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He Y, Ning Z, Zhu X, Zhang Y, Liu C, Jiang S, Yuan Z, Zhang H. Plant lncRNA-miRNA Interaction Prediction Based on Counterfactual Heterogeneous Graph Attention Network. Interdiscip Sci 2024:10.1007/s12539-024-00652-9. [PMID: 39382820 DOI: 10.1007/s12539-024-00652-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 08/10/2024] [Accepted: 08/12/2024] [Indexed: 10/10/2024]
Abstract
Identifying interactions between long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) provides a new perspective for understanding regulatory relationships in plant life processes. Recently, computational methods based on graph neural networks (GNNs) have been widely employed to predict lncRNA-miRNA interactions (LMIs), which compensate for the inadequacy of biological experiments. However, the low-semantic and noise of graph limit the performance of existing GNN-based methods. In this paper, we develop a novel Counterfactual Heterogeneous Graph Attention Network (CFHAN) to improve the robustness to against the noise and the prediction of plant LMIs. Firstly, we construct a real-world based lncRNA-miRNA (L-M) heterogeneous network. Secondly, CFHAN utilizes the node-level attention, the semantic-level attention, and the counterfactual links to enhance the node embeddings learning. Finally, these embeddings are used as inputs for Multilayer Perceptron (MLP) to predict the interactions between lncRNAs and miRNAs. Evaluating our method on a benchmark dataset of plant LMIs, CFHAN outperforms five state-of-the-art methods, and achieves an average AUC and average ACC of 0.9953 and 0.9733, respectively. This demonstrates CFHAN's ability to predict plant LMIs and exhibits promising cross-species prediction ability, offering valuable insights for experimental LMI researches.
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Affiliation(s)
- Yu He
- College of Information and Intelligence, Hunan Agricultural University, Changsha, 410128, China
| | - ZiLan Ning
- College of Information and Intelligence, Hunan Agricultural University, Changsha, 410128, China
| | - XingHui Zhu
- College of Information and Intelligence, Hunan Agricultural University, Changsha, 410128, China
| | - YinQiong Zhang
- College of Information and Intelligence, Hunan Agricultural University, Changsha, 410128, China
| | - ChunHai Liu
- Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China
| | - SiWei Jiang
- College of Information and Intelligence, Hunan Agricultural University, Changsha, 410128, China
| | - ZheMing Yuan
- Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China.
| | - HongYan Zhang
- College of Information and Intelligence, Hunan Agricultural University, Changsha, 410128, China.
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2
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Yajnik KN, Singh IK, Singh A. lncRNAs and epigenetics regulate plant's resilience against biotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108892. [PMID: 38964086 DOI: 10.1016/j.plaphy.2024.108892] [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: 07/13/2023] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024]
Abstract
With the advent of transcriptomic techniques involving single-stranded RNA sequencing and chromatin isolation by RNA purification-based sequencing, transcriptomic studies of coding and non-coding RNAs have been executed efficiently. These studies acknowledged the role of non-coding RNAs in modulating gene expression. Long non-coding RNAs (lncRNAs) are a kind of non-coding RNAs having lengths of >200 nucleotides, playing numerous roles in plant developmental processes such as photomorphogenesis, epigenetic changes, reproductive tissue development, and in regulating biotic and abiotic stresses. Epigenetic changes further control gene expression by changing their state to "ON-OFF" and also regulate stress memory and its transgenerational inheritance. With well-established regulatory mechanisms, they act as guides, scaffolds, signals, and decoys to modulate gene expression. They act as a major operator of post-transcriptional modifications such as histone and epigenetic modifications, and DNA methylations. The review elaborates on the roles of lncRNAs in plant immunity and also discusses how epigenetic markers alter gene expression in response to pest/pathogen attack and influences chromatin-associated stress memory as well as transgenerational inheritance of epigenetic imprints in plants. The review further summarizes some research studies on how histone modifications and DNA methylations resist pathogenic and pest attacks by activating defense-related genes.
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Affiliation(s)
- Kalpesh Nath Yajnik
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India; Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Archana Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India; Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India; Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, India.
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3
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Shen E, Zhao T, Zhu QH. Are miRNAs applicable for balancing crop growth and defense trade-off? THE NEW PHYTOLOGIST 2024; 243:1670-1680. [PMID: 38952260 DOI: 10.1111/nph.19939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024]
Abstract
Securing agricultural supplies for the increasing population without negative impacts on environment demands new crop varieties with higher yields, better quality, and stronger stress resilience. But breeding such super crop varieties is restrained by growth-defense (G-D) trade-off. MicroRNAs (miRNAs) are versatile regulators of plant growth and immune responses, with several being demonstrated to simultaneously regulate crop growth and defense against biotic stresses and to balance G-D trade-off. Increasing evidence also links miRNAs to the metabolism and signaling of phytohormones, another type of master regulator of plant growth and defense. Here, we synthesize the reported functions of miRNAs in crop growth, development, and responses to bio-stressors, summarize the regulatory scenarios of miRNAs based on their relationship with target(s), and discuss how miRNAs, particularly those involved in crosstalk with phytohormones, can be applied in balancing G-D trade-off in crops. We also propose several open questions to be addressed for adopting miRNAs in balancing crop G-D trade-off.
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Affiliation(s)
- Enhui Shen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- The Rural Development Academy, Zhejiang University, Hangzhou, 310058, China
| | - Tianlun Zhao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Institute of Hainan, Zhejiang University, Hangzhou, 310058, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
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Bai Y, He J, Yao Y, An L, Cui Y, Li X, Yao X, Xiao S, Wu K. Identification and functional analysis of long non-coding RNA (lncRNA) and metabolites response to mowing in hulless barley (Hordeum vulgare L. var. nudum hook. f.). BMC PLANT BIOLOGY 2024; 24:666. [PMID: 38997634 PMCID: PMC11241897 DOI: 10.1186/s12870-024-05334-8] [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: 03/06/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND Hulless barley (Hordeum vulgare L. var. nudum Hook. f.) is a significant cereal crop and a substantial source of forage for livestock. Long non-coding RNAs (lncRNAs) and metabolites play crucial roles in the nutrient accumulation and regeneration of hulless barley plants following mowing. The study aimed to identify differentially expressed lncRNAs and metabolites in hulless barley plants by analyzing transcriptomic and metabolomic datasets at 2 h, 24 h, and 72 h following mowing. RESULTS The study revealed that 190, 90, and 438 lncRNA genes were differentially expressed at the 2 h, 24 h, and 72 h time points compared to the non-mowing control. We identified 14 lncRNA genes-11 downregulated and 3 upregulated-showing consistently significant differential expression across all time points after mowing. These differentially expressed lncRNAs target genes involved in critical processes such as cytokinin signaling, cell wall degradation, storage protein accumulation, and biomass increase. In addition, we identified ten differentially expressed metabolites targeting diverse metabolic pathways, including plant hormones, alkaloids, and flavonoids, before and after mowing at various time points. Endogenous hormone analysis revealed that cytokinin most likely played a crucial role in the regeneration of hulless barley after mowing. CONCLUSIONS This study created a comprehensive dataset of lncRNAs, metabolites, and hormones in hulless barley after mowing, revealing valuable insights into the functional characteristics of lncRNAs, metabolites, and hormones in regulating plant regeneration. The results indicated that cytokinin plays a significant role in facilitating the regeneration process of hulless barley after mowing. This comprehensive dataset is an invaluable resource for better understanding the complex mechanisms that underlie plant regeneration, with significant implications for crop improvement.
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Affiliation(s)
- Yixiong Bai
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Jiaqi He
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Youhua Yao
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Likun An
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Yongmei Cui
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Xin Li
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Xiaohua Yao
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Shanshan Xiao
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China
| | - Kunlun Wu
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Xining, Qinghai Province, 810016, China.
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Ren F, Huang J, Yang Y. Unveiling the impact of microplastics and nanoplastics on vascular plants: A cellular metabolomic and transcriptomic review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 279:116490. [PMID: 38795417 DOI: 10.1016/j.ecoenv.2024.116490] [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: 04/07/2023] [Revised: 05/03/2024] [Accepted: 05/19/2024] [Indexed: 05/28/2024]
Abstract
With increasing plastic manufacture and consumption, microplastics/nanoplastics (MP/NP) pollution has become one of the world's pressing global environmental issues, which poses significant threats to ecosystems and human health. In recent years, sharp increasing researches have confirmed that MP/NP had direct or indirect effects on vegetative growth and sexual process of vascular plant. But the potential mechanisms remain ambiguous. MP/NP particles can be adsorbed and/or absorbed by plant roots or leaves and thus cause diverse effects on plant. This holistic review aims to discuss the direct effects of MP/NP on vascular plant, with special emphasis on the changes of metabolic and molecular levels. MP/NP can alter substance and energy metabolism, as well as shifts in gene expression patterns. Key aspects affected by MP/NP stress include carbon and nitrogen metabolism, amino acids biosynthesis and plant hormone signal transduction, expression of stress related genes, carbon and nitrogen metabolism related genes, as well as those involved in pathogen defense. Additionally, the review provides updated insights into the growth and physiological responses of plants exposed to MP/NP, encompassing phenomena such as seed/spore germination, photosynthesis, oxidative stress, cytotoxicity, and genotoxicity. By examining the direct impact of MP/NP from both physiological and molecular perspectives, this review sets the stage for future investigations into the complex interactions between plants and plastic pollutants.
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Affiliation(s)
- Fugang Ren
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China; College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, China
| | - Jing Huang
- Department of Vocal Performance, Sichuan Conservatory of Music, Chengdu 610021, China
| | - Yongqing Yang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China.
