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Cheng B, Pei W, Wan K, Pan R, Zhang W. LncRNA cis- and trans-regulation provides new insight into drought stress responses in wild barley. PHYSIOLOGIA PLANTARUM 2024; 176:e14424. [PMID: 38973627 DOI: 10.1111/ppl.14424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/11/2024] [Accepted: 06/20/2024] [Indexed: 07/09/2024]
Abstract
Drought is one of the most common abiotic stresses that affect barley productivity. Long noncoding RNA (lncRNA) has been reported to be widely involved in abiotic stress, however, its function in the drought stress response in wild barley remains unclear. In this study, RNA sequencing was performed to identify differentially expressed lncRNAs (DElncRNA) among two wild barley and two cultivated barley genotypes. Then, the cis-regulatory networks were according to the chromosome position and the expression level correction. The GO annotation indicates that these cis-target genes are mainly involved in "ion transport transporter activity" and "metal ion transport transporter activity". Through weighted gene co-expression network analysis (WGCNA), 10 drought-related modules were identified to contract trans-regulatory networks. The KEGG annotation demonstrated that these trans-target genes were enriched for photosynthetic physiology, brassinosteroid biosynthesis, and flavonoid metabolism. In addition, we constructed the lncRNA-mediated ceRNA regulatory network by predicting the microRNA response elements (MREs). Furthermore, the expressions of lncRNAs were verified by RT-qPCR. Functional verification of a candidate lncRNA, MSTRG.32128, demonstrated its positive role in drought response and root growth and development regulation. Hormone content analysis provided insights into the regulatory mechanisms of MSTRG.32128 in root development, revealing its involvement in auxin and ethylene signal transduction pathways. These findings advance our understanding of lncRNA-mediated regulatory mechanisms in barley under drought stress. Our results will provide new insights into the functions of lncRNAs in barley responding to drought stress.
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Affiliation(s)
- Bingyun Cheng
- Research Center of Crop Stresses Resistance Technologies/ MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Yangtze University, Jingzhou, China
| | - Wenyu Pei
- Research Center of Crop Stresses Resistance Technologies/ MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Yangtze University, Jingzhou, China
| | - Kui Wan
- Research Center of Crop Stresses Resistance Technologies/ MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Yangtze University, Jingzhou, China
| | - Rui Pan
- Research Center of Crop Stresses Resistance Technologies/ MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Yangtze University, Jingzhou, China
| | - Wenying Zhang
- Research Center of Crop Stresses Resistance Technologies/ MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Yangtze University, Jingzhou, China
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Li S, Wang J, Ren G. CircRNA: An emerging star in plant research: A review. Int J Biol Macromol 2024; 272:132800. [PMID: 38825271 DOI: 10.1016/j.ijbiomac.2024.132800] [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: 02/23/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
CircRNAs are a class of covalently closed non-coding RNA formed by linking the 5' terminus and the 3' terminus after reverse splicing. CircRNAs are widely found in eukaryotes, and they are highly conserved, with spatio-temporal expression specificity and stability. CircRNAs can act as miRNA sponges to regulate the expression of downstream target genes, regulating the transcription of parental genes and some can even be translated into peptides or proteins. Research on circRNAs in plants is still in its infancy compared to that in animals. With the deepening of research, the results of a variety of plant circRNAs suggest that they play an important role in growth and development, and tolerance towards abiotic stresses such as salt, drought, low temperature, high temperature and other adverse environments. In this review paper, we elaborated the molecular characteristics, mechanism of action, function and bioinformatics databases of plant circRNAs, combined with the progress of circRNA research in animals, discussed the potential mechanism of action of plant circRNAs, and proposed the unsolved problems and prospects for future application of plant circRNAs.
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Affiliation(s)
- Simin Li
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Jingyi Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Guocheng Ren
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; Dongying Institute, Shandong Normal University, Dongying 257000, China.
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Shi D, Huang H, Zhang Y, Qian Z, Du J, Huang L, Yan X, Lin S. The roles of non-coding RNAs in male reproductive development and abiotic stress responses during this unique process in flowering plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:111995. [PMID: 38266717 DOI: 10.1016/j.plantsci.2024.111995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Successful male reproductive development is the guarantee for sexual reproduction of flowering plants. Male reproductive development is a complicated and multi-stage process that integrates physiological processes and adaptation and tolerance to a myriad of environmental stresses. This well-coordinated process is governed by genetic and epigenetic machineries. Non-coding RNAs (ncRNAs) play pleiotropic roles in the plant growth and development. The identification, characterization and functional analysis of ncRNAs and their target genes have opened a new avenue for comprehensively revealing the regulatory network of male reproductive development and its response to environmental stresses in plants. This review briefly addresses the types, origin, biogenesis and mechanisms of ncRNAs in plants, highlights important updates on the roles of ncRNAs in regulating male reproductive development and emphasizes the contribution of ncRNAs, especially miRNAs and lncRNAs, in responses to abiotic stresses during this unique process in flowering plants.
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Affiliation(s)
- Dexi Shi
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Huiting Huang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Yuting Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Zhihao Qian
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Jiao Du
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xiufeng Yan
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China.
| | - Sue Lin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China.
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4
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Wang H, Jia Y, Bai X, Wang J, Liu G, Wang H, Wu Y, Xin J, Ma H, Liu Z, Zou D, Zhao H. Whole-transcriptome profiling and identification of cold tolerance-related ceRNA networks in japonica rice varieties. FRONTIERS IN PLANT SCIENCE 2024; 15:1260591. [PMID: 38567126 PMCID: PMC10985246 DOI: 10.3389/fpls.2024.1260591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/02/2024] [Indexed: 04/04/2024]
Abstract
Introduction Low-temperature stress negatively impacts rice yield, posing a significant risk to food security. While previous studies have explored the physiological and linear gene expression alterations in rice under low-temperature conditions, the changes in competing endogenous RNA (ceRNA) networks remain largely unexamined. Methods We conducted RNA sequencing on two japonica rice varieties with differing cold-tolerance capabilities to establish ceRNA networks. This enabled us to investigate the transcriptional regulatory network and molecular mechanisms that rice employs in response to low-temperature stress. Results We identified 364 differentially expressed circular RNAs (circRNAs), 224 differentially expressed microRNAs (miRNAs), and 12,183 differentially expressed messenger RNAs (mRNAs). WRKY family was the most prominent transcription factor family involved in cold tolerance. Based on the expression patterns and targeted relationships of these differentially expressed RNAs, we discerned five potential ceRNA networks related to low-temperature stress in rice: osa-miR166j-5p from the miR166 family was associated with cold tolerance; osa-miR528-3p and osa-miR156j-3p were linked to stress response; and osa-miR156j-3p was involved in the antioxidant system. In addition, Os03g0152000 in the antioxidant system, as well as Os12g0491800 and Os05g0381400, correlated with the corresponding stress response and circRNAs in the network. A gene sequence difference analysis and phenotypic validation of Os11g0685700 (OsWRKY61) within the WRKY family suggested its potential role in regulating cold tolerance in rice. Discussion and conclusion We identified Os11g0685700 (OsWRKY61) as a promising candidate gene for enhancing cold tolerance in japonica rice. The candidate miRNAs, mRNAs, and circRNAs uncovered in this study are valuable targets for researchers and breeders. Our findings will facilitate the development of cold-tolerant rice varieties from multiple angles and provide critical directions for future research into the functions of cold-tolerance-related miRNAs, mRNAs, and circRNAs in rice.
