decreased the luciferase activity of the wild EHHADH, whereas no effect on the mutational EHHADH was found. 4. This study identified miRNA expression profiles in the Tibetan chicken and suggested that miR-34 c-5p acts as a novel miRNA associated with hypoxic adaptation. This facilitates the understanding of molecular mechanisms that underlie long-term exposure to hypoxia.
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Affiliation(s)
- Z Zhang
- Poultry Research Institute, Sichuan Animal Science Academy , Chengdu, Sichuan, China.,Poultry Research Institute, Animal Breeding and Genetics Key Laboratory of Sichuan Province , Chengdu, Sichuan, China
| | - M Qiu
- Poultry Research Institute, Sichuan Animal Science Academy , Chengdu, Sichuan, China
| | - H Du
- Poultry Research Institute, Sichuan Animal Science Academy , Chengdu, Sichuan, China
| | - Q Li
- Poultry Research Institute, Sichuan Animal Science Academy , Chengdu, Sichuan, China
| | - C Yu
- Poultry Research Institute, Sichuan Animal Science Academy , Chengdu, Sichuan, China
| | - W Gan
- Poultry Research Institute, Shanghai Ying Biotechnology Company , Shanghai, China
| | - H Peng
- Poultry Research Institute, Sichuan Animal Science Academy , Chengdu, Sichuan, China
| | - B Xia
- Poultry Research Institute, Sichuan Animal Science Academy , Chengdu, Sichuan, China
| | - X Xiong
- Poultry Research Institute, Sichuan Animal Science Academy , Chengdu, Sichuan, China
| | - X Song
- Poultry Research Institute, Sichuan Animal Science Academy , Chengdu, Sichuan, China
| | - L Yang
- Poultry Research Institute, Sichuan Animal Science Academy , Chengdu, Sichuan, China
| | - C Hu
- Poultry Research Institute, Sichuan Animal Science Academy , Chengdu, Sichuan, China
| | - J Chen
- Poultry Research Institute, Sichuan Animal Science Academy , Chengdu, Sichuan, China
| | - C Yang
- Poultry Research Institute, Sichuan Animal Science Academy , Chengdu, Sichuan, China
| | - X Jiang
- Poultry Research Institute, Sichuan Animal Science Academy , Chengdu, Sichuan, China.,Poultry Research Institute, Animal Breeding and Genetics Key Laboratory of Sichuan Province , Chengdu, Sichuan, China
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6
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Liang Y, Zhang Y, Xu L, Zhou D, Jin Z, Zhou H, Lin S, Cao J, Huang L. CircRNA Expression Pattern and ceRNA and miRNA-mRNA Networks Involved in Anther Development in the CMS Line of Brassica campestris. Int J Mol Sci 2019; 20:ijms20194808. [PMID: 31569708 PMCID: PMC6801457 DOI: 10.3390/ijms20194808] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/20/2019] [Accepted: 09/24/2019] [Indexed: 12/16/2022] Open
Abstract
Male-sterile plants provide an important breeding tool for the heterosis of hybrid crops, such as Brassicaceae. In the last decade, circular RNAs (circRNAs), as a novel class of covalently closed and single-stranded endogenous non-coding RNAs (ncRNAs), have received much attention because of their functions as “microRNA (miRNA) sponges” and “competing endogenous RNAs” (ceRNAs). However, the information about circRNAs in the regulation of male-sterility and anther development is limited. In this study, we established the Polima cytoplasm male sterility (CMS) line “Bcpol97-05A”, and the fertile line, “Bcajh97-01B”, in Brassicacampestris L. ssp. chinensis Makino, syn. B. rapa ssp. chinensis, and performed RNA expression profiling comparisons between the flower buds of the sterile line and fertile line by whole-transcriptome sequencing. A total of 31 differentially expressed (DE) circRNAs, 47 DE miRNAs, and 4779 DE mRNAs were identified. By using Cytoscape, the miRNA-mediated regulatory network and ceRNA network were constructed, and the circRNA A02:23507399|23531438 was hypothesized to be an important circRNA regulating anther development at the post-transcriptional level. The gene ontology (GO) analysis demonstrated that miRNAs and circRNAs could regulate the orderly secretion and deposition of cellulose, sporopollenin, pectin, and tryphine; the timely degradation of lipids; and the programmed cell death (PCD) of tapetum cells, which play key roles in anther development. Our study revealed a new circRNA–miRNA–mRNA network, which is involved in the anther development of B. campestris, which enriched the understanding of CMS in flowering plants, and laid a foundation for further study on the functions of circRNAs and miRNAs during anther development.
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Affiliation(s)
- Yuwei Liang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Yuzhi Zhang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Liai Xu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Dong Zhou
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Zongmin Jin
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Huiyan Zhou
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Sue Lin
- Institute of Life Sciences, Wenzhou University, Wenzhou 325000, China.
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China.