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Rashwan HH, Taher AM, Hassan HA, Awaji AA, Kiriacos CJ, Assal RA, Youness RA. Harnessing the supremacy of MEG3 LncRNA to defeat gastrointestinal malignancies. Pathol Res Pract 2024; 256:155223. [PMID: 38452587 DOI: 10.1016/j.prp.2024.155223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/09/2024]
Abstract
Evidence suggests that long non-coding RNAs (lncRNAs) play a pivotal role in the carcinogenesis and progression of various human malignancies including gastrointestinal malignancies. This comprehensive review reports the functions and mechanisms of the lncRNA maternally expressed gene 3 (MEG3) involved in gastrointestinal malignancies. It summarizes its roles in mediating the regulation of cellular proliferation, apoptosis, migration, invasiveness, epithelial-to-mesenchymal transition, and drug resistance in several gastrointestinal cancers such as colorectal cancer, gall bladder cancer, pancreatic cancer, gastric cancer, esophageal cancer, cholangiocarcinoma, gastrointestinal stromal tumors and most importantly, hepatocellular carcinoma. In addition, the authors briefly highlight its implicated mechanistic role and interactions with different non-coding RNAs and oncogenic signaling cascades. This review presents the rationale for developing non coding RNA-based anticancer therapy via harnessing the power of MEG3 in gastrointestinal malignancies.
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Affiliation(s)
- H H Rashwan
- Molecular Genetics and Biochemistry Department, Molecular Genetics Research Team (MGRT), Faculty of Biotechnology, German International University (GIU), Cairo 11835, Egypt; Bioinformatics Group, Center for Informatics Science (CIS), School of Information Technology and Computer Science (ITCS), Nile University, 12677, Giza, Egypt
| | - A M Taher
- Molecular Genetics and Biochemistry Department, Molecular Genetics Research Team (MGRT), Faculty of Biotechnology, German International University (GIU), Cairo 11835, Egypt
| | - H A Hassan
- Molecular Genetics and Biochemistry Department, Molecular Genetics Research Team (MGRT), Faculty of Biotechnology, German International University (GIU), Cairo 11835, Egypt
| | - A A Awaji
- Department of Biology, Faculty of Science, University College of Taymaa, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - C J Kiriacos
- Molecular Genetics and Biochemistry Department, Molecular Genetics Research Team (MGRT), Faculty of Biotechnology, German International University (GIU), Cairo 11835, Egypt
| | - R A Assal
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Heliopolis University for Sustainable Development, Cairo, Egypt
| | - R A Youness
- Molecular Genetics and Biochemistry Department, Molecular Genetics Research Team (MGRT), Faculty of Biotechnology, German International University (GIU), Cairo 11835, Egypt.
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7
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Yadav A, Mathan J, Dubey AK, Singh A. The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling. Noncoding RNA 2024; 10:13. [PMID: 38392968 PMCID: PMC10893181 DOI: 10.3390/ncrna10010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research.
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Affiliation(s)
- Amit Yadav
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
| | - Jyotirmaya Mathan
- Sashi Bhusan Rath Government Autonomous Women’s College, Brahmapur 760001, India;
| | - Arvind Kumar Dubey
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Anuradha Singh
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, USA
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8
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Li M, Yu H, Zhou B, Gan L, Li S, Zhang C, Yu B. JANUS, a spliceosome-associated protein, promotes miRNA biogenesis in Arabidopsis. Nucleic Acids Res 2024; 52:420-430. [PMID: 37994727 PMCID: PMC10783502 DOI: 10.1093/nar/gkad1105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
MicroRNAs (miRNAs) are important regulators of genes expression. Their levels are precisely controlled through modulating the activity of the microprocesser complex (MC). Here, we report that JANUS, a homology of the conserved U2 snRNP assembly factor in yeast and human, is required for miRNA accumulation. JANUS associates with MC components Dicer-like 1 (DCL1) and SERRATE (SE) and directly binds the stem-loop of pri-miRNAs. In a hypomorphic janus mutant, the activity of DCL1, the numbers of MC, and the interaction of primary miRNA transcript (pri-miRNAs) with MC are reduced. These data suggest that JANUS promotes the assembly and activity of MC through its interaction with MC and/or pri-miRNAs. In addition, JANUS modulates the transcription of some pri-miRNAs as it binds the promoter of pri-miRNAs and facilitates Pol II occupancy of at their promoters. Moreover, global splicing defects are detected in janus. Taken together, our study reveals a novel role of a conserved splicing factor in miRNA biogenesis.
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Affiliation(s)
- Mu Li
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Huihui Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Bangjun Zhou
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Lu Gan
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Shengjun Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao New Energy Shangdong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Bin Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
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9
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Nasser JS, Altahoo N, Almosawi S, Alhermi A, Butler AE. The Role of MicroRNA, Long Non-Coding RNA and Circular RNA in the Pathogenesis of Polycystic Ovary Syndrome: A Literature Review. Int J Mol Sci 2024; 25:903. [PMID: 38255975 PMCID: PMC10815174 DOI: 10.3390/ijms25020903] [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: 12/03/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Polycystic ovary syndrome (PCOS) is the most common endocrine-metabolic disease in females of reproductive age, affecting 4-20% of pre-menopausal women worldwide. MicroRNAs (miRNAs) are endogenous, single-stranded, non-coding, regulatory ribonucleic acid molecules found in eukaryotic cells. Abnormal miRNA expression has been associated with several diseases and could possibly explain their underlying pathophysiology. MiRNAs have been extensively studied for their potential diagnostic, prognostic, and therapeutic uses in many diseases, such as type 2 diabetes, obesity, cardiovascular disease, PCOS, and endometriosis. In women with PCOS, miRNAs were found to be abnormally expressed in theca cells, follicular fluid, granulosa cells, peripheral blood leukocytes, serum, and adipose tissue when compared to those without PCOS, making miRNAs a useful potential biomarker for the disease. Key pathways involved in PCOS, such as folliculogenesis, steroidogenesis, and cellular adhesion, are regulated by miRNA. This also highlights their importance as potential prognostic markers. In addition, recent evidence suggests a role for miRNAs in regulating the circadian rhythm (CR). CR is crucial for regulating reproduction through the various functions of the hypothalamic-pituitary-gonadal (HPG) axis and the ovaries. A disordered CR affects reproductive outcomes by inducing insulin resistance, oxidative stress, and systemic inflammation. Moreover, miRNAs were demonstrated to interact with lncRNA and circRNAs, which are thought to play a role in the pathogenesis of PCOS. This review discusses what is currently understood about miRNAs in PCOS, the cellular pathways involved, and their potential role as biomarkers and therapeutic targets.
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Affiliation(s)
- Jenan Sh. Nasser
- School of Medicine, Royal College of Surgeons of Ireland, Busaiteen, Adliya 15503, Bahrain; (J.S.N.); (N.A.); (S.A.); (A.A.)
| | - Noor Altahoo
- School of Medicine, Royal College of Surgeons of Ireland, Busaiteen, Adliya 15503, Bahrain; (J.S.N.); (N.A.); (S.A.); (A.A.)
| | - Sayed Almosawi
- School of Medicine, Royal College of Surgeons of Ireland, Busaiteen, Adliya 15503, Bahrain; (J.S.N.); (N.A.); (S.A.); (A.A.)
| | - Abrar Alhermi
- School of Medicine, Royal College of Surgeons of Ireland, Busaiteen, Adliya 15503, Bahrain; (J.S.N.); (N.A.); (S.A.); (A.A.)
| | - Alexandra E. Butler
- Research Department, Royal College of Surgeons of Ireland, Busaiteen, Adliya 15503, Bahrain
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10
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Hussein MA, Valinezhad K, Adel E, Munirathinam G. MALAT-1 Is a Key Regulator of Epithelial-Mesenchymal Transition in Cancer: A Potential Therapeutic Target for Metastasis. Cancers (Basel) 2024; 16:234. [PMID: 38201661 PMCID: PMC10778055 DOI: 10.3390/cancers16010234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/29/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript-1 (MALAT-1) is a long intergenic non-coding RNA (lncRNA) located on chr11q13. It is overexpressed in several cancers and controls gene expression through chromatin modification, transcriptional regulation, and post-transcriptional regulation. Importantly, MALAT-1 stimulates cell proliferation, migration, and metastasis and serves a vital role in driving the epithelial-to-mesenchymal transition (EMT), subsequently acquiring cancer stem cell-like properties and developing drug resistance. MALAT-1 modulates EMT by interacting with various intracellular signaling pathways, notably the phosphoinositide 3-kinase (PI3K)/Akt and Wnt/β-catenin pathways. It also behaves like a sponge for microRNAs, preventing their interaction with target genes and promoting EMT. In addition, we have used bioinformatics online tools to highlight the disparities in the expression of MALAT-1 between normal and cancer samples using data from The Cancer Genome Atlas (TCGA). Furthermore, the intricate interplay of MALAT-1 with several essential targets of cancer progression and metastasis renders it a good candidate for therapeutic interventions. Several innovative approaches have been exploited to target MALAT-1, such as short hairpin RNAs (shRNAs), antisense oligonucleotides (ASOs), and natural products. This review emphasizes the interplay between MALAT-1 and EMT in modulating cancer metastasis, stemness, and chemoresistance in different cancers.