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Affiliation(s)
- Hao Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Yan Jia
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Xu Bai
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Jin Wang
- Bei Da Huang Kenfeng Seed Limited Company, Research and Breeding Center, Harbin, China
| | - Ge Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Haixing Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Yulong Wu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Junying Xin
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Huimiao Ma
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Zhenyu Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Hongwei Zhao
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, China
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Wang R, Zhang M, Wang H, Chen L, Zhang X, Guo L, Qi T, Tang H, Shahzad K, Wang H, Qiao X, Wu J, Xing C. Identification and characterization of circular RNAs involved in the fertility stability of cotton CMS-D2 restorer line under heat stress. BMC PLANT BIOLOGY 2024; 24:32. [PMID: 38183049 PMCID: PMC10768462 DOI: 10.1186/s12870-023-04706-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/25/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND As a vital type of noncoding RNAs, circular RNAs (circRNAs) play important roles in plant growth and development and stress response. However, little is known about the biological roles of circRNAs in regulating the stability of male fertility restoration for cytoplasmic male sterility (CMS) conditioned by Gossypium harknessii cytoplasm (CMS-D2) cotton under high-temperature (HT) stress. RESULTS In this study, RNA-sequencing and bioinformatics analysis were performed on pollen grains of isonuclear alloplasmic near-isogenic restorer lines NH [N(Rf1rf1)] and SH [S(Rf1rf1)] with obvious differences in fertility stability under HT stress at two environments. A total of 967 circRNAs were identified, with 250 differentially expressed under HT stress. We confirmed the back-splicing sites of eight selected circRNAs using divergent primers and Sanger sequencing. Tissue-specific expression patterns of five differentially expressed circRNAs (DECs) were also verified by RT-PCR and qRT-PCR. Functional enrichment and metabolic pathway analysis revealed that the parental genes of DECs were significantly enriched in fertility-related biological processes such as pollen tube guidance and cell wall organization, as well as the Pentose and glucuronate interconversions, Steroid biosynthesis, and N-Glycan biosynthesis pathways. Moreover, we also constructed a putative circRNA-mediated competing endogenous RNA (ceRNA) network consisting of 21 DECs, eight predicted circRNA-binding miRNAs, and their corresponding 22 mRNA targets, especially the two ceRNA modules circRNA346-miR159a-MYB33 and circRNA484-miR319e-MYB33, which might play important biological roles in regulating pollen fertility stability of cotton CMS-D2 restorer line under HT stress. CONCLUSIONS Through systematic analysis of the abundance, characteristics and expression patterns of circRNAs, as well as the potential functions of their parent genes, our findings suggested that circRNAs and their mediated ceRNA networks acted vital biological roles in cotton pollen development, and might be also essential regulators for fertility stability of CMS-D2 restorer line under heat stress. This study will open a new door for further unlocking complex regulatory mechanisms underpinning the fertility restoration stability for CMS-D2 in cotton.
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Affiliation(s)
- Ruijie Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Meng Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China.
| | - Hui Wang
- Xiangyang Vocational and Technical College, Xiangyang, 441050, Hubei, China
| | - Liangliang Chen
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Xuexian Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Liping Guo
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Tingxiang Qi
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Huini Tang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Kashif Shahzad
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Hailin Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Xiuqin Qiao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Jianyong Wu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China.
| | - Chaozhu Xing
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, 38 Huanghe Dadao, Anyang, 455000, Henan, China.
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Vashisht I, Dhaka N, Jain R, Sood A, Sharma N, Sharma MK, Sharma R. Non-coding RNAs-mediated environmental surveillance determines male fertility in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108030. [PMID: 37708711 DOI: 10.1016/j.plaphy.2023.108030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/16/2023]
Abstract
Plants are continuously exposed to environmental stresses leading to significant yield losses. With the changing climatic conditions, the intensity and duration of these stresses are expected to increase, posing a severe threat to crop productivity worldwide. Male gametogenesis is one of the most sensitive developmental stages. Exposure to environmental stresses during this stage leads to male sterility and yield loss. Elucidating the underlying molecular mechanism of environment-affected male sterility is essential to address this challenge. High-throughput RNA sequencing studies, loss-of-function phenotypes of sRNA biogenesis genes and functional genomics studies with non-coding RNAs have started to unveil the roles of small RNAs, long non-coding RNAs and the complex regulatory interactions between them in regulating male fertility under different growth regimes. Here, we discuss the current understanding of the non-coding RNA-mediated environmental stress surveillance and regulation of male fertility in plants. The candidate ncRNAs emerging from these studies can be leveraged to generate environment-sensitive male sterile lines for hybrid breeding or mitigate the impact of climate change on male fertility, as the situation demands.
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Affiliation(s)
- Ira Vashisht
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Namrata Dhaka
- Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana, 123031, India
| | - Rubi Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India; Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Akanksha Sood
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Niharika Sharma
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, 2800, Australia
| | - Manoj K Sharma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rita Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan, 333031, India.
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Babaei S, Singh MB, Bhalla PL. Circular RNAs modulate the floral fate acquisition in soybean shoot apical meristem. BMC PLANT BIOLOGY 2023; 23:322. [PMID: 37328881 DOI: 10.1186/s12870-023-04319-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/26/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Soybean (Glycine max), a major oilseed and protein source, requires a short-day photoperiod for floral induction. Though key transcription factors controlling flowering have been identified, the role of the non-coding genome is limited. Circular RNAs (circRNAs) recently emerged as a novel class of RNAs with critical regulatory functions. However, a study on circRNAs during the floral transition of a crop plant is lacking. We investigated the expression and potential function of circRNAs in floral fate acquisition by soybean shoot apical meristem in response to short-day treatment. RESULTS Using deep sequencing and in-silico analysis, we denoted 384 circRNAs, with 129 exhibiting short-day treatment-specific expression patterns. We also identified 38 circRNAs with predicted binding sites for miRNAs that could affect the expression of diverse downstream genes through the circRNA-miRNA-mRNA network. Notably, four different circRNAs with potential binding sites for an important microRNA module regulating developmental phase transition in plants, miR156 and miR172, were identified. We also identified circRNAs arising from hormonal signaling pathway genes, especially abscisic acid, and auxin, suggesting an intricate network leading to floral transition. CONCLUSIONS This study highlights the gene regulatory complexity during the vegetative to reproductive transition and paves the way to unlock floral transition in a crop plant.
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Affiliation(s)
- Saeid Babaei
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Science, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Science, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Science, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia.