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7
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Dhaka N, Sharma S, Vashisht I, Kandpal M, Sharma MK, Sharma R. Small RNA profiling from meiotic and post-meiotic anthers reveals prospective miRNA-target modules for engineering male fertility in sorghum. Genomics 2019; 112:1598-1610. [PMID: 31521711 DOI: 10.1016/j.ygeno.2019.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/30/2019] [Accepted: 09/11/2019] [Indexed: 02/06/2023]
Abstract
Understanding male gametophyte development is essential to augment hybrid production in sorghum. Although small RNAs are known to critically influence anther/pollen development, their roles in sorghum reproduction have not been deciphered yet. Here, we report small RNA profiling and high-confidence annotation of microRNAs (miRNAs) from meiotic and post-meiotic anthers in sorghum. We identified 262 miRNAs (82 known and 180 novel), out of which 58 (35 known and 23 novel) exhibited differential expression between two stages. Out of 35 differentially expressed known miRNAs, 13 are known to regulate anther/pollen development in other plant species. We also demonstrated conserved spatiotemporal patterns of 21- and 24-nt phasiRNAs and their respective triggers, miR2118 and miR2275, in sorghum anthers as evidenced in other monocots. miRNA target identification yielded 5622 modules, of which 46 modules comprising 16 known and 8 novel miRNA families with 38 target genes are prospective candidates for engineering male fertility in grasses.
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Affiliation(s)
- Namrata Dhaka
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Shalini Sharma
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Ira Vashisht
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Manu Kandpal
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Manoj Kumar Sharma
- Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India
| | - Rita Sharma
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi 110067, India.
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8
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Sun G, Li F, Ma X, Sun J, Jiang R, Tian Y, Han R, Li G, Wang Y, Li Z, Kang X, Li W. gga-miRNA-18b-3p Inhibits Intramuscular Adipocytes Differentiation in Chicken by Targeting the ACOT13 Gene. Cells 2019; 8:E556. [PMID: 31181634 PMCID: PMC6627633 DOI: 10.3390/cells8060556] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 12/13/2022] Open
Abstract
Intramuscular fat (IMF) is the most important evaluating indicator of chicken meat quality, the content of which is positively correlated with tenderness, flavor, and succulence of the meat. Chicken IMF deposition process is regulated by many factors, including genetic, nutrition, and environment. Although large number of omics' studies focused on the IMF deposition process, the molecular mechanism of chicken IMF deposition is still poorly understood. In order to study the role of miRNAs in chicken intramuscular adipogenesis, the intramuscular adipocyte differentiation model (IMF-preadipocytes and IMF-adipocytes) was established and subject to miRNA-Seq. A total of 117 differentially expressed miRNAs between two groups were obtained. Target genes prediction and functional enrichment analysis revealed that eight pathways involved in lipid metabolism related processes, such as fatty acid metabolism and fatty acid elongation. Meanwhile a putative miRNA, gga-miR-18b-3p, was identified be served a function in the intramuscular adipocyte differentiation. Luciferase assay suggested that the gga-miR-18b-3p targeted to the 3'UTR of ACOT13. Subsequent functional experiments demonstrated that gga-miR-18b-3p acted as an inhibitor of intramuscular adipocyte differentiation by targeting ACOT13. Our findings laid a new theoretical foundation for the study of lipid metabolism, and also provided a potential target to improve the meat quality in the poultry industry.
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Affiliation(s)
- Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Fang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Xiangfei Ma
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Junwei Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Ruirui Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Yanbin Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Wenting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
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Štorchová H. The Role of Non-Coding RNAs in Cytoplasmic Male Sterility in Flowering Plants. Int J Mol Sci 2017; 18:E2429. [PMID: 29144434 PMCID: PMC5713397 DOI: 10.3390/ijms18112429] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 11/17/2022] Open
Abstract
The interactions between mitochondria and nucleus substantially influence plant development, stress response and morphological features. The prominent example of a mitochondrial-nuclear interaction is cytoplasmic male sterility (CMS), when plants produce aborted anthers or inviable pollen. The genes responsible for CMS are located in mitochondrial genome, but their expression is controlled by nuclear genes, called fertility restorers. Recent explosion of high-throughput sequencing methods enabled to study transcriptomic alterations in the level of non-coding RNAs under CMS biogenesis. We summarize current knowledge of the role of nucleus encoded regulatory non-coding RNAs (long non-coding RNA, microRNA as well as small interfering RNA) in CMS. We also focus on the emerging data of non-coding RNAs encoded by mitochondrial genome and their possible involvement in mitochondrial-nuclear interactions and CMS development.
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Affiliation(s)
- Helena Štorchová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic.