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Affiliation(s)
- Mohamed Ali Hussein
- Department of Pharmaceutical Services, Children’s Cancer Hospital Egypt, Cairo 57357, Egypt;
- Department of Biology, School of Sciences and Engineering, American University in Cairo, New Cairo 11835, Egypt;
| | - Kamyab Valinezhad
- Department of Biomedical Sciences, College of Medicine, University of Illinois, Rockford, IL 61107, USA;
| | - Eman Adel
- Department of Biology, School of Sciences and Engineering, American University in Cairo, New Cairo 11835, Egypt;
| | - Gnanasekar Munirathinam
- Department of Biomedical Sciences, College of Medicine, University of Illinois, Rockford, IL 61107, USA;
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11
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Zhou D, Zhao S, Zhou H, Chen J, Huang L. A lncRNA bra-miR156HG regulates flowering time and leaf morphology as a precursor of miR156 in Brassica campestris and Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 337:111889. [PMID: 37805055 DOI: 10.1016/j.plantsci.2023.111889] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Long non-coding RNAs (lncRNAs) are important regulators in plant growth and development. Here the function of a lncRNA fragment was studied, which was predicted as an endogenous target mimic (eTM) of miR156 in Brassica campesrtis. Unexpectedly, the transformation of this lncRNA into Arabidopsis thaliana neither inhibited the expression of miR156a nor resulted in any phenotypes that differed from the control plants (CK). The full-length sequence of the lncRNA (named bra-miR156HG) was then obtained using RACE and transferred into A. thaliana. The transgenic plants displayed a delay in flowering time, an increasing number of rosette leaves, and a changed morphology of cauline leaves, which was similar to the plants that expressed bra-miR156a. In contrast, the overexpression of bra-miR156HG in B. campestris resulted in an increased tip angle of leaves and changed the length-width ratio of leaves at different nodes, suggesting that bra-miR156HG may be involved in regulating the leaf morphology. Collectively, our study showed that bra-miR156HG functions as a precursor of bra-miR156a involved in regulating plant flowering time and leaf development under different biological backgrounds. The secondary structure of lncRNA is essential not only for the normal roles that it plays but also for expanding the functional diversities.
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Affiliation(s)
- Dong Zhou
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310000, China
| | - Shengke Zhao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310000, China
| | - Huiyan Zhou
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310000, China
| | - Jingwen Chen
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310000, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310000, China.
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Sheng N, Huang L, Gao L, Cao Y, Xie X, Wang Y. A Survey of Computational Methods and Databases for lncRNA-MiRNA Interaction Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:2810-2826. [PMID: 37030713 DOI: 10.1109/tcbb.2023.3264254] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are two prevalent non-coding RNAs in current research. They play critical regulatory roles in the life processes of animals and plants. Studies have shown that lncRNAs can interact with miRNAs to participate in post-transcriptional regulatory processes, mainly involved in regulating cancer development, metastatic progression, and drug resistance. Additionally, these interactions have significant effects on plant growth, development, and responses to biotic and abiotic stresses. Deciphering the potential relationships between lncRNAs and miRNAs may provide new insights into our understanding of the biological functions of lncRNAs and miRNAs, and the pathogenesis of complex diseases. In contrast, gathering information on lncRNA-miRNA interactions (LMIs) through biological experiments is expensive and time-consuming. With the accumulation of multi-omics data, computational models are extremely attractive in systematically exploring potential LMIs. To the best of our knowledge, this is the first comprehensive review of computational methods for identifying LMIs. Specifically, we first summarized the available public databases for predicting animal and plant LMIs. Second, we comprehensively reviewed the computational methods for predicting LMIs and classified them into two categories, including network-based methods and sequence-based methods. Third, we analyzed the standard evaluation methods and metrics used in LMI prediction. Finally, we pointed out some problems in the current study and discuss future research directions. Relevant databases and the latest advances in LMI prediction are summarized in a GitHub repository https://github.com/sheng-n/lncRNA-miRNA-interaction-methods, and we'll keep it updated.
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Rehman OU, Uzair M, Farooq MS, Saleem B, Attacha S, Attia KA, Farooq U, Fiaz S, El-Kallawy WH, Kimiko I, Khan MR. Comprehensive insights into the regulatory mechanisms of lncRNA in alkaline-salt stress tolerance in rice. Mol Biol Rep 2023; 50:7381-7392. [PMID: 37450076 DOI: 10.1007/s11033-023-08648-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Alkaline-salt is one of the abiotic stresses that slows plant growth and developmental processes and threatens crop yield. Long non-coding RNAs (lncRNAs) are endogenous RNA found in plants that engage in a variety of cellular functions and stress responses. METHOD lncRNAs act as competing endogenous RNAs (ceRNA) and constitute a new set of gene control. The precise regulatory mechanism by which lncRNAs function as ceRNAs in response to alkaline-salt stress remains unclear. We identified alkaline-salt responsive lncRNAs using transcriptome-wide analysis of two varieties including alkaline-salt tolerant [WD20342 (WD)] and alkaline-salt sensitive [Caidao (CD)] rice cultivar under control and alkaline-salt stress treated [WD20342 (WDT, and Caidao (CDT)] conditions. RESULTS Investigating the competitive relationships between mRNAs and lncRNAs, we next built a ceRNA network involving lncRNAs based on the ceRNA hypothesis. Expression profiles revealed that a total of 65, 34, and 1549 differentially expressed (DE) lncRNAs, miRNAs, and mRNAs were identified in alkaline-salt tolerant WD (Control) vs. WDT (Treated). Similarly, 75 DE-lncRNAs, 34 DE-miRNAs, and 1725 DE-mRNAs (including up-regulated and down-regulated) were identified in alkaline-salt sensitive CD (Control) vs. CDT (Treated), respectively. An alkaline-salt stress ceRNA network discovered 321 lncRNA-miRNA-mRNA triplets in CD and CDT, with 32 lncRNAs, 121 miRNAs, and 111 mRNAs. Likewise, 217 lncRNA-miRNA-mRNA triplets in WD and WDT revealed the NONOSAT000455-osa_miR5809b-LOC_Os11g01210 triplet with the highest degree as a hub node with the most significant positive correlation in alkaline-salt stress response. CONCLUSION The results of our investigation indicate that osa-miR5809b is dysregulated and plays a part in regulating the defense response of rice against alkaline-salt stress. Our study highlights the regulatory functions of lncRNAs acting as ceRNAs in the mechanisms underlying alkaline-salt resistance in rice.
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Affiliation(s)
- Obaid Ur Rehman
- Food Science and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan.
| | - Muhammad Shahbaz Farooq
- Food Science and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Bilal Saleem
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Safira Attacha
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Kotb A Attia
- Department of Biochemistry, Science College, King Saud University, POX, Riyadh, 2455-11451, Saudi Arabia.
| | - Umer Farooq
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan
| | - Wael H El-Kallawy
- Agriculture Research Center, (ARC), Rice Research and Training Center, (RRTC) Sakha, Field Crop Research Institute, Sakha, Egypt
| | - Itoh Kimiko
- Institute of Science and Technology, Niigata University, Ikarashi-2, Nishi-ku, Niigata, 950-2181, Japan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, 45500, Pakistan.
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14
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Farzaneh M, Abouali Gale Dari M, Anbiyaiee A, Najafi S, Dayer D, Mousavi Salehi A, Keivan M, Ghafourian M, Uddin S, Azizidoost S. Emerging roles of the long non-coding RNA NEAT1 in gynecologic cancers. J Cell Commun Signal 2023; 17:531-547. [PMID: 37310654 PMCID: PMC10409959 DOI: 10.1007/s12079-023-00746-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/10/2023] [Indexed: 06/14/2023] Open
Abstract
Gynecologic cancers are a worldwide problem among women. Recently, molecular targeted therapy opened up an avenue for cancer diagnosis and treatment. Long non-coding RNAs (lncRNAs) are RNA molecules (> 200 nt) that are not translated into protein, and interact with DNA, RNA, and proteins. LncRNAs were found to play pivotal roles in cancer tumorigenesis and progression. Nuclear paraspeckle assembly transcript 1 (NEAT1) is a lncRNA that mediates cell proliferation, migration, and EMT in gynecologic cancers by targeting several miRNAs/mRNA axes. Therefore, NEAT1 may function as a potent biomarker for the prediction and treatment of breast, ovarian, cervical, and endometrial cancers. In this narrative review, we summarized various NEAT1-related signaling pathways that are critical in gynecologic cancers. Long non-coding RNA (lncRNA) by targeting various signaling pathways involved in its target genes can regulate the occurrence of gynecologic cancers.
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Affiliation(s)
- Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mahrokh Abouali Gale Dari
- Department of Obstetrics and Gynecology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Amir Anbiyaiee
- Department of Surgery, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Dian Dayer
- Fertility and Infertility Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Abdolah Mousavi Salehi
- Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mona Keivan
- Department of Immunology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mehri Ghafourian
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, 3050, Doha, Qatar
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh 22602 India
| | - Shirin Azizidoost
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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15
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Dey A. Structural Modifications and Novel Protein-Binding Sites in Pre-miR-675-Explaining Its Regulatory Mechanism in Carcinogenesis. Noncoding RNA 2023; 9:45. [PMID: 37624037 PMCID: PMC10457854 DOI: 10.3390/ncrna9040045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Pre-miR-675 is a microRNA expressed from the exon 1 of H19 long noncoding RNA, and the atypical expression of pre-miR-675 has been linked with several diseases and disorders including cancer. To execute its function inside the cell, pre-miR-675 is folded into a particular conformation, which aids in its interaction with several other biological molecules. However, the exact folding dynamics of pre-miR-675 and its protein-binding motifs are currently unknown. Moreover, how H19 lncRNA and pre-miR-675 crosstalk and modulate each other's activities is also unclear. The detailed structural analysis of pre-miR-675 in this study determines its earlier unknown conformation and identifies novel protein-binding sites on pre-miR-675, thus making it an excellent therapeutic target against cancer. Co-folding analysis between H19 lncRNA and pre-miR-675 determine structural transformations in pre-miR-675, thus describing the earlier unknown mechanism of interaction between these two molecules. Comprehensively, this study details the conformation of pre-miR-675 and its protein-binding sites and explains its relationship with H19 lncRNA, which can be interpreted to understand the role of pre-miR-675 in the development and progression of tumorigenesis and designing new therapeutics against cancers.