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Liu J, Zhang C, Jiang M, Ni Y, Xu Y, Wu W, Huang L, Newmaster SG, Kole C, Wu B, Liu C. Identification of circular RNAs of Cannabis sativa L. potentially involved in the biosynthesis of cannabinoids. PLANTA 2023; 257:72. [PMID: 36862222 DOI: 10.1007/s00425-023-04104-4] [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: 10/14/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
We identified circRNAs in the Cannabis sativa L. genome and examined their association with 28 cannabinoids in three tissues of C. sativa. Nine circRNAs are potentially involved in the biosynthesis of six cannabinoids. Cannabis sativa L. has been widely used in the production of medicine, textiles, and food for over 2500 years. The main bioactive compounds in C. sativa are cannabinoids, which have multiple important pharmacological actions. Circular RNAs (circRNAs) play essential roles in growth and development, stress resistance, and the biosynthesis of secondary metabolites. However, the circRNAs in C. sativa remain unknown. In this study, to explore the role of circRNAs in cannabinoid biosynthesis, we performed RNA-Seq and metabolomics analysis on the leaves, roots, and stems of C. sativa. We identified 741 overlapping circRNAs by three tools, of which 717, 16, and 8 circRNAs were derived from exonic, intronic, and intergenic, respectively. Functional enrichment analysis indicated that the parental genes (PGs) of circRNAs were enriched in many processes related to biological stress responses. We found that most of the circRNAs showed tissue-specific expression and 65 circRNAs were significantly correlated with their PGs (P < 0.05, |r|≥ 0.5). We also determined 28 cannabinoids by High-performance liquid chromatography-ESI-triple quadrupole-linear ion trap mass spectrometry. Ten circRNAs, including ciR0159, ciR0212, ciR0153, ciR0149, ciR0016, ciR0044, ciR0022, ciR0381, ciR0006, and ciR0025 were found to be associated with six cannabinoids by weighted gene co-expression network analysis. Twenty-nine of 53 candidate circRNAs, including 9 cannabinoids related were validated successfully using PCR amplification and Sanger sequencing. Taken together, all these results would help to enhance our acknowledge of the regulation of circRNAs, and lay the foundation for breeding new C. sativa cultivars with high cannabinoids through manipulating circRNAs.
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Affiliation(s)
- Jingting Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Chang Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Mei Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Yang Ni
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Yicen Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Wuwei Wu
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, People's Republic of China
| | - Linfang Huang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Steven G Newmaster
- Natural Health Product Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Chittaranjan Kole
- International Climate Resilient Crop Genomics Consortium and International Phytomedomics and Nutriomics Consortium, Kolkata, 700094, India
| | - Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China.
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China.
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Yue Z, Pan X, Li J, Si F, Yin L, Hou Y, Chen X, Li X, Zhang Y, Ma J, Yang J, Li H, Luan F, Huang W, Zhang X, Yuan L, Zhang R, Wei C. Whole-transcriptome analyses identify key differentially expressed mRNAs, lncRNAs, and miRNAs associated with male sterility in watermelon. FRONTIERS IN PLANT SCIENCE 2023; 14:1138415. [PMID: 36938061 PMCID: PMC10019506 DOI: 10.3389/fpls.2023.1138415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Male sterility is a valuable trait for watermelon breeding, as watermelon hybrids exhibit obvious heterosis. However, the underlying regulatory mechanism is still largely unknown, especially regarding the related non-coding genes. In the present study, approximately 1035 differentially expressed genes (DEGs), as well as 80 DE-lncRNAs and 10 DE-miRNAs, were identified, with the overwhelming majority down-regulated in male-sterile floral buds. Enrichment analyses revealed that the general phenylpropanoid pathway as well as its related metabolisms was predicted to be altered in a mutant compared to its fertile progenitor. Meanwhile, the conserved genetic pathway DYT1-TDF1-AMS-MS188-MS1, as well as the causal gene ClAMT1 for the male-sterile mutant Se18, was substantially disrupted during male reproductive development. In addition, some targets of the key regulators AMS and MS188 in tapetum development were also down-regulated at a transcriptional level, such as ABCG26 (Cla004479), ACOS5 (Cla022956), CYP703A2 (Cla021151), PKSA (Cla021099), and TKPR1 (Cla002563). Considering lncRNAs may act as functional endogenous target mimics of miRNAs, competitive endogenous RNA networks were subsequently constructed, with the most complex one containing three DE-miRNAs, two DE-lncRNAs, and 21 DEGs. Collectively, these findings not only contribute to a better understanding of genetic regulatory networks underlying male sterility in watermelon, but also provide valuable candidates for future research.
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Affiliation(s)
- Zhen Yue
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaona Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiayue Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Fengfei Si
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Lijuan Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Yinjie Hou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoyao Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Xin Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Yong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Jianxiang Ma
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Jianqiang Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Hao Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Wenfeng Huang
- Vegetable Research Institute of Hainan Academy of Agricultural Sciences, Haikou, Hainan, China
| | - Xian Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin, China
| | - Li Yuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruimin Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Chunhua Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
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Liu R, Ma Y, Guo T, Li G. Identification, biogenesis, function, and mechanism of action of circular RNAs in plants. PLANT COMMUNICATIONS 2023; 4:100430. [PMID: 36081344 PMCID: PMC9860190 DOI: 10.1016/j.xplc.2022.100430] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/11/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Circular RNAs (circRNAs) are a class of single-stranded, closed RNA molecules with unique functions that are ubiquitously expressed in all eukaryotes. The biogenesis of circRNAs is regulated by specific cis-acting elements and trans-acting factors in humans and animals. circRNAs mainly exert their biological functions by acting as microRNA sponges, forming R-loops, interacting with RNA-binding proteins, or being translated into polypeptides or proteins in human and animal cells. Genome-wide identification of circRNAs has been performed in multiple plant species, and the results suggest that circRNAs are abundant and ubiquitously expressed in plants. There is emerging compelling evidence to suggest that circRNAs play essential roles during plant growth and development as well as in the responses to biotic and abiotic stress. However, compared with recent advances in human and animal systems, the roles of most circRNAs in plants are unclear at present. Here we review the identification, biogenesis, function, and mechanism of action of plant circRNAs, which will provide a fundamental understanding of the characteristics and complexity of circRNAs in plants.
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Affiliation(s)
- Ruiqi Liu
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Yu Ma
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Tao Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China.
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11
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Jin H, Yang Z, Luo J, Li C, Chen J, Lim KJ, Wang Z. Comprehensive identification and analysis of circRNAs during hickory ( Carya cathayensis Sarg.) flower bud differentiation. FRONTIERS IN PLANT SCIENCE 2023; 13:1000489. [PMID: 36684801 PMCID: PMC9846342 DOI: 10.3389/fpls.2022.1000489] [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: 07/22/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Flower bud differentiation represents a crucial transition from vegetative growth to reproductive development. Carya cathayensis (hickory) is an important economic species in China, with a long juvenile period that hinders its commercial development. In recent years, circular RNAs (circRNAs) have been widely studied and identified as sponges for miRNA regulation of mRNA expression. However, little is known regarding the role of circRNAs in flower buds. In this study, we sequenced circRNAs at three developmental stages (undifferentiated, differentiating, and fully differentiated) in both female and male buds. A total of 6,931 circRNAs were identified in the three developmental stages and 4,449 and 2,209 circRNAs were differentially expressed in female and male buds, respectively. Gene ontology demonstrated that many circRNA host genes participated in various processes, for example, cellular and intracellular pH regulation. Function annotation identified 46 differentially expressed circRNAs involved in flowering regulation, with 28 circRNAs found only in female buds, 4 found only in male buds, and 11 found in both female and male buds. A circRNA-miRNA-mRNA network was predicted based on 13 flowering-related circRNAs and their seven putative interacting miRNAs to describe the regulatory mechanism. Our preliminary results demonstrated a potential involvement of circRNA in bud differentiation. They provided a preliminary theoretical basis for how circRNA might participate in flower development in hickory, perhaps in woody plants.
