1
|
He S, Bing J, Zhong Y, Zheng X, Zhou Z, Wang Y, Hu J, Sun X. PlantCircRNA: a comprehensive database for plant circular RNAs. Nucleic Acids Res 2024:gkae709. [PMID: 39189447 DOI: 10.1093/nar/gkae709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/11/2024] [Accepted: 08/02/2024] [Indexed: 08/28/2024] Open
Abstract
Circular RNAs (circRNAs) represent recently discovered novel regulatory non-coding RNAs. While they are present in many eukaryotes, there has been limited research on plant circRNAs. We developed PlantCircRNA (https://plant.deepbiology.cn/PlantCircRNA/) to fill this gap. The two most important features of PlantCircRNA are (i) it incorporates circRNAs from 94 plant species based on 39 245 RNA-sequencing samples and (ii) it imports the original AtCircDB and CropCircDB databases. We manually curated all circRNAs from published articles, and imported them into the database. Furthermore, we added detailed information of tissue as well as abiotic stresses to the database. To help users understand these circRNAs, the database includes a detection score to measure their consistency and a naming system following the guidelines recently proposed for eukaryotes. Finally, we developed a comprehensive platform for users to visualize, analyze, and download data regarding specific circRNAs. This resource will serve as a home for plant circRNAs and provide the community with unprecedented insights into these mysterious molecule.
Collapse
Affiliation(s)
- Shutian He
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Jianhao Bing
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Yang Zhong
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Xiaoyang Zheng
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Ziyu Zhou
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Yifei Wang
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Jiming Hu
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Xiaoyong Sun
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| |
Collapse
|
2
|
Wang Y, Wu Y, Yang S, Gao R, Lv X, Yang Z, Jiao P, Zhang N, Loor JJ, Chen Z. m 6A Methylation Mediates the Function of the circRNA-08436/miR-195/ELOVL6 Axis in Regards to Lipid Metabolism in Dairy Goat Mammary Glands. Animals (Basel) 2024; 14:1715. [PMID: 38929334 PMCID: PMC11201019 DOI: 10.3390/ani14121715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
The nutritional value of goat milk is determined by the composition of its fatty acids, with particular importance placed on the role of unsaturated fatty acids in promoting human health. CircRNAs have been known to affect fatty acid metabolism through different pathways. In this study, high-throughput sequencing was employed to construct expression profiles of mammary tissue harvested during the dry period and peak lactation stages of dairy goats. Differentially expressed circRNAs and mRNAs were screened, revealing significantly higher expression levels of circRNA-08436 and ELOVL6 during the peak lactation period compared with the dry period. Thus, circRNA-08436 and ELOVL6 were chosen for subsequent studies. The findings demonstrated that circRNA-08436 not only promotes the synthesis of triglyceride (TAG) and cholesterol in goat mammary epithelial cells (GMECs), but also increases the concentrations of saturated fatty acids in the cells. Through the utilization of software prediction, the dual luciferase reporter system, and qRT-PCR, it was observed that circRNA-08436 binds to miR-195, with its overexpression reducing the expression levels of miR-195 and inhibiting TAG synthesis. In addition, circRNA-08436 upregulated the expression levels of the miR-195 target gene ELOVL6. The data also revealed that YTHDC1 facilitated the transport of circRNA-08436 from the nucleus to the cytoplasm, while YTHDC2 in the cytoplasm functioned as a "reader" to identify and degrade circRNA-08436. Taken together, these findings contribute to a better understanding of the molecular regulation of fatty acid metabolism in the mammary glands of dairy goats, thus offering a sound theoretical basis for the production of high-quality goat milk.
Collapse
Affiliation(s)
- Yu Wang
- Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi 830000, China; (Y.W.); (N.Z.)
- Key Laboratory of Genetics Breeding and Reproduction of Grass Feeding Livestock, Minisitry of Agriculture and Rural Affairs, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi 830000, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.W.); (S.Y.); (R.G.); (X.L.); (Z.Y.)
| | - Yanni Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.W.); (S.Y.); (R.G.); (X.L.); (Z.Y.)
| | - Sitian Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.W.); (S.Y.); (R.G.); (X.L.); (Z.Y.)
| | - Rui Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.W.); (S.Y.); (R.G.); (X.L.); (Z.Y.)
| | - Xiaoyang Lv
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.W.); (S.Y.); (R.G.); (X.L.); (Z.Y.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.W.); (S.Y.); (R.G.); (X.L.); (Z.Y.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Peixin Jiao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China;
| | - Ning Zhang
- Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi 830000, China; (Y.W.); (N.Z.)
- Key Laboratory of Genetics Breeding and Reproduction of Grass Feeding Livestock, Minisitry of Agriculture and Rural Affairs, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi 830000, China
| | - Juan J. Loor
- Mammalian Nutrition Physiology Genomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Zhi Chen
- Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi 830000, China; (Y.W.); (N.Z.)