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Affiliation(s)
- Abhishek Dey
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER-R)-Raebareli, Lucknow 226002, India
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16
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Bhattacharjee R, Prabhakar N, Kumar L, Bhattacharjee A, Kar S, Malik S, Kumar D, Ruokolainen J, Negi A, Jha NK, Kesari KK. Crosstalk between long noncoding RNA and microRNA in Cancer. Cell Oncol (Dordr) 2023; 46:885-908. [PMID: 37245177 PMCID: PMC10356678 DOI: 10.1007/s13402-023-00806-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2023] [Indexed: 05/29/2023] Open
Abstract
miRNAs and lncRNAs play a central role in cancer-associated gene regulations. The dysregulated expression of lncRNAs has been reported as a hallmark of cancer progression, acting as an independent prediction marker for an individual cancer patient. The interplay of miRNA and lncRNA decides the variation of tumorigenesis that could be mediated by acting as sponges for endogenous RNAs, regulating miRNA decay, mediating intra-chromosomal interactions, and modulating epigenetic components. This paper focuses on the influence of crosstalk between lncRNA and miRNA on cancer hallmarks such as epithelial-mesenchymal transition, hijacking cell death, metastasis, and invasion. Other cellular roles of crosstalks, such as neovascularization, vascular mimicry, and angiogenesis were also discussed. Additionally, we reviewed crosstalk mechanism with specific host immune responses and targeting interplay (between lncRNA and miRNA) in cancer diagnosis and management.
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Affiliation(s)
- Rahul Bhattacharjee
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Neeraj Prabhakar
- Centre for Structural System Biology, Department of Physics, University of Hamburg, c/o DESY, Building 15, Notkestr. 852267, Hamburg, Germany
- Pharmacy, Abo Akademi University, Tykistökatu 6A, Turku, Finland
| | - Lamha Kumar
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, India
| | - Arkadyuti Bhattacharjee
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Sulagna Kar
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Sumira Malik
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi, Jharkhand, 834001, India
| | - Dhruv Kumar
- School of Health Sciences and Technology (SoHST), UPES University, Dehradun, Uttarakhand, India
| | - Janne Ruokolainen
- Department of Applied Physics, School of Science, Aalto University, Espoo, 00076, Finland
| | - Arvind Negi
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, Espoo, 00076, Finland.
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering and Technology (SET), Sharda University, Greater Noida, 201310, UP, India.
- School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, 144411, India.
- Department of Biotechnology, School of Applied & Life Sciences (SALS), Uttaranchal University, Dehradun, 248007, India.
| | - Kavindra Kumar Kesari
- Department of Applied Physics, School of Science, Aalto University, Espoo, 00076, Finland.
- Faculty of Biological and Environmental Sciences, University of Helsinki, Biocentre 3, Helsinki, Finland.
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17
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Alsaab HO. Pathological role of long non-coding (lnc) RNA in the regulation of Wnt/β-catenin signaling pathway during epithelial-mesenchymal transition (EMT). Pathol Res Pract 2023; 248:154566. [PMID: 37285735 DOI: 10.1016/j.prp.2023.154566] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023]
Abstract
The term "epithelial-mesenchymal transition" (EMT) describes a biological process wherein epithelial cells acquire mesenchymal cell characteristics. This process enables the metastatic cells to migrate and invasion. Recent studies have established the connections between the EMT process and Wnt/β-catenin signaling in cancer. Key cellular functions such as differentiation, proliferation, migration, genetic stability, apoptosis, and stem cell renewal are modulated via Wnt/ β-catenin signaling pathway. Up-regulation of this evolutionarily conserved signal pathway leads to EMT. On the other hand, recent investigations have indicated that non-coding RNAs including microRNAs (miRNAs) and long non-coding RNA (lncRNAs) are involved in regulating of Wnt/β-catenin pathway. A high level of lncRNAs mainly has a positive correlation with EMT. However, lncRNA down-regulation has been observed in promoting EMT. It seems that depending on the specific targets, up-or down-regulation of lncRNAs can stimulate EMT by activating the Wnt/ β-catenin pathway. The evaluation of interactions between lncRNAs and the Wnt/ β-catenin signaling pathway in the regulation of EMT during metastasis can be fascinating. Herein, for the first time, the crucial role of lncRNAs-mediated regulation of the Wnt/ β-catenin signaling pathway in the EMT process of human tumors has been summarized.
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Affiliation(s)
- Hashem O Alsaab
- Pharmaceutics and Pharmaceutical Technology, Taif University, Taif, Saudi Arabia.
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18
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Singh A, AT V, Gupta K, Sharma S, Kumar S. Long non-coding RNA and microRNA landscape of two major domesticated cotton species. Comput Struct Biotechnol J 2023; 21:3032-3044. [PMID: 37266406 PMCID: PMC10229759 DOI: 10.1016/j.csbj.2023.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/03/2023] Open
Abstract
Allotetraploid cotton plants Gossypium hirsutum and Gossypium barbadense have been widely cultivated for their natural, renewable textile fibres. Even though ncRNAs in domesticated cotton species have been extensively studied, systematic identification and annotation of lncRNAs and miRNAs expressed in various tissues and developmental stages under various biological contexts are limited. This influences the comprehension of their functions and future research on these cotton species. Here, we report high confidence lncRNAs and miRNA collection from G. hirsutum accession and G. barbadense accession using large-scale RNA-seq and small RNA-seq datasets incorporated into a user-friendly database, CoNCRAtlas. This database provides a wide range and depth of lncRNA and miRNA annotation based on the systematic integration of extensive annotations such as expression patterns derived from transcriptome data analysis in thousands of samples, as well as multi-omics annotations. We assume this comprehensive resource will accelerate evolutionary and functional studies in ncRNAs and inform future breeding programs for cotton improvement. CoNCRAtlas is accessible at http://www.nipgr.ac.in/CoNCRAtlas/.
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Affiliation(s)
- Ajeet Singh
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
- Postdoctoral Associate, Ophthalmology, Baylor College of Medicine, Houston, TX, USA
| | - Vivek AT
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Kanika Gupta
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Shruti Sharma
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Shailesh Kumar
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
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19
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Yang X, Liu C, Tang Q, Zhang T, Wang L, Han L, Zhang J, Pei X. Identification of LncRNAs and Functional Analysis of ceRNA Related to Fatty Acid Synthesis during Flax Seed Development. Genes (Basel) 2023; 14:genes14050967. [PMID: 37239327 DOI: 10.3390/genes14050967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/01/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Flax is a flowering plant cultivated for its oil and contains various unsaturated fatty acids. Linseed oil is known as the "deep-sea fish oil" of plants, and is beneficial to brain and blood lipids, among other positive effects. Long non-coding RNAs (lncRNAs) play an important role in plant growth and development. There are not many studies assessing how lncRNAs are related to the fatty acid synthesis of flax. The relative oil contents of the seeds of the variety Heiya NO.14 (for fiber) and the variety Macbeth (for oil) were determined at 5 day, 10 day, 20 day, and 30 day after flowering. We found that 10-20 day is an important period for ALA accumulation in the Macbeth variety. The strand-specific transcriptome data were analyzed at these four time points, and a series of lncRNAs related to flax seed development were screened. A competing endogenous RNA (ceRNA) network was constructed and the accuracy of the network was verified using qRT-PCR. MSTRG.20631.1 could act with miR156 on the same target, squamosa promoter-binding-like protein (SPL), to influence fatty acid biosynthesis through a gluconeogenesis-related pathway during flax seed development. This study provides a theoretical basis for future studies assessing the potential functions of lncRNAs during seed development.
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Affiliation(s)
- Xinsen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Caiyue Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiaoling Tang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tianbao Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Limin Wang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Lida Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianping Zhang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Kumar B, Saha B, Jaiswal S, Angadi UB, Rai A, Iquebal MA. Genome-wide identification and characterization of tissue-specific non-coding RNAs in black pepper ( Piper nigrum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1079221. [PMID: 37008483 PMCID: PMC10060637 DOI: 10.3389/fpls.2023.1079221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/08/2023] [Indexed: 06/19/2023]
Abstract
Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are the two classes of non-coding RNAs (ncRNAs) present predominantly in plant cells and have various gene regulatory functions at pre- and post-transcriptional levels. Previously deemed as "junk", these ncRNAs have now been reported to be an important player in gene expression regulation, especially in stress conditions in many plant species. Black pepper, scientifically known as Piper nigrum L., despite being one of the most economically important spice crops, lacks studies related to these ncRNAs. From a panel of 53 RNA-Seq datasets of black pepper from six tissues, namely, flower, fruit, leaf, panicle, root, and stem of six black pepper cultivars, covering eight BioProjects across four countries, we identified and characterized a total of 6406 lncRNAs. Further downstream analysis inferred that these lncRNAs regulated 781 black pepper genes/gene products via miRNA-lncRNA-mRNA network interactions, thus working as competitive endogenous RNAs (ceRNAs). The interactions may be various mechanisms like miRNA-mediated gene silencing or lncRNAs acting as endogenous target mimics (eTMs) of the miRNAs. A total of 35 lncRNAs were also identified to be potential precursors of 94 miRNAs after being acted upon by endonucleases like Drosha and Dicer. Tissue-wise transcriptome analysis revealed 4621 circRNAs. Further, miRNA-circRNA-mRNA network analysis showed 432 circRNAs combining with 619 miRNAs and competing for the binding sites on 744 mRNAs in different black pepper tissues. These findings can help researchers to get a better insight to the yield regulation and responses to stress in black pepper in endeavor of higher production and improved breeding programs in black pepper varieties.