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12
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Wei J, Chen Q, Lin J, Chen F, Chen R, Liu H, Chu P, Lu Z, Li S, Yu G. Genome-wide identification and expression analysis of tomato glycoside hydrolase family 1 β-glucosidase genes in response to abiotic stresses. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2072767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Jinpeng Wei
- Ministry of Agriculture and Rural Affairs Agro-products and Processed Products Quality Supervision, Inspection and Testing Center, Daqing, Heilongjiang, PR China
- Key Lab of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Qiusen Chen
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Jiaxin Lin
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Fengqiong Chen
- Ministry of Agriculture and Rural Affairs Agro-products and Processed Products Quality Supervision, Inspection and Testing Center, Daqing, Heilongjiang, PR China
| | - Runan Chen
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Hanlin Liu
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Peiyu Chu
- Ministry of Agriculture and Rural Affairs Agro-products and Processed Products Quality Supervision, Inspection and Testing Center, Daqing, Heilongjiang, PR China
| | - Zhiyong Lu
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Shaozhe Li
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
| | - Gaobo Yu
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, PR China
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Zhang P, Dai M. CircRNA: a rising star in plant biology. J Genet Genomics 2022; 49:1081-1092. [PMID: 35644325 DOI: 10.1016/j.jgg.2022.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 01/14/2023]
Abstract
Circular RNAs (circRNAs) are covalently closed single-stranded RNA molecules, which are widespread in eukaryotic cells. As regulatory molecules, circRNAs have various functions, such as regulating gene expression, binding miRNAs or proteins, and being translated into proteins, which are important for cell proliferation and cell differentiation, individual growth and development, as well as many other biological processes. However, compared with that in animal models, studies of circRNAs in plants lags behind and, particularly, the regulatory mechanisms of biogenesis and molecular functions of plant circRNAs remain elusive. Recent studies have shown that circRNAs are wide spread in plants with tissue- or development-specific expression patterns and are responsive to a variety of environmental stresses. In this review, we summarize these advances, focusing on the regulatory mechanisms of biogenesis, molecular and biological functions of circRNAs, and the methods for investigating circRNAs. We also discuss the challenges and the prospects of plant circRNA studies.
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Affiliation(s)
- Pei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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14
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Peng Y, Pan R, Liu Y, Medison MB, Shalmani A, Yang X, Zhang W. LncRNA-mediated ceRNA regulatory network provides new insight into chlorogenic acid synthesis in sweet potato. PHYSIOLOGIA PLANTARUM 2022; 174:e13826. [PMID: 36377281 DOI: 10.1111/ppl.13826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Sweet potato (Ipomoea batatas L.) is considered a highly nutritional and economical crop due to its high contents of bioactive substances, such as anthocyanin and chlorogenic acid (CGA), especially in leaves and stems. The roles of noncoding RNAs (ncRNA), including long noncoding RNA (lncRNA) and microRNA (miRNA), in CGA synthesis, are still unknown. In this study, the differentially expressed (DE) mRNAs, miRNAs, and lncRNAs in two leafy vegetable genotypes "FS7-6-14-7" (high CGA content) and "FS7-6" (low CGA content) were identified. The cis-regulation between lncRNA and mRNA was analyzed. Then, the CGA synthesis-related modules MEBlue and MEYellow were identified to detect trans-regulation mRNA-lncRNA pairs. The GO and KEGG annotations suggested that mRNA in these two modules was significantly enriched in the secondary metabolite synthesis biosynthesis category. A competing endogenous RNAs (ceRNA) network, including 8730 miRNA-mRNA and 444 miRNA-lncRNA pairs, was constructed by DEmiRNA target prediction. Then, a CGA synthesis-related ceRNA network was obtained with lncRNA and mRNA from MEBlue and MEYellow. Finally, one relational pair, MSTRG.47662.1/mes-miR398/itb04g00990, was selected for functional validation. Overexpression of lncRNA MSTRG.47662.1 and mRNA itb04g00990 increased CGA content in both tobacco and sweet potato callus, while overexpression of miRNA mes-miR398 decreased CGA content. Meanwhile, regression analysis of the expression patterns demonstrated that MSTRG.47662.1, acting as a ceRNA, promoted itb04g00990 expression by competitively binding mes-miR398 in CGA synthesis in sweet potato. Our results provide insights into how ncRNA-mediated ceRNA regulatory networks likely contribute to CGA synthesis in leafy sweet potato.
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Affiliation(s)
- Ying Peng
- Research Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Rui Pan
- Research Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Yi Liu
- Research Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
- Institute of Food Crops/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Milca Banda Medison
- Research Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Abdullah Shalmani
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xinsun Yang
- Institute of Food Crops/Hubei Engineering and Technology Research Centre of Sweet Potato/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Wenying Zhang
- Research Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
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Zhu Z, Wang J, Fan X, Long Q, Chen H, Ye Y, Zhang K, Ren Z, Zhang Y, Niu Q, Chen D, Guo R. CircRNA-regulated immune responses of asian honey bee workers to microsporidian infection. Front Genet 2022; 13:1013239. [PMID: 36267412 PMCID: PMC9577369 DOI: 10.3389/fgene.2022.1013239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Nosema ceranae is a widespread fungal parasite for honey bees, causing bee nosemosis. Based on deep sequencing and bioinformatics, identification of circular RNAs (circRNAs) in Apis cerana workers’ midguts and circRNA-regulated immune response of host to N. ceranae invasion were conducted in this current work, followed by molecular verification of back-splicing sites and expression trends of circRNAs. Here, 10185 and 7405 circRNAs were identified in the midguts of workers at 7 days (AcT1) and 10 days (AcT2) post inoculation days post-inoculation with N. ceranae. PCR amplification result verified the back-splicing sites within three specific circRNAs (novel_circ_005123, novel_circ_007177, and novel_circ_015140) expressed in N. ceranae-inoculated midgut. In combination with transcriptome data from corresponding un-inoculated midguts (AcCK1 and AcCK2), 2266 circRNAs were found to be shared by the aforementioned four groups, whereas the numbers of specific ones were 2618, 1917, 5691, and 3723 respectively. Further, 83 52) differentially expressed circRNAs (DEcircRNAs) were identified in AcCK1 vs. AcT1 (AcCK2 vs. AcT2) comparison group. Source genes of DEcircRNAs in workers’ midgut at seven dpi were involved in two cellular immune-related pathways such as endocytosis and ubiquitin mediated proteolysis. Additionally, competing endogenous RNA (ceRNA) network analysis showed that 23 13) DEcircRNAs in AcCK1 vs. AcT1 (AcCK2 vs. AcT2) comparison group could target 18 14) miRNAs and further link to 1111 (1093) mRNAs. These target mRNAs were annotated to six cellular immunity pathways including endocytosis, lysosome, phagosome, ubiquitin mediated proteolysis, metabolism of xenobiotics by cytochrome P450, and insect hormone biosynthesis. Moreover, 284 164) internal ribosome entry site and 54 26) ORFs were identified from DEcircRNAs in AcCK1 vs. AcT1 (AcCK2 vs. AcT2) comparison group; additionally, ORFs in DEcircRNAs in midgut at seven dpi with N. ceranae were associated with several cellular immune pathways including endocytosis and ubiquitin-mediated proteolysis. Ultimately, RT-qPCR results showed that the expression trends of six DEcircRNAs were consistent with those in transcriptome data. These results demonstrated that N. ceranae altered the expression pattern of circRNAs in A. c. cerana workers’ midguts, and DEcircRNAs were likely to regulate host cellular and humoral immune response to microsporidian infection. Our findings lay a foundation for clarifying the mechanism underlying host immune response to N. ceranae infection and provide a new insight into interaction between Asian honey bee and microsporidian.