- Key Laboratory of Genetics Breeding and Reproduction of Grass Feeding Livestock, Minisitry of Agriculture and Rural Affairs, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi 830000, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Y.W.); (S.Y.); (R.G.); (X.L.); (Z.Y.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
| |
Collapse
|
3
|
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: 4] [Impact Index Per Article: 4.0] [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.
Collapse
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.
| |
Collapse
|
4
|
Zhang Z, Jin S, Tian H, Wang Z, Jiang R, Liu C, Xin D, Wu X, Chen Q, Zhu R. Identifying the Soybean microRNAs Related to Phytophthora sojae Based on RNA Sequencing and Bioinformatics Analysis. Int J Mol Sci 2023; 24:ijms24108546. [PMID: 37239903 DOI: 10.3390/ijms24108546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Phytophthora root rot in soybeans is caused by a pathogen called Phytophthora sojae (P. sojae), which results in a significant decrease in soybean production within affected regions. MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that play a key post-transcriptional regulatory role in eukaryotes. In this paper, the miRNAs that respond to P. sojae were analyzed from the gene level to complement the study of molecular resistance mechanisms in soybean. The study utilized high-throughput sequencing of soybean data to predict miRNAs that respond to P. sojae, analyze their specific functions, and verify regulatory relationships using qRT-PCR. The results showed that the miRNAs in soybean respond to P. sojae infection. MiRNAs can be transcribed independently, suggesting the presence of transcription factor binding sites in the promoter regions. Additionally, we performed an evolutionary analysis on conserved miRNAs that respond to P. sojae. Finally, we investigated the regulatory relationships among miRNAs, genes, and transcription factors, and identified five regulatory patterns. These findings lay the groundwork for future studies on the evolution of miRNAs responsive to P. sojae.
Collapse
Affiliation(s)
- Zhanguo Zhang
- College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
- National Research Center of Soybean Engineering and Technology, Harbin 150030, China
| | - Song Jin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Huilin Tian
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Zhihao Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Rui Jiang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Rongsheng Zhu
- College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| |
Collapse
|
5
|
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: 11] [Impact Index Per Article: 11.0] [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.
Collapse
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.
| |
Collapse
|
6
|
Jiao Y, Sha C, Xie R, Shu Q. Comparative analysis of the potential physiological and molecular mechanisms involved in the response to root zone hypoxia in two rootstock seedlings of the Chinese bayberry via transcriptomic analysis. Funct Integr Genomics 2022; 23:11. [PMID: 36542181 DOI: 10.1007/s10142-022-00944-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 08/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
The negative effects of waterlogging can be effectively improved through the use of waterlogging-resistant rootstocks. However, the underlying physiological and molecular mechanisms of Chinese bayberry (Morella rubra) rootstock tolerance to waterlogging have not yet been investigated. This study aims to unravel the molecular regulation mechanisms underlying waterlogging-tolerant rootstocks. Two rootstocks, Morella cerifera (tolerant) and Morella rubra (sensitive), were selected for root zone hypoxia treatments, assessments of hormone levels and antioxidant enzyme activity, and transcriptomic analysis. While the contents of abscisic acid (ABA) and brassinosteroid (BR) in the roots of M. rubra decreased significantly after root zone hypoxia treatment, there were no significant changes in M. cerifera. Both the superoxide dismutase (SOD) activity and malondialdehyde (MDA) content increased in M. cerifera but were decreased in M. rubra. Transcriptome sequencing identified 1,925 (928 up- and 997 downregulated) and 733 (278 up- and 455 downregulated) differentially expressed genes (DEGs) in the two rootstocks. The gene set enrichment analysis showed that 84 gene sets were enriched after root zone hypoxia treatment, including 57 (35 up- and 22 downregulated) and 14 (five up- and nine downregulated) gene sets derived from M. cerifera and M. rubra, respectively, while the remaining 13 gene sets were shared. KEGG pathway analysis showed specific enrichment in six pathways in M. cerifera, including the mitogen-activated protein kinase (MAPK), tyrosine metabolism, glycolysis/gluconeogenesis, ribosome, cyanoamino acid metabolism, and plant-pathogen interaction pathways. Overall, these results provide preliminary insights into the molecular mechanisms of Chinese bayberry tolerance to waterlogging.
Collapse
Affiliation(s)
- Yun Jiao
- Institute of Forestry, Ningbo Academy of Agricultural Science, Ningbo, 315040, China.
| | - Cunlong Sha
- Haishu District Agricultural Technology Management Service Station, Ningbo, 315100, China
| | - Rangjin Xie
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, China
| | - Qiaoyun Shu
- Institute of Forestry, Ningbo Academy of Agricultural Science, Ningbo, 315040, China
| |
Collapse
|