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Praveen A, Dubey S, Singh S, Sharma VK. Abiotic stress tolerance in plants: a fascinating action of defense mechanisms. 3 Biotech 2023; 13:102. [PMID: 36866326 PMCID: PMC9971429 DOI: 10.1007/s13205-023-03519-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
Climate fluctuation mediated abiotic stress consequences loss in crop yields. These stresses have a negative impact on plant growth and development by causing physiological and molecular changes. In this review, we have attempted to outline recent studies (5 years) associated with abiotic stress resistance in plants. We investigated the various factors that contribute to coping with abiotic challenges, such as transcription factors (TFs), microRNAs (miRNAs), epigenetic changes, chemical priming, transgenic breeding, autophagy, and non-coding RNAs. Stress responsive genes are regulated mostly by TFs, and these can be used to enhance stress resistance in plants. Plants express some miRNA during stress imposition that act on stress-related target genes to help them survive. Epigenetic alterations govern gene expression and facilitate stress tolerance. Chemical priming enhances growth in plants by modulating physiological parameters. Transgenic breeding enables identification of genes involved in precise plant responses during stressful situations. In addition to protein coding genes, non-coding RNAs also influence the growth of the plant by causing alterations at gene expression levels. For achieving sustainable agriculture for a rising world population, it is crucial to develop abiotic-resistant crops with anticipated agronomical traits. To achieve this objective, understanding the diverse mechanisms by which plants protect themselves against abiotic stresses is imperative. This review emphasizes on recent progress and future prospects for abiotic stress tolerance and productivity in plants.
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Affiliation(s)
- Afsana Praveen
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Yamuna Expressway, Sector 17A, Gautam Budh Nagar, Uttar Pradesh 203201 India
| | - Sonali Dubey
- National Botanical Research Institute, Uttar Pradesh, Lukhnow, 226001 India
| | - Shilpy Singh
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Yamuna Expressway, Sector 17A, Gautam Budh Nagar, Uttar Pradesh 203201 India
| | - Varun Kumar Sharma
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Yamuna Expressway, Sector 17A, Gautam Budh Nagar, Uttar Pradesh 203201 India
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22
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Long Non-Coding RNAs of Plants in Response to Abiotic Stresses and Their Regulating Roles in Promoting Environmental Adaption. Cells 2023; 12:cells12050729. [PMID: 36899864 PMCID: PMC10001313 DOI: 10.3390/cells12050729] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/10/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Abiotic stresses triggered by climate change and human activity cause substantial agricultural and environmental problems which hamper plant growth. Plants have evolved sophisticated mechanisms in response to abiotic stresses, such as stress perception, epigenetic modification, and regulation of transcription and translation. Over the past decade, a large body of literature has revealed the various regulatory roles of long non-coding RNAs (lncRNAs) in the plant response to abiotic stresses and their irreplaceable functions in environmental adaptation. LncRNAs are recognized as a class of ncRNAs that are longer than 200 nucleotides, influencing a variety of biological processes. In this review, we mainly focused on the recent progress of plant lncRNAs, outlining their features, evolution, and functions of plant lncRNAs in response to drought, low or high temperature, salt, and heavy metal stress. The approaches to characterize the function of lncRNAs and the mechanisms of how they regulate plant responses to abiotic stresses were further reviewed. Moreover, we discuss the accumulating discoveries regarding the biological functions of lncRNAs on plant stress memory as well. The present review provides updated information and directions for us to characterize the potential functions of lncRNAs in abiotic stresses in the future.
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23
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Nie H, Cheng C, Kong J, Li H, Hua J. Plant non-coding RNAs function in pollen development and male sterility. FRONTIERS IN PLANT SCIENCE 2023; 14:1109941. [PMID: 36875603 PMCID: PMC9975556 DOI: 10.3389/fpls.2023.1109941] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Male sterility is classified as either cytoplasmic male sterility (CMS) or genic male sterility (GMS). Generally, CMS involves mitochondrial genomes interacting with the nuclear genome, while GMS is caused by nuclear genes alone. Male sterility is regulated by multilevel mechanisms in which non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and phased small interfering RNAs (phasiRNAs), which have been proven to be critical elements. The development of high-throughput sequencing technology offers new opportunities to evaluate the genetic mechanism of ncRNAs in plant male sterility. In this review, we summarize the critical ncRNAs that regulate gene expression in ways dependent on or independent of hormones, which involve the differentiation of the stamen primordia, degradation of the tapetum, formation of microspores, and the release of pollen. In addition, the key mechanisms of the miRNA-lncRNA-mRNA interaction networks mediating male sterility in plants are elaborated. We present a different perspective on exploring the ncRNA-mediated regulatory pathways that control CMS in plants and create male-sterile lines through hormones or genome editing. A refined understanding of the ncRNA regulatory mechanisms in plant male sterility for the development of new sterile lines would be conducive to improve hybridization breeding.
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Affiliation(s)
- Hushuai Nie
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, China
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Cheng Cheng
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Huijing Li
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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Erdem MG, Unlu O, Demirci M. Could Long Non-Coding RNA MEG3 and PTENP1 Interact with miR-21 in the Pathogenesis of Non-Alcoholic Fatty Liver Disease? Biomedicines 2023; 11:biomedicines11020574. [PMID: 36831110 PMCID: PMC9953690 DOI: 10.3390/biomedicines11020574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
NAFLD is the most common cause of chronic liver disease worldwide. The miRNAs and lncRNAs are important endogenous ncRNAs families that can regulate molecular mechanisms. The aim of this study was to analyze the miRNA and lncRNA expression profiles in serum samples of NAFLD patients with different types of hepatosteatosis compared to healthy controls by the qPCR method. A total of180 NAFLD patients and 60 healthy controls were included. miRCURY LNA miRNA miRNome PCR human panel I + II kit and LncProfiler qPCR Array Kit were used to detect miRNA and lncRNA expression, respectively. DIANA miRPath and DIANA-lncBase web servers were used for interaction analysis. As a result, 75 miRNA and 24 lncRNA expression changes were determined. For miRNAs and lncRNAs, 30 and 5 were downregulated and 45 and 19 were upregulated, respectively. hsa-miR-21 was upregulated 2-fold whereas miR-197 was downregulated 0.25-fold. Among lncRNAs, NEAT1 was upregulated 2.9-fold while lncRNA MEG3 was downregulated 0.41-fold. A weak correlation was found between hsa-miR-122 and lncRNA MALAT1. As a conclusion, it is clear that lncRNA-miRNA interaction is involved in the molecular mechanisms of the emergence of NAFLD. The lncRNAs MEG3 and PTENP1 interacted with hsa-miR-21. It was thought that this interaction should be investigated as a biomarker for the development of NAFLD.
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Affiliation(s)
- Mustafa Genco Erdem
- Department of Internal Medicine, Faculty of Medicine, Beykent University, İstanbul 34398, Türkiye
| | - Ozge Unlu
- Department of Medical Microbiology, Faculty of Medicine, Istanbul Atlas University, İstanbul 34403, Türkiye
| | - Mehmet Demirci
- Department of Medical Microbiology, Faculty of Medicine, Kirklareli University, Kırklareli 39100, Türkiye
- Correspondence: ; Tel.: +90-(288)-444-40-39; Fax: +90-(288)-212-96-79
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25
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Long Noncoding RNA: A Novel Insight into the Pathogenesis of Acute Lung Injury. J Clin Med 2023; 12:jcm12020604. [PMID: 36675533 PMCID: PMC9861694 DOI: 10.3390/jcm12020604] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/03/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Acute lung injury (ALI) and its severe form, acute respiratory distress syndrome (ARDS), represent an acute stage of lung inflammation where the alveolar epithelium loses its functionality. ALI has a devastating impact on the population as it not only has a high rate of incidence, but also has high rates of morbidity and mortality. Due to the involvement of multiple factors, the pathogenesis of ALI is complex and is not fully understood yet. Long noncoding RNAs (lncRNAs) are a group of non-protein-coding transcripts longer than 200 nucleotides. Growing evidence has shown that lncRNAs have a decisive role in the pathogenesis of ALI. LncRNAs can either promote or hinder the development of ALI in various cell types in the lungs. Mechanistically, current studies have found that lncRNAs play crucial roles in the pathogenesis of ALI via the regulation of small RNAs (e.g., microRNAs) or downstream proteins. Undoubtedly, lncRNAs not only have the potential to reveal the underlying mechanisms of ALI pathogenesis but also serve as diagnostic and therapeutic targets for the therapy of ALI.
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Yang W, Bai Q, Li Y, Chen J, Liu C. Epigenetic modifications: Allusive clues of lncRNA functions in plants. Comput Struct Biotechnol J 2023; 21:1989-1994. [PMID: 36950220 PMCID: PMC10025020 DOI: 10.1016/j.csbj.2023.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 02/25/2023] [Accepted: 03/08/2023] [Indexed: 03/13/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been verified as flexible and important factors in various biological processes of multicellular eukaryotes, including plants. The respective intricate crosstalk among multiple epigenetic modifications has been examined to some extent. However, only a small proportion of lncRNAs has been functionally well characterized. Moreover, the relationship between lncRNAs and other epigenetic modifications has not been systematically studied. In this mini-review, we briefly summarize the representative biological functions of lncRNAs in developmental programs and environmental responses in plants. In addition, we particularly discuss the intimate relationship between lncRNAs and other epigenetic modifications, and we outline the underlying avenues and challenges for future research on plant lncRNAs.