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Affiliation(s)
- Zhiwei Zhu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jie Wang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qi Long
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huazhi Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yaping Ye
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kaiyao Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhongmin Ren
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yang Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qingsheng Niu
- Apitherapy Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
- Apiculture Science Institute of Jilin Province, Jilin, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, China
- Apiculture Science Institute of Jilin Province, Jilin, China
- *Correspondence: Rui Guo,
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Identification and Characterization of Circular RNAs Involved in the Flower Development and Senescence of Rhododendron delavayi Franch. Int J Mol Sci 2022; 23:ijms231911214. [PMID: 36232515 PMCID: PMC9569710 DOI: 10.3390/ijms231911214] [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: 08/16/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
Floral development and senescence are a crucial determinant for economic and ornamental value. CircRNAs play an essential role in regulating plant growth and development; however, there is no systematic identification of circRNAs during the lifespan of flowers. This study aims to explore the expression profile and functional role of circRNAs in the full flowering stages of Rhododendron delavayi Franch. We carried out transcriptome sequencing of the six stages of Rhododendron delavayi Franch flowers to identify the circular RNA expression profile. In addition, using bioinformatics methods, we explored the functions of circRNAs, including analysis of the circRNA-miRNA-mRNA network, short time-series expression miner (STEM), and so on. We identified 146 circRNAs, of which 79 were differentially expressed from the budding to fading stages. Furthermore, using STEM analysis, one of the 42 circRNA expression model profiles was significantly upregulated during the senescence stage, including 16 circRNAs. Additionally, 7 circRNA-miRNA-mRNA networks were constructed with 10 differentially expressed circRNAs, in which some target mRNA may regulate the development and senescence of the Rhododendron flowers. Finally, by analyzing the correlation between circRNAs and mRNA, combined with existing reports, we proposed that circRNAs play a regulatory role during flower development and senescence by mediating the jasmonate signaling pathway. Overall, these results provide new clues to the potential mechanism of circRNAs acting as novel post-transcriptional regulators in the development and senescence process of flowers.
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Chen H, Wang T, Gong Z, Lu H, Chen Y, Deng F, Ren W. Low Light Conditions Alter Genome-Wide Profiles of Circular RNAs in Rice Grains during Grain Filling. PLANTS 2022; 11:plants11091272. [PMID: 35567273 PMCID: PMC9102277 DOI: 10.3390/plants11091272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022]
Abstract
In animals and plants, circRNAs regulate gene expression and act as sponges that inhibit the activity of microRNAs. This study aimed to determine how specific circRNAs are expressed in rice grains at different stages of grain filling, under normal and low light conditions. We extracted total RNA from rice grains under low and sufficient light conditions. Deep sequencing was performed using circRNA libraries, and bioinformatics tools were used to identify the circRNAs. In addition, we analyzed targeted messenger RNA functions using two databases to predict the processes involved in rice grain development, and we conducted real-time PCR on 15 of the circRNAs as well as Sanger sequencing. During the grain development process, 8015 candidate circRNAs were isolated, among which the number of known circRNAs was 1661. We also found that the number of circRNAs changed with the time of development. Among them, six circRNAs acted as sponges that targeted more than two microRNAs at different stages of development, and these circRNAs showed a regulatory pattern consistent with the transcriptome sequencing results. More circRNA diversity was found under low light treatment compared to normal light. These findings reveal a possible link between circRNA regulation and the expression of the functional genes associated with photosignal-mediated rice grain development.
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Affiliation(s)
- Hong Chen
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 621000, China; (H.C.); (T.W.); (Z.G.); (H.L.); (Y.C.); (F.D.)
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Tao Wang
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 621000, China; (H.C.); (T.W.); (Z.G.); (H.L.); (Y.C.); (F.D.)
| | - Zhiyou Gong
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 621000, China; (H.C.); (T.W.); (Z.G.); (H.L.); (Y.C.); (F.D.)
| | - Hui Lu
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 621000, China; (H.C.); (T.W.); (Z.G.); (H.L.); (Y.C.); (F.D.)
| | - Yong Chen
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 621000, China; (H.C.); (T.W.); (Z.G.); (H.L.); (Y.C.); (F.D.)
| | - Fei Deng
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 621000, China; (H.C.); (T.W.); (Z.G.); (H.L.); (Y.C.); (F.D.)
| | - Wanjun Ren
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 621000, China; (H.C.); (T.W.); (Z.G.); (H.L.); (Y.C.); (F.D.)
- Correspondence:
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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] [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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Xu W, Bao W, Liu H, Chen C, Bai H, Huang M, Zhu G, Zhao H, Gou N, Chen Y, Wang L, Wuyun TN. Insights Into the Molecular Mechanisms of Late Flowering in Prunus sibirica by Whole-Genome and Transcriptome Analyses. FRONTIERS IN PLANT SCIENCE 2022; 12:802827. [PMID: 35145534 PMCID: PMC8821173 DOI: 10.3389/fpls.2021.802827] [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: 10/27/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Freezing during the flowering of Prunus sibirica is detrimental to fruit production. The late flowering (LF) type, which is delayed by 7-15 days compared with the normal flowering (NF) type, avoids damages at low temperature, but the molecular mechanism of LF remains unclear. Therefore, this study was conducted to comprehensively characterize floral bud differentiation. A histological analysis showed that initial floral bud differentiation was delayed in the LF type compared to the NF type. Genome-wide associated studies (GWAS) showed that a candidate gene (PaF106G0600023738.01) was significantly associated with LF type. It was identified as trehalose-6-phosphate phosphatase (PsTPPF), which is involved in trehalose-6-phosphate (Tre6P) signaling pathway and acts on floral transition. A whole-transcriptome RNA sequencing analysis was conducted, and a total of 6,110 differential expression (DE) mRNAs, 1,351 DE lncRNAs, and 148 DE miRNAs were identified. In addition, 24 DE mRNAs related with floral transition were predicted, and these involved the following: three interactions between DE lncRNAs and DE mRNAs of photoperiod pathway with two mRNAs (COP1, PaF106G0400018289.01 and CO3, MXLOC_025744) and three lncRNAs (CCLR, LTCONS_00031803, COCLR1, LTCONS_00046726, and COCLR2, LTCONS_00046731); one interaction between DE miRNAs and DE mRNAs with one mRNA, encoding trehalose-6-phosphate synthase (PsTPS1, PaF106G0100001132.01), and one miRNA (miRNA167h). Combined with the expression profiles and Tre6P levels, functions of PsTPPF and PsTPS1 in Tre6P regulation were considered to be associated with flowering time. A new network of ceRNAs correlated with LF was constructed, and it consisted of one mRNA (PsTPS1), one lncRNA (TCLR, LTCONS_00034157), and one miRNA (miR167h). This study provided insight into the molecular regulatory mechanism of LF in Prunus sibirica.