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10
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Kakar KU, Nawaz Z, Kakar K, Ali E, Almoneafy AA, Ullah R, Ren XL, Shu QY. Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: novel insights into synteny, structures, and transcript profiles. BMC Genomics 2017; 18:869. [PMID: 29132315 PMCID: PMC5683364 DOI: 10.1186/s12864-017-4244-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/31/2017] [Indexed: 12/12/2022] Open
Abstract
Background The cyclic nucleotide-gated ion channel (CNGC) family affects the uptake of cations, growth, pathogen defence, and thermotolerance in plants. However, the systematic identification, origin and function of this gene family has not been performed in Brassica oleracea, an important vegetable crop and genomic model organism. Results In present study, we identified 26 CNGC genes in B. oleracea genome, which are non-randomly localized on eight chromosomes, and classified into four major (I-IV) and two sub-groups (i.e., IV-a and IV-b). The BoCNGC family is asymmetrically fractioned into the following three sub-genomes: least fractionated (14 genes), most fractionated-I (10), and most fractionated-II (2). The syntenic map of BoCNGC genes exhibited strong relationships with the model Arabidopsis thaliana and B. rapa CNGC genes and provided markers for defining the regions of conserved synteny among the three genomes. Both whole-genome triplication along with segmental and tandem duplications contributed to the expansion of this gene family. We predicted the characteristics of BoCNGCs regarding exon-intron organisations, motif compositions and post-translational modifications, which diversified their structures and functions. Using orthologous Arabidopsis CNGCs as a reference, we found that most CNGCs were associated with various protein–protein interaction networks involving CNGCs and other signalling and stress related proteins. We revealed that five microRNAs (i.e., bol-miR5021, bol-miR838d, bol-miR414b, bol-miR4234, and bol-miR_new2) have target sites in nine BoCNGC genes. The BoCNGC genes were differentially expressed in seven B. oleracea tissues including leaf, stem, callus, silique, bud, root and flower. The transcript abundance levels quantified by qRT-PCR assays revealed that BoCNGC genes from phylogenetic Groups I and IV were particularly sensitive to cold stress and infections with bacterial pathogen Xanthomonas campestris pv. campestris, suggesting their importance in abiotic and biotic stress responses. Conclusion Our comprehensive genome-wide analysis represents a rich data resource for studying new plant gene families. Our data may also be useful for breeding new B. oleracea cultivars with improved productivity, quality, and stress resistance. Electronic supplementary material The online version of this article (10.1186/s12864-017-4244-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kaleem U Kakar
- State Key Laboratory of Rice Biology, Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.,Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Zarqa Nawaz
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China.,Wuxi Hupper Bioseed Technology Academy Ltd., Wuxi, 214000, China
| | - Khadija Kakar
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Essa Ali
- State Key Laboratory of Rice Biology, Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Abdulwareth A Almoneafy
- Department of Biological sciences, College of Education and Science, Albaydaa University, Rada'a, Yemen
| | - Raqeeb Ullah
- Department of Environmental Sciences, Quaid -i- Azam University, Islamabad, Pakistan
| | - Xue-Liang Ren
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China. .,Guizhou Academy of Tobacco Science, Longtanba Road No. 29, Guanshanhu District, Guiyang, (550081), Guizhou, People's Republic of China.
| | - Qing-Yao Shu
- State Key Laboratory of Rice Biology, Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China. .,Institute of Crop Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310029, China.
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Wang Y, Liu J, Wang X, Liu S, Wang G, Zhou J, Yuan Y, Chen T, Jiang C, Zha L, Huang L. Validation of Suitable Reference Genes for Assessing Gene Expression of MicroRNAs in Lonicera japonica. FRONTIERS IN PLANT SCIENCE 2016; 7:1101. [PMID: 27507983 PMCID: PMC4961011 DOI: 10.3389/fpls.2016.01101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/11/2016] [Indexed: 06/06/2023]
Abstract
MicroRNAs (miRNAs), which play crucial regulatory roles in plant secondary metabolism and responses to the environment, could be developed as promising biomarkers for different varieties and production areas of herbal medicines. However, limited information is available for miRNAs from Lonicera japonica, which is widely used in East Asian countries owing to various pharmaceutically active secondary metabolites. Selection of suitable reference genes for quantification of target miRNA expression through quantitative real-time (qRT)-PCR is important for elucidating the molecular mechanisms of secondary metabolic regulation in different tissues and varieties of L. japonica. For precise normalization of gene expression data in L. japonica, 16 candidate miRNAs were examined in three tissues, as well as 21 cultivated varieties collected from 16 production areas, using GeNorm, NormFinder, and RefFinder algorithms. Our results revealed combination of u534122 and u3868172 as the best reference genes across all samples. Their specificity was confirmed by detecting the cycling threshold (C t) value ranges in different varieties of L. japonica collected from diverse production areas, suggesting the use of these two reference miRNAs is sufficient for accurate transcript normalization with different tissues, varieties, and production areas. To our knowledge, this is the first report on validation of reference miRNAs in honeysuckle (Lonicera spp.). Restuls from this study can further facilitate discovery of functional regulatory miRNAs in different varieties of L. japonica.
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Affiliation(s)
- Yaolong Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Juan Liu
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Xumin Wang
- Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
| | - Shuang Liu
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Guoliang Wang
- Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
| | - Junhui Zhou
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Yuan Yuan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Tiying Chen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Chao Jiang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Liangping Zha
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
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Guo XY, Lu M, Chen XQ, He FD, Li A. Correlation study of biological characteristics of non-small cell lung cancer A549 cells after transfecting plasmid by microbubble ultrasound contrast agent. ASIAN PAC J TROP MED 2016; 9:582-6. [DOI: 10.1016/j.apjtm.2016.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/16/2016] [Indexed: 10/21/2022] Open
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