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Affiliation(s)
- Wenjing Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quanzi Bai
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yan Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, China
- Corresponding author at: CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China.
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Ye Y, Fan X, Long Q, Wang J, Zhang W, Cai Z, Sun M, Gu X, Zou P, Chen D, Guo R. Comprehensive investigation and regulatory function of lncRNAs engaged in western honey bee larval immune response to Ascosphaera apis invasion. Front Physiol 2022; 13:1082522. [PMID: 36589426 PMCID: PMC9800914 DOI: 10.3389/fphys.2022.1082522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Ascosphaera apis is a fungal pathogen that exclusively infects bee larvae, causing chalkbrood disease, which results in severe damage for beekeeping industry. Long non-coding RNAs (lncRNAs) are versatile regulators in various biological processes such as immune defense and host-pathogen interaction. However, expression pattern and regulatory role of lncRNAs involved in immune response of bee host to A. apis invasion is still very limited. Here, the gut tissues of Apis mellifera ligustica 4-, 5-, and 6-day-old larvae inoculated by A. apis spores (AmT1, AmT2, and AmT3 groups) and corresponding un-inoculated larval guts (AmCK1, AmCK2, and AmCK3 groups) were prepared and subjected to deep sequencing, followed by identification of lncRNAs, analysis of differentially expressed lncRNAs (DElncRNAs), and investigation of competing endogenous RNA (ceRNA) network. In total, 3,746 A. m. ligustica lncRNAs were identified, including 78 sense lncRNAs, 891 antisense lncRNAs, 1,893 intergenic lncRNAs, 346 bidirectional lncRNAs, and 210 intronic lncRNAs. In the 4-, 5-, and 6- comparison groups, 357, 236, and 505 DElncRNAs were discovered. Additionally, 217, 129, and 272 DElncRNAs were respectively predicted to regulate neighboring genes via cis-acting manner, and these targets were associated with a series of GO terms and KEGG pathways of great importance, such as response to stimulus and Jak-STAT signaling pathway. Moreover, 197, 95, and 356 DElncRNAs were observed to target 10, eight, and 21 DEmiRNAs and further target 147, 79, and 315 DEmRNAs, forming complex regulatory networks. Further investigation suggested that these targets were engaged in several key cellular and humoral immune pathways, such as phagosome and MAPK signaling pathway. Ultimately, the expression trends of nine randomly selected DElncRNAs were verified by RT-qPCR, confirming the authenticity and reliability of our transcriptome data. Findings in this current work not only provide candidate DElncRNAs for functional study, but also lay a foundation for unclosing the mechanism underlying DElncRNA-regulated larval immune responses to A. apis invasion.
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Affiliation(s)
- Yaping Ye
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Qi Long
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jie Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wende Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zongbing Cai
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Minghui Sun
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaoyu Gu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Peiyuan Zou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Babaei S, Singh MB, Bhalla PL. Role of long non-coding RNAs in rice reproductive development. FRONTIERS IN PLANT SCIENCE 2022; 13:1040366. [PMID: 36457537 PMCID: PMC9705774 DOI: 10.3389/fpls.2022.1040366] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/28/2022] [Indexed: 05/13/2023]
Abstract
Rice is a staple crop, feeding over half of the global population. The future demand of population growth and climate change requires substantial rice improvement. Recent advances in rice genomics have highlighted the vital role of the non-coding part of the genome. The protein-coding regions account for only a tiny portion of the eukaryotic genome, and most of the genomic regions transcribe copious amounts of non-coding RNAs. Of these, the long non-coding RNAs, including linear non-coding RNAs (lncRNAs) and circular non-coding RNAs (circRNAs), have been shown to play critical roles in various developmental processes by regulating the expression of genes and functions of proteins at transcriptional, post-transcriptional and post-translational levels. With the advances in next-generation sequencing technologies, a substantial number of long non-coding RNAs have been found to be expressed in plant reproductive organs in a cell- and tissue-specific manner suggesting their reproductive development-related functions. Accumulating evidence points towards the critical role of these non-coding RNAs in flowering, anther, and pollen development, ovule and seed development and photoperiod and temperature regulation of male fertility. In this mini review, we provide a brief overview of the role of the linear and circular long non-coding RNAs in rice reproductive development and control of fertility and crop yield.
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Affiliation(s)
| | | | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
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29
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Zafar J, Huang J, Xu X, Jin F. Analysis of Long Non-Coding RNA-Mediated Regulatory Networks of Plutella xylostella in Response to Metarhizium anisopliae Infection. INSECTS 2022; 13:916. [PMID: 36292864 PMCID: PMC9604237 DOI: 10.3390/insects13100916] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) represent a diverse class of RNAs that are structurally similar to messenger RNAs (mRNAs) but do not encode proteins. Growing evidence suggests that in response to biotic and abiotic stresses, the lncRNAs play crucial regulatory roles in plants and animals. However, the potential role of lncRNAs during fungal infection has yet to be characterized in Plutella xylostella, a devastating pest of cruciferous crops. In the current study, we performed a strand-specific RNA sequencing of Metarhizium anisopliae-infected (Px36hT, Px72hT) and uninfected (Px36hCK, Px72hCK) P. xylostella fat body tissues. Comprehensive bioinformatic analysis revealed a total of 5665 and 4941 lncRNAs at 36 and 72-h post-infection (hpi), including 563 (Px36hT), 532 (Px72hT) known and 5102 (Px36hT), 4409 (Px72hT) novel lncRNA transcripts. These lncRNAs shared structural similarities with their counterparts in other species, including shorter exon and intron length, fewer exon numbers, and a lower expression profile than mRNAs. LncRNAs regulate the expression of neighboring protein-coding genes by acting in a cis and trans manner. Functional annotation and pathway analysis of cis-acting lncRNAs revealed their role in several immune-related genes, including Toll, serpin, transferrin, βGRP etc. Furthermore, we identified multiple lncRNAs acting as microRNA (miRNA) precursors. These miRNAs can potentially regulate the expression of mRNAs involved in immunity and development, suggesting a crucial lncRNA-miRNA-mRNA complex. Our findings will provide a genetic resource for future functional studies of lncRNAs involved in P. xylostella immune responses to M. anisopliae infection and shed light on understanding insect host-pathogen interactions.
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Affiliation(s)
| | | | - Xiaoxia Xu
- Correspondence: (X.X.); (F.J.); Tel.: +86-135-6047-8369 (F.J.)
| | - Fengliang Jin
- Correspondence: (X.X.); (F.J.); Tel.: +86-135-6047-8369 (F.J.)
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30
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Baruah C, Nath P, Barah P. LncRNAs in neuropsychiatric disorders and computational insights for their prediction. Mol Biol Rep 2022; 49:11515-11534. [PMID: 36097122 DOI: 10.1007/s11033-022-07819-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/20/2022] [Accepted: 07/24/2022] [Indexed: 12/06/2022]
Abstract
Long non-coding RNAs (lncRNAs) are 200 nucleotide extended transcripts that do not encode proteins or possess limited coding ability. LncRNAs epigenetically control several biological functions such as gene regulation, transcription, mRNA splicing, protein interaction, and genomic imprinting. Over the years, drastic progress in understanding the role of lncRNAs in diverse biological processes has been made. LncRNAs are reported to show tissue-specific expression patterns suggesting their potential as novel candidate biomarkers for diseases. Among all other non-coding RNAs, lncRNAs are highly expressed within the brain-enriched or brain-specific regions of the neural tissues. They are abundantly expressed in the neocortex and pre-mature frontal regions of the brain. LncRNAs are co-expressed with the protein-coding genes and have a significant role in the evolution of functions of the brain. Any deregulation in the lncRNAs contributes to disruptions in normal brain functions resulting in multiple neurological disorders. Neuropsychiatric disorders such as schizophrenia, bipolar disease, autism spectrum disorders, and anxiety are associated with the abnormal expression and regulation of lncRNAs. This review aims to highlight the understanding of lncRNAs concerning normal brain functions and their deregulation associated with neuropsychiatric disorders. We have also provided a survey on the available computational tools for the prediction of lncRNAs, their protein coding potentials, and sub-cellular locations, along with a section on existing online databases with known lncRNAs, and their interactions with other molecules.
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Affiliation(s)
- Cinmoyee Baruah
- Department of Molecular Biology and Biotechnology, Tezpur University, 784028, Napaam, Sonitpur, Assam, India
| | - Prangan Nath
- Department of Molecular Biology and Biotechnology, Tezpur University, 784028, Napaam, Sonitpur, Assam, India
| | - Pankaj Barah
- Department of Molecular Biology and Biotechnology, Tezpur University, 784028, Napaam, Sonitpur, Assam, India.