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Affiliation(s)
- Wanyu Xu
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou, China
| | - Wenquan Bao
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, China
| | - Huimin Liu
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou, China
| | - Chen Chen
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou, China
| | - Haikun Bai
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou, China
| | - Mengzhen Huang
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou, China
| | - Gaopu Zhu
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou, China
| | - Han Zhao
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou, China
| | - Ningning Gou
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou, China
| | - Yixiao Chen
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou, China
| | - Lin Wang
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou, China
| | - Ta-Na Wuyun
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China
- Kernel-Apricot Engineering and Technology Research Center of State Forestry and Grassland Administration, Zhengzhou, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Zhengzhou, China
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20
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Li Z, Guo Y, Ndandala CB, Chen H, Huang C, Zhao G, Huang H, Li G, Chen H. Analysis of circRNA and miRNA expression profiles in IGF3-induced ovarian maturation in spotted scat ( Scatophagus argus). Front Endocrinol (Lausanne) 2022; 13:998207. [PMID: 36506051 PMCID: PMC9732426 DOI: 10.3389/fendo.2022.998207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/03/2022] [Indexed: 11/26/2022] Open
Abstract
Insulin-like growth factor 3 (IGF3) induces ovarian maturation in teleosts; however, research on its molecular regulatory mechanism remains deficient. Circular RNAs (circRNAs) and microRNAs (miRNAs) are involved in various biological processes, including reproduction. In this study, circRNAs and miRNAs involved in IGF3-induced ovarian maturation were evaluated in spotted scat (Scatophagus argus). In ovarian tissues, we identified 176 differentially expressed (DE) circRNAs and 52 DE miRNAs between IGF3 treatment and control groups. Gene Ontology (GO) enrichment analyses showed that host genes of DE circRNAs and target genes of DE miRNAs were enriched for various processes with a high degree of overlap, including cellular process, reproduction, reproductive process, biological adhesion, growth, extracellular region, cell junction, catalytic activity, and transcription factor activity. Enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways included cell adhesion molecules, ECM-receptor interaction, regulation of actin cytoskeleton, focal adhesion, cell cycle, Hedgehog signaling pathway, phosphatidylinositol signaling system, PI3K-Akt signaling pathway, Apelin signaling pathway, Notch signaling pathway, insulin signaling pathway, and Rap1 signaling pathway. A circRNA-miRNA-mRNA regulatory network was constructed, including DE genes involved in reproduction (e.g., oocyte maturation, oocyte meiosis, and ECM remodeling), such as ccnd2, hecw2, dnm2, irs1, adam12, and cdh13. According to the regulatory network and tissue distribution, we identified one circRNA (Lachesis_group5:6245955|6270787) and three miRNAs (novel_miR_622, novel_miR_980, and novel_miR_64) that may exert regulatory effects in IGF3-induced ovarian maturation in S. argus. Taken together, this study provides a novel insight into the molecular mechanisms by which IGF3 functions in ovaries and highlights the effects of circRNAs and miRNAs in reproduction in S. argus.
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Affiliation(s)
- Zhiyuan Li
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Yuwen Guo
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Charles Brighton Ndandala
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Huadong Chen
- Guangdong Havwii Agriculture Group Co., LTD, Zhanjiang, China
| | | | | | - Hai Huang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya, China
- *Correspondence: Huapu Chen, ; Hai Huang,
| | - Guangli Li
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Huapu Chen
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources of Ministry of Education, Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya, China
- *Correspondence: Huapu Chen, ; Hai Huang,
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21
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Analyses of Lysin-motif Receptor-like Kinase ( LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study. Cells 2021; 11:cells11010037. [PMID: 35011598 PMCID: PMC8750388 DOI: 10.3390/cells11010037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/10/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022] Open
Abstract
The LysM receptor-like kinases (LysM-RLKs) play a crucial role in plant symbiosis and response to environmental stresses. Brassica napus, B. rapa, and B. oleracea are utilized as valuable vegetables. Different biotic and abiotic stressors affect these crops, resulting in yield losses. Therefore, genome-wide analysis of the LysM-RLK gene family was conducted. From the genome of the examined species, 33 LysM-RLK have been found. The conserved domains of Brassica LysM-RLKs were divided into three groups: LYK, LYP, and LysMn. In the BrassicaLysM-RLK gene family, only segmental duplication has occurred. The Ka/Ks ratio for the duplicated pair of genes was less than one indicating that the genes’ function had not changed over time. The BrassicaLysM-RLKs contain 70 cis-elements, indicating that they are involved in stress response. 39 miRNA molecules were responsible for the post-transcriptional regulation of 12 Brassica LysM-RLKs. A total of 22 SSR loci were discovered in 16 Brassica LysM-RLKs. According to RNA-seq data, the highest expression in response to biotic stresses was related to BnLYP6. According to the docking simulations, several residues in the active sites of BnLYP6 are in direct contact with the docked chitin and could be useful in future studies to develop pathogen-resistant B. napus. This research reveals comprehensive information that could lead to the identification of potential genes for Brassica species genetic manipulation.
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22
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Gaffo E, Buratin A, Dal Molin A, Bortoluzzi S. Sensitive, reliable and robust circRNA detection from RNA-seq with CirComPara2. Brief Bioinform 2021; 23:6409697. [PMID: 34698333 PMCID: PMC8769706 DOI: 10.1093/bib/bbab418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/09/2021] [Accepted: 09/12/2021] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) are a large class of covalently closed RNA molecules originating by a process called back-splicing. CircRNAs are emerging as functional RNAs involved in the regulation of biological processes as well as in disease and cancer mechanisms. Current computational methods for circRNA identification from RNA-seq experiments are characterized by low discovery rates and performance dependent on the analysed data set. We developed CirComPara2 (https://github.com/egaffo/CirComPara2), a new automated computational pipeline for circRNA discovery and quantification, which consistently achieves high recall rates without losing precision by combining multiple circRNA detection methods. In our benchmark analysis, CirComPara2 outperformed state-of-the-art circRNA discovery tools and proved to be a reliable and robust method for comprehensive transcriptome characterization.
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Affiliation(s)
- Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Alessia Buratin
- Department of Molecular Medicine, University of Padova, Padova, Italy; Department of Biology, University of Padova, Padova, Italy
| | - Anna Dal Molin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Stefania Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padova, Italy; Interdepartmental Center For Innovative Biotechnologies, University of Padova, Padova, Italy
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23
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Babaei S, Singh MB, Bhalla PL. Circular RNAs Repertoire and Expression Profile during Brassica rapa Pollen Development. Int J Mol Sci 2021; 22:ijms221910297. [PMID: 34638635 PMCID: PMC8508787 DOI: 10.3390/ijms221910297] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 12/16/2022] Open
Abstract
Circular RNAs (circRNAs) are covalently closed RNA molecules generated by the back-splicing of exons from linear precursor mRNAs. Though various linear RNAs have been shown to play important regulatory roles in many biological and developmental processes, little is known about the role of their circular counterparts. In this study, we performed high-throughput RNA sequencing to delineate the expression profile and potential function of circRNAs during the five stages of pollen development in Brassica rapa. A total of 1180 circRNAs were detected in pollen development, of which 367 showed stage-specific expression patterns. Functional enrichment and metabolic pathway analysis showed that the parent genes of circRNAs were mainly involved in pollen-related molecular and biological processes such as mitotic and meiotic cell division, DNA processes, protein synthesis, protein modification, and polysaccharide biosynthesis. Moreover, by predicting the circRNA–miRNA network from our differentially expressed circRNAs, we found 88 circRNAs with potential miRNA binding sites, suggesting their role in post-transcriptional regulation of the genes. Finally, we confirmed the back-splicing sites of nine selected circRNAs using divergent primers and Sanger sequencing. Our study presents the systematic analysis of circular RNAs during pollen development and forms the basis of future studies for unlocking complex gene regulatory networks underpinning reproduction in flowering plants.
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24
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Wu P, Kong Y, Dai Z, Liu W, Zhao Z. The circular RNA circCRIM1 inhibits osteosarcoma progression through sponging miR-513. Mamm Genome 2021; 32:495-502. [PMID: 34480205 DOI: 10.1007/s00335-021-09903-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/06/2021] [Indexed: 01/16/2023]
Abstract
Numerous studies have suggested that the abnormal expression of circular RNAs plays an essential role in the pathological progression of numerous tumors. Nonetheless, the functions and underlying mechanisms of the circular RNA circCRIM1 in osteosarcoma (OS) are still not fully understood. In this study, 47 classes of OS tissues and adjoining normal tissues were obtained from patients. Real-time PCR was employed to measure circCRIM1 expression levels in both OS tissues and cell lines. The proliferation, migration, and invasion ability in OS cell lines were measured by MTT assays, EDU assays, transwell migration experiments, and transwell invasion assays. The results demonstrated that the expression of circCRIM1 was notably decreased both in OS tissues and cell lines. Depressed circCRIM1 expression was correlated with lymph node metastasis, advanced FIGO stage, and low overall survival of OS patients. In addition, the results indicated that circCRIM1 could decrease the migration, invasion, and growth of OS cells. Further mechanistic studies indicated that circCRIM1 served as a competing endogenous RNA (ceRNA) of miR-513, leading to decreases in the proliferation, migration, and invasion of OS cells. Taken together, our data uncovered a significant role of the circCRIM1/miR-513 pathway in the proliferation, migration, and invasion of OS cell lines and suggested that circCRIM1 may serve as a possible therapeutic target for OS treatment.
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Affiliation(s)
- Pengfei Wu
- Department of Orthopaedics, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, No.1, Huanghe West Road, Huaiyin District, Huaian, 223300, Jiangsu, China
| | - Yinghui Kong
- Department of Orthopaedics, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, No.1, Huanghe West Road, Huaiyin District, Huaian, 223300, Jiangsu, China.
| | - Zhitang Dai
- Department of Orthopaedics, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, No.1, Huanghe West Road, Huaiyin District, Huaian, 223300, Jiangsu, China
| | - Weidong Liu
- Department of Orthopaedics, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, No.1, Huanghe West Road, Huaiyin District, Huaian, 223300, Jiangsu, China
| | - Zexue Zhao
- Department of Orthopaedics, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, No.1, Huanghe West Road, Huaiyin District, Huaian, 223300, Jiangsu, China
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25
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NGS Methodologies and Computational Algorithms for the Prediction and Analysis of Plant Circular RNAs. Methods Mol Biol 2021; 2362:119-145. [PMID: 34195961 DOI: 10.1007/978-1-0716-1645-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Circular RNAs (circRNAs) are a class of single-stranded RNAs derived from exonic, intronic, and intergenic regions from precursor messenger RNAs (pre-mRNA), where a noncanonical back-splicing event occurs, in which the 5' and 3' ends are attached by covalent bond. CircRNAs participate in the regulation of gene expression at the transcriptional and posttranscriptional level primarily as miRNA and RNA-binding protein (RBP) sponges, but also involved in the regulation of alternative RNA splicing and transcription. CircRNAs are widespread and abundant in plants where they have been involved in stress responses and development. Through the analysis of all publications in this field in the last five years, we can summarize that the identification of these molecules is carried out through next generation sequencing studies, where samples have been previously treated to eliminate DNA, rRNA, and linear RNAs as a means to enrich circRNAs. Once libraries are prepared, they are sequenced and subsequently studied from a bioinformatics point of view. Among the different tools for identifying circRNAs, we can highlight CIRI as the most used (in 60% of the published studies), as well as CIRCExplorer (20%) and find_circ (20%). Although it is recommended to use more than one program in combination, and preferably developed specifically to treat with plant samples, this is not always the case. It should also be noted that after identifying these circular RNAs, most of the authors validate their findings in the laboratory in order to obtain bona fide results.