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Zhao Z, Zang S, Zou W, Pan YB, Yao W, You C, Que Y. Long Non-Coding RNAs: New Players in Plants. Int J Mol Sci 2022; 23:ijms23169301. [PMID: 36012566 PMCID: PMC9409372 DOI: 10.3390/ijms23169301] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
During the process of growth and development, plants are prone to various biotic and abiotic stresses. They have evolved a variety of strategies to resist the adverse effects of these stresses. lncRNAs (long non-coding RNAs) are a type of less conserved RNA molecules of more than 200 nt (nucleotides) in length. lncRNAs do not code for any protein, but interact with DNA, RNA, and protein to affect transcriptional, posttranscriptional, and epigenetic modulation events. As a new regulatory element, lncRNAs play a critical role in coping with environmental pressure during plant growth and development. This article presents a comprehensive review on the types of plant lncRNAs, the role and mechanism of lncRNAs at different molecular levels, the coordination between lncRNA and miRNA (microRNA) in plant immune responses, the latest research progress of lncRNAs in plant growth and development, and their response to biotic and abiotic stresses. We conclude with a discussion on future direction for the elaboration of the function and mechanism of lncRNAs.
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Affiliation(s)
- Zhennan Zhao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yong-Bao Pan
- Sugarcane Research Unit, USDA-ARS, Houma, LA 70360, USA
| | - Wei Yao
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi University, Nanning 530005, China
| | - Cuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (C.Y.); (Y.Q.); Tel.: +86-591-8385-2547 (C.Y. & Y.Q.)
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (C.Y.); (Y.Q.); Tel.: +86-591-8385-2547 (C.Y. & Y.Q.)
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Dey SS, Sharma PK, Munshi AD, Jaiswal S, Behera TK, Kumari K, G. B, Iquebal MA, Bhattacharya RC, Rai A, Kumar D. Genome wide identification of lncRNAs and circRNAs having regulatory role in fruit shelf life in health crop cucumber ( Cucumis sativus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:884476. [PMID: 35991462 PMCID: PMC9383263 DOI: 10.3389/fpls.2022.884476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Cucumber is an extremely perishable vegetable; however, under room conditions, the fruits become unfit for consumption 2-3 days after harvesting. One natural variant, DC-48 with an extended shelf-life was identified, fruits of which can be stored up to 10-15 days under room temperature. The genes involved in this economically important trait are regulated by non-coding RNAs. The study aims to identify the long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) by taking two contrasting genotypes, DC-48 and DC-83, at two different fruit developmental stages. The upper epidermis of the fruits was collected at 5 days and 10 days after pollination (DAP) for high throughput RNA sequencing. The differential expression analysis was performed to identify differentially expressed (DE) lncRNAs and circRNAs along with the network analysis of lncRNA, miRNA, circRNA, and mRNA interactions. A total of 97 DElncRNAs were identified where 18 were common under both the developmental stages (8 down regulated and 10 upregulated). Based on the back-spliced reads, 238 circRNAs were found to be distributed uniformly throughout the cucumber genomes with the highest numbers (71) in chromosome 4. The majority of the circRNAs (49%) were exonic in origin followed by inter-genic (47%) and intronic (4%) origin. The genes related to fruit firmness, namely, polygalacturonase, expansin, pectate lyase, and xyloglucan glycosyltransferase were present in the target sites and co-localized networks indicating the role of the lncRNA and circRNAs in their regulation. Genes related to fruit ripening, namely, trehalose-6-phosphate synthase, squamosa promoter binding protein, WRKY domain transcription factors, MADS box proteins, abscisic stress ripening inhibitors, and different classes of heat shock proteins (HSPs) were also found to be regulated by the identified lncRNA and circRNAs. Besides, ethylene biosynthesis and chlorophyll metabolisms were also found to be regulated by DElncRNAs and circRNAs. A total of 17 transcripts were also successfully validated through RT PCR data. These results would help the breeders to identify the complex molecular network and regulatory role of the lncRNAs and circRNAs in determining the shelf-life of cucumbers.
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Affiliation(s)
- Shyam S. Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Parva Kumar Sharma
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - A. D. Munshi
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - T. K. Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Khushboo Kumari
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Boopalakrishnan G.
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Zhang H, Liu Z, Hu A, Wu H, Zhu J, Wang F, Cao P, Yang X, Zhang H. Full-Length Transcriptome Analysis of the Halophyte Nitraria sibirica Pall. Genes (Basel) 2022; 13:genes13040661. [PMID: 35456467 PMCID: PMC9032868 DOI: 10.3390/genes13040661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Nitraria sibirica Pall. is one of the pioneer tree species in saline–alkali areas due to its extreme salt tolerance. However, the lack of information on its genome limits the further exploration of the molecular mechanisms in N. sibirica under salt stress. Methods: In this study, we used single-molecule real-time (SMRT) technology based on the PacBio Iso-Seq platform to obtain transcriptome data from N. sibirica under salt treatment for the first time, which is helpful for our in-depth analysis of the salt tolerance and molecular characteristics of N. sibirica. Results: Our results suggested that a total of 234,508 circular consensus sequences (CCSs) with a mean read length of 2121 bp were obtained from the 19.26 Gb raw data. Furthermore, based on transcript cluster analysis, 93,713 consensus isoforms were obtained, including 92,116 high-quality isoforms. After removing redundant sequences, 49,240 non-redundant transcripts were obtained from high-quality isoforms. A total of 37,261 SSRs, 1816 LncRNAs and 47,314 CDSs, of which 40,160 carried complete ORFs, were obtained. Based on our transcriptome data, we also analyzed the coding genes of H+-PPase, and the results of both bioinformatics and functional analyses indicated that the gene prediction via full-length transcripts obtained by SMRT technology is reliable and effective. In summary, our research data obtained by SMRT technology provides more reliable and accurate information for the further analysis of the regulatory network and molecular mechanism of N. sibirica under salt stress.
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Affiliation(s)
- Huilong Zhang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, Dongying 257000, China
| | - Zhen Liu
- Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou 061001, China
- Academy of Agriculture and Forestry Sciences, Cangzhou 061001, China
| | - Aishuang Hu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, China
- Institute of Coastal Agriculture, Hebei Academy of Agriculture and Forestry Sciences, Tangshan 063299, China
| | - Haiwen Wu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, Dongying 257000, China
| | - Jianfeng Zhu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, Dongying 257000, China
| | - Fengzhi Wang
- Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou 061001, China
- Academy of Agriculture and Forestry Sciences, Cangzhou 061001, China
| | - Pingping Cao
- Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou 061001, China
- Academy of Agriculture and Forestry Sciences, Cangzhou 061001, China
| | - Xiuyan Yang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, Dongying 257000, China
| | - Huaxin Zhang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing 100091, China
- The Comprehensive Experimental Center of Chinese Academy of Forestry in Yellow River Delta, Dongying 257000, China
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Ma X, Zhao F, Zhou B. The Characters of Non-Coding RNAs and Their Biological Roles in Plant Development and Abiotic Stress Response. Int J Mol Sci 2022; 23:ijms23084124. [PMID: 35456943 PMCID: PMC9032736 DOI: 10.3390/ijms23084124] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 02/07/2023] Open
Abstract
Plant growth and development are greatly affected by the environment. Many genes have been identified to be involved in regulating plant development and adaption of abiotic stress. Apart from protein-coding genes, more and more evidence indicates that non-coding RNAs (ncRNAs), including small RNAs and long ncRNAs (lncRNAs), can target plant developmental and stress-responsive mRNAs, regulatory genes, DNA regulatory regions, and proteins to regulate the transcription of various genes at the transcriptional, posttranscriptional, and epigenetic level. Currently, the molecular regulatory mechanisms of sRNAs and lncRNAs controlling plant development and abiotic response are being deeply explored. In this review, we summarize the recent research progress of small RNAs and lncRNAs in plants, focusing on the signal factors, expression characters, targets functions, and interplay network of ncRNAs and their targets in plant development and abiotic stress responses. The complex molecular regulatory pathways among small RNAs, lncRNAs, and targets in plants are also discussed. Understanding molecular mechanisms and functional implications of ncRNAs in various abiotic stress responses and development will benefit us in regard to the use of ncRNAs as potential character-determining factors in molecular plant breeding.
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Affiliation(s)
- Xu Ma
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Ministry of Education, Harbin 150040, China;
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Fei Zhao
- Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
- Correspondence: (F.Z.); (B.Z.); Tel.: +86-0538-8243-965 (F.Z.); +86-0451-8219-1738 (B.Z.)
| | - Bo Zhou
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Ministry of Education, Harbin 150040, China;
- College of Life Science, Northeast Forestry University, Harbin 150040, China
- Correspondence: (F.Z.); (B.Z.); Tel.: +86-0538-8243-965 (F.Z.); +86-0451-8219-1738 (B.Z.)
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Ku YS, Cheung MY, Cheng SS, Nadeem MA, Chung G, Lam HM. Using the Knowledge of Post-transcriptional Regulations to Guide Gene Selections for Molecular Breeding in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:867731. [PMID: 35432392 PMCID: PMC9009170 DOI: 10.3389/fpls.2022.867731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
The omics approaches allow the scientific community to successfully identify genomic regions associated with traits of interest for marker-assisted breeding. Agronomic traits such as seed color, yield, growth habit, and stress tolerance have been the targets for soybean molecular breeding. Genes governing these traits often undergo post-transcriptional modifications, which should be taken into consideration when choosing elite genes for molecular breeding. Post-transcriptional regulations of genes include transcript regulations, protein modifications, and even the regulation of the translational machinery. Transcript regulations involve elements such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) for the maintenance of transcript stability or regulation of translation efficiency. Protein modifications involve molecular modifications of target proteins and the alterations of their interacting partners. Regulations of the translational machinery include those on translation factors and the ribosomal protein complex. Post-transcriptional regulations usually involve a set of genes instead of a single gene. Such a property may facilitate molecular breeding. In this review, we will discuss the post-transcriptional modifications of genes related to favorable agronomic traits such as stress tolerance, growth, and nutrient uptake, using examples from soybean as well as other crops. The examples from other crops may guide the selection of genes for marker-assisted breeding in soybean.