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Xu S, Song Y, Shao Y, Zhou H. Comprehensive analysis of circular RNA in oral leukoplakia: upregulated circHLA-C as a potential biomarker for diagnosis and prognosis. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1375. [PMID: 33313120 PMCID: PMC7723659 DOI: 10.21037/atm-20-3840] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background Emerging evidence indicates that circular RNAs (circRNAs) play an indispensable role in a variety of tumors, yet the function of circRNAs in premalignant lesions is still obscure. Oral leukoplakia (OLK) is one of the most common premalignant lesions of the oral mucosa. Our study aimed to comprehensively investigate whether circRNAs contribute to the occurrence and development of OLK. Methods We obtained six pairs of OLK and normal oral mucosal (NOM) tissue samples and subjected them to high-throughput sequencing to detect the expression of circRNA. In total, 26 pairs of NOM and OLK tissues were used for validation. Key circRNAs were selected and further validated by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), ribonuclease (RNase) R digestion, and Sanger sequencing. Visualization analysis of circular human leukocyte antigen-C (circHLA-C) was performed in the UCSC Genome Browser (genome.ucsc.edu). Functional analysis of differentially expressed (DE) circRNAs were processed by Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Furthermore, TargetScan (www.targetscan.org) was applied to predict targeted micro RNAs (miRNAs) and messenger RNAs (mRNAs) of circRNAs and a competing endogenous RNA (ceRNA) network related with identified circRNAs was constructed in Cytoscape (v2.8.0). Results Profile data showed that 366 circRNAs were significantly altered in OLK tissues, including 65 upregulated and 301 downregulated circRNA transcripts. Compared with sequencing results, seven selected circRNAs expressed the same changing tendency. The amplest upregulated circRNA in our sequencing data, circHLA-C, was confirmed through back-splice junction sequences by Sanger sequencing after RNase R digestion. Correlation analysis demonstrated that circHLA-C correlated positively with the degree of dysplasia. Furthermore, receiver operating characteristic (ROC) curve analysis indicated that circHLA-C had potential diagnostic value with excellent accuracy and specificity. Conclusions According to the literature, we were the first to uncover the expression profiles of circRNAs in OLK. Our research performed a comprehensive bioinformatics analysis of DE circRNAs in OLK and identified circHLA-C as a promising diagnostic biomarker with potential as a therapeutic genetic target for OLK.
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Affiliation(s)
- Siming Xu
- Department of Oral Mucosal Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Yuhan Song
- Department of Oral Mucosal Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Yanxiong Shao
- Department of Oral Mucosal Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Haiwen Zhou
- Department of Oral Mucosal Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai, China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
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27
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Hong W, Xue M, Jiang J, Zhang Y, Gao X. Circular RNA circ-CPA4/ let-7 miRNA/PD-L1 axis regulates cell growth, stemness, drug resistance and immune evasion in non-small cell lung cancer (NSCLC). J Exp Clin Cancer Res 2020; 39:149. [PMID: 32746878 PMCID: PMC7397626 DOI: 10.1186/s13046-020-01648-1] [Citation(s) in RCA: 204] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/21/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) cells derived intracellular and extracellular programmed cell death ligand 1 (PD-L1) promoted cancer progression and drug resistance, and facilitated tumor immune evasion. However, the detailed molecular mechanisms are still largely unknown. In the present study, we aimed to explore the role of circular RNA circ-CPA4/let-7 miRNA/PD-L1 axis in the regulation of NSCLC progression, drug resistance and tumor immune microenvironment. METHODS Real-Time qPCR and Western Blot analysis were conducted to examine gene expressions at transcriptional and translated levels, respectively. The regulatory mechanisms of circ-CPA4, let-7 miRNA and PD-L1 were validated by dual-luciferase reporter gene system and RNA pull-down assay. Cell growth and apoptosis were determined by CCK-8 assay, colony formation assay and Annexin V-FITC/PI double staining assay. Cell mobility was evaluated by transwell assay. RESULTS Circ-CPA4 and PD-L1 were high-expressed, while let-7 miRNA was low-expressed in NSCLC cells and cancer tissues compared to the human bronchial epithelial (HBE) cells and their paired clinical normal adjacent tissues, respectively. Besides, knock-down of circ-CPA4 inhibited cell growth, mobility and epithelial-mesenchymal transition (EMT), and promoted cell death in NSCLC cells by downregulating PD-L1 through serving as a RNA sponge for let-7 miRNA. In addition, the NSCLC cells derived PD-L1-containing exosomes promoted cell stemness and increased resistance of NSCLC cells to cisplatin. Notably, by co-culturing the NSCLC cells with CD8+ T cells isolated from human peripheral blood mononuclear cells (hPBMCs) in a transwell co-culturing system, we found that NSCLC cells inactivated CD8+ T cells in a secreted PD-L1-dependent manner. Further results suggested that circ-CPA4 also positively regulated exosomal PD-L1, and the NSCLC cells with circ-CPA4 ablation re-activated CD8+ T cells in the co-culturing system. CONCLUSION Taken together, circ-CPA4 regulated cell growth, mobility, stemness and drug resistance in NSCLC cells and inactivated CD8+ T cells in the tumor immune microenvironment through let-7 miRNA/PD-L1 axis.
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MESH Headings
- Animals
- Apoptosis
- B7-H1 Antigen/genetics
- B7-H1 Antigen/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carboxypeptidases A/genetics
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/secondary
- Cell Movement
- Cell Proliferation
- Drug Resistance, Neoplasm
- Epithelial-Mesenchymal Transition
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Immune Evasion
- Leukocytes, Mononuclear
- Lung Neoplasms/drug therapy
- Lung Neoplasms/immunology
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Male
- Mice
- Mice, Nude
- MicroRNAs/genetics
- Middle Aged
- Neoplasm Invasiveness
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Prognosis
- RNA, Circular/genetics
- Survival Rate
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Weijun Hong
- Department of Respiratory Medicine, Minhang Hospital, Fudan University, 170 Xin-Song Road, Shanghai, 201199 China
| | - Min Xue
- Department of Respiratory Medicine, Minhang Hospital, Fudan University, 170 Xin-Song Road, Shanghai, 201199 China
| | - Jun Jiang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Yajuan Zhang
- Department of Respiratory Medicine, Minhang Hospital, Fudan University, 170 Xin-Song Road, Shanghai, 201199 China
| | - Xiwen Gao
- Department of Respiratory Medicine, Minhang Hospital, Fudan University, 170 Xin-Song Road, Shanghai, 201199 China
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Identification and Characterization of circRNAs Responsive to Methyl Jasmonate in Arabidopsis thaliana. Int J Mol Sci 2020; 21:ijms21030792. [PMID: 31991793 PMCID: PMC7037704 DOI: 10.3390/ijms21030792] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/09/2020] [Accepted: 01/23/2020] [Indexed: 12/23/2022] Open
Abstract
Circular RNAs (circRNAs) are endogenous noncoding RNAs with covalently closed continuous loop structures that are formed by 3′–5′ ligation during splicing. These molecules are involved in diverse physiological and developmental processes in eukaryotic cells. Jasmonic acid (JA) is a critical hormonal regulator of plant growth and defense. However, the roles of circRNAs in the JA regulatory network are unclear. In this study, we performed high-throughput sequencing of Arabidopsis thaliana at 24 h, 48 h, and 96 h after methyl JA (MeJA) treatment. A total of 8588 circRNAs, which were distributed on almost all chromosomes, were identified, and the majority of circRNAs had lengths between 200 and 800 bp. We identified 385 differentially expressed circRNAs (DEcircRNAs) by comparing data between MeJA-treated and untreated samples. Gene Ontology (GO) enrichment analysis of the host genes that produced the DEcircRNAs showed that the DEcircRNAs are mainly involved in response to stimulation and metabolism. Additionally, some DEcircRNAs were predicted to act as miRNA decoys. Eight DEcircRNAs were validated by qRT-PCR with divergent primers, and the junction sites of five DEcircRNAs were validated by PCR analysis and Sanger sequencing. Our results provide insight into the potential roles of circRNAs in the MeJA regulation network.
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