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Affiliation(s)
- Yee-Shan Ku
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Yan Cheung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Sau-Shan Cheng
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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Zhou D, Chen C, Jin Z, Chen J, Lin S, Lyu T, Liu D, Xiong X, Cao J, Huang L. Transcript Profiling Analysis and ncRNAs' Identification of Male-Sterile Systems of Brassica campestris Reveal New Insights Into the Mechanism Underlying Anther and Pollen Development. FRONTIERS IN PLANT SCIENCE 2022; 13:806865. [PMID: 35211139 PMCID: PMC8861278 DOI: 10.3389/fpls.2022.806865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Male-sterile mutants are useful materials to study the anther and pollen development. Here, whole transcriptome sequencing was performed for inflorescences in three sterile lines of Chinese cabbage (Brassica campestris L. ssp. chinensis Makino, syn. B. rapa ssp. chinensis), the genic male-sterile line (A line), the Polima cytoplasmic male-sterile (CMS) line (P line), and the Ogura CMS line (O line) along with their maintainer line (B line). In total, 7,136 differentially expressed genes (DEGs), 361 differentially expressed long non-coding RNAs (lncRNAs) (DELs), 56 differentially expressed microRNAs (miRNAs) (DEMs) were selected out. Specific regulatory networks related to anther cell differentiation, meiosis cytokinesis, pollen wall formation, and tapetum development were constructed based on the abortion characteristics of male-sterile lines. Candidate genes and lncRNAs related to cell differentiation were identified in sporocyteless P line, sixteen of which were common to the DEGs in Arabidopsis spl/nzz mutant. Genes and lncRNAs concerning cell plate formation were selected in A line that is defected in meiosis cytokinesis. Also, the orthologs of pollen wall formation and tapetum development genes in Arabidopsis showed distinct expression patterns in the three different sterile lines. Among 361 DELs, 35 were predicted to interact with miRNAs, including 28 targets, 47 endogenous target mimics, and five precursors for miRNAs. Two lncRNAs were further proved to be functional precursors for bra-miR156 and bra-miR5718, respectively. Overexpression of bra-miR5718HG in B. campestris slowed down the growth of pollen tubes, caused shorter pollen tubes, and ultimately affected the seed set. Our study provides new insights into molecular regulation especially the ncRNA interaction during pollen development in Brassica crops.
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Affiliation(s)
- Dong Zhou
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Caizhi Chen
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Zongmin Jin
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Jingwen Chen
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Sue Lin
- Institute of Life Sciences, Wenzhou University, Wenzhou, China
| | - Tao Lyu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Dandan Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Xinpeng Xiong
- College of Bioengineering, Jingchu University of Technology, Jingmen, China
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
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Liu J, Chang C. Concerto on Chromatin: Interplays of Different Epigenetic Mechanisms in Plant Development and Environmental Adaptation. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122766. [PMID: 34961235 PMCID: PMC8705648 DOI: 10.3390/plants10122766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 05/26/2023]
Abstract
Epigenetic mechanisms such as DNA methylation, histone post-translational modifications, chromatin remodeling, and noncoding RNAs, play important roles in regulating plant gene expression, which is involved in various biological processes including plant development and stress responses. Increasing evidence reveals that these different epigenetic mechanisms are highly interconnected, thereby contributing to the complexity of transcriptional reprogramming in plant development processes and responses to environmental stresses. Here, we provide an overview of recent advances in understanding the epigenetic regulation of plant gene expression and highlight the crosstalk among different epigenetic mechanisms in making plant developmental and stress-responsive decisions. Structural, physical, transcriptional and metabolic bases for these epigenetic interplays are discussed.
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Khoei MA, Karimi M, Karamian R, Amini S, Soorni A. Identification of the Complex Interplay Between Nematode-Related lncRNAs and Their Target Genes in Glycine max L. FRONTIERS IN PLANT SCIENCE 2021; 12:779597. [PMID: 34956274 PMCID: PMC8705754 DOI: 10.3389/fpls.2021.779597] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/08/2021] [Indexed: 05/26/2023]
Abstract
Soybean (Glycine max) is a major plant protein source and oilseed crop. However, plant-parasitic nematodes (PPNs) affect its annual yield. In the current study, in order to better understand the regulation of defense mechanism against PPNs in soybean, we investigated the role of long non-coding RNAs (lncRNAs) in response to two nematode species, Heterodera glycines (SCN: soybean cyst nematode) and Rotylenchulus reniformis (reniform). To this end, two publicly available RNA-seq data sets (SCN data set and RAD: reniform-associated data set) were employed to discover the lncRNAome profile of soybean under SCN and reniform infection, respectively. Upon identification of unannotated transcripts in these data sets, a seven-step pipeline was utilized to sieve these transcripts, which ended up in 384 and 283 potential lncRNAs in SCN data set and RAD, respectively. These transcripts were then used to predict cis and trans nematode-related targets in soybean genome. Computational prediction of target genes function, some of which were also among differentially expressed genes, revealed the involvement of putative nematode-responsive genes as well as enrichment of multiple stress responses in both data sets. Finally, 15 and six lncRNAs were proposed to be involved in microRNA-mediated regulation of gene expression in soybean in response to SNC and reniform infection, respectively. Collectively, this study provides a novel insight into the signaling and regulatory network of soybean-pathogen interactions and opens a new window for further research.
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Affiliation(s)
| | | | - Roya Karamian
- Department of Biology, Faculty of Sciences, Bu-Ali Sina University, Hamedan, Iran
| | | | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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Expression Patterns and Regulation of Non-Coding RNAs during Synthesis of Cellulose in Eucalyptus grandis Hill. FORESTS 2021. [DOI: 10.3390/f12111565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cellulose, an essential structural component in the plant cell wall and a renewable biomass resource, plays a significant role in nature. Eucalyptus’s excellent timber tree species (including Eucalyptus grandis Hill) provide many raw materials for the paper and wood industries. The synthesis of cellulose is a very complex process involving multiple genes and regulated by various biological networks. However, research on regulating associated genes and non-coding RNAs during cellulose synthesis in E. grandis remains lacking. In this study, the wood anatomical characteristics and chemical indexes of E. grandis were analyzed by taking three different parts (diameter at breast height (DBH), middle and upper part of the trunk) from the main stem of E. grandis as raw materials. The role of non-coding RNAs (Long non-coding RNA, lncRNA; Micro RNA, miRNA; Circle RNA, circRNA) on regulating candidate genes was presented, and the network map of ceRNA (Competing endogenous RNA) regulation during wood cellulose biosynthesis of E. grandis was constructed. The transcriptome sequencing of nine samples obtained from the trunk of the immature xylem in E. grandis at DBH, middle and upper parts had a 95.81 G clean reading, 57,480 transcripts, 7365 lncRNAs, and 5180 circRNAs. Each sample had 172–306 known miRNAs and 1644–3508 new miRNAs. A total of 190 DE-lncRNAs (Differentially expressed long non-coding RNAs), 174 DE-miRNAs (Differentially expressed micro RNAs), and 270 DE-circRNAs (Differentially expressed circle RNAs) were obtained by comparing transcript expression levels. Four lncRNAs and nine miRNAs were screened out, and the ceRNA regulatory network was constructed. LncRNA1 and lncRNA4 regulated the genes responsible for cellulose synthesis in E. grandis, which were overexpressed in 84K (Populus Alba × Populus glandulosa) poplar. The cellulose and lignin content in lncRNA4-oe were significantly higher than wild type 84K poplar and lncRNA1-oe. The average plant height, middle and basal part of the stem diameter in lncRNA4-oe were significantly higher than the wild type. However, there was no significant difference between the growth of lncRNA1-oe and the wild type. Further studies are warranted to explore the molecular regulatory mechanism of cellulose biosynthesis in Eucalyptus species.
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Waterlogging-Stress-Responsive LncRNAs, Their Regulatory Relationships with miRNAs and Target Genes in Cucumber ( Cucumis sativus L.). Int J Mol Sci 2021; 22:ijms22158197. [PMID: 34360961 PMCID: PMC8348067 DOI: 10.3390/ijms22158197] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022] Open
Abstract
Low oxygen level is a phenomenon often occurring during the cucumber cultivation period. Genes involved in adaptations to stress can be regulated by non-coding RNA. The aim was the identification of long non-coding RNAs (lncRNAs) involved in the response to long-term waterlogging stress in two cucumber haploid lines, i.e., DH2 (waterlogging tolerant—WL-T) and DH4 (waterlogging sensitive—WL-S). Plants, at the juvenile stage, were waterlogged for 7 days (non-primed, 1xH), and after a 14-day recovery period, plants were stressed again for another 7 days (primed, 2xH). Roots were collected for high-throughput RNA sequencing. Implementation of the bioinformatic pipeline made it possible to determine specific lncRNAs for non-primed and primed plants of both accessions, highlighting differential responses to hypoxia stress. In total, 3738 lncRNA molecules were identified. The highest number (1476) of unique lncRNAs was determined for non-primed WL-S plants. Seventy-one lncRNAs were depicted as potentially being involved in acquiring tolerance to hypoxia in cucumber. Understanding the mechanism of gene regulation under long-term waterlogging by lncRNAs and their interactions with miRNAs provides sufficient information in terms of adaptation to the oxygen deprivation in cucumber. To the best of our knowledge, this is the first report concerning the role of lncRNAs in the regulation of long-term waterlogging tolerance by priming application in cucumber